Mock Version: 2.15 Mock Version: 2.15 Mock Version: 2.15 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/f40-build-764390-122869/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=604800uid=991gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1701993600 Wrote: /builddir/build/SRPMS/percolator-3.06.04-1.fc40.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/f40-build-764390-122869/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=604800uid=991gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1701993600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fiO3so + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf percolator-rel-3-06-04 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-06-04.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd percolator-rel-3-06-04 + rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + tar -xvf /builddir/build/SOURCES/yeast-01.sqt.tar.gz yeast-01.shuffled2.sqt yeast-01.shuffled.sqt yeast-01.sqt + find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';' + find . -type f -name '*.h' -exec chmod 0644 '{}' ';' + find . -type f -name '*.xx' -exec chmod 0644 '{}' ';' + find . -type f -name '*.txt' -exec chmod 0644 '{}' ';' + chmod a-x src/converters/MSToolkit/RAMP/README + mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README + mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt + cp -p /builddir/build/SOURCES/percolator-RAMP_license_lgpl-2.1.txt RAMP_license_lgpl-2.1.txt + sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.ulJTY5 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd percolator-rel-3-06-04 + export 'CXXFLAGS=-std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer' + CXXFLAGS='-std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer' + mkdir -p percolator ~/build/BUILD/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-rel-3-06-04 + pushd percolator + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=riscv64 .. -- The C compiler identification is GNU 13.2.1 -- The CXX compiler identification is GNU 13.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- -- ------------------------------------------------------------------------------- -- Building PERCOLATOR: -- change a configuration variable with: cmake -D= -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- CMAKE_PREFIX_PATH = ../ -- XML_SUPPORT = ON -- GOOGLE_TEST = -- GOOGLE_TEST_PATH = -- TARGET_ARCH = riscv64 -- TOOL CHAIN FILE = -- PROFILING = -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages: -- Found Xerces-C: /usr/lib64/libxerces-c.so -- : /usr/include -- Version: 3.2.3 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Locating CodeSynthesis library with XSDDIR set to -- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx -- RPC found, will include headers from: /usr/include/tirpc -- and libraries from : /usr/lib64/libtirpc.so -- Found Boost: /usr/lib64/cmake/Boost-1.81.0/BoostConfig.cmake (found suitable version "1.81.0", minimum required is "1.46.0") found components: filesystem system -- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.14.0") -- Using installed GoogleTest at: -- Found Boost: /usr/lib64/cmake/Boost-1.81.0/BoostConfig.cmake (found suitable version "1.81.0", minimum required is "1.46.0") -- Configuring done (9.6s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/percolator + cd src + xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../../src/xml/percolator_in.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../../src/xml/percolator_out.xsd + cd .. + /usr/bin/make -O -j4 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/percolator//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src 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/builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 4%] Building C object src/blas/CMakeFiles/blas.dir/daxpy.c.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/daxpy.c.o -MF CMakeFiles/blas.dir/daxpy.c.o.d -o CMakeFiles/blas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/daxpy.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 5%] Building C object src/blas/CMakeFiles/blas.dir/ddot.c.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/ddot.c.o -MF CMakeFiles/blas.dir/ddot.c.o.d -o CMakeFiles/blas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/ddot.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 6%] Building C object src/blas/CMakeFiles/blas.dir/dgemv.c.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dgemv.c.o -MF CMakeFiles/blas.dir/dgemv.c.o.d -o CMakeFiles/blas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dgemv.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 8%] Building C object src/blas/CMakeFiles/blas.dir/dnrm2.c.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dnrm2.c.o -MF CMakeFiles/blas.dir/dnrm2.c.o.d -o CMakeFiles/blas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dnrm2.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 9%] Building C object src/blas/CMakeFiles/blas.dir/dscal.c.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dscal.c.o -MF CMakeFiles/blas.dir/dscal.c.o.d -o CMakeFiles/blas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dscal.c make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 10%] Linking C static library libblas.a cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/cmake -P CMakeFiles/blas.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/cmake -E cmake_link_script CMakeFiles/blas.dir/link.txt --verbose=1 /usr/bin/ar rcv libblas.a CMakeFiles/blas.dir/daxpy.c.o CMakeFiles/blas.dir/ddot.c.o CMakeFiles/blas.dir/dgemv.c.o CMakeFiles/blas.dir/dnrm2.c.o CMakeFiles/blas.dir/dscal.c.o a - CMakeFiles/blas.dir/daxpy.c.o a - CMakeFiles/blas.dir/ddot.c.o a - CMakeFiles/blas.dir/dgemv.c.o a - CMakeFiles/blas.dir/dnrm2.c.o a - CMakeFiles/blas.dir/dscal.c.o /usr/bin/ranlib libblas.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 10%] Built target blas make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 4%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 12%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 13%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 16%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Database.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 18%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/PeptideConstraint.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/PeptideSrc.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 4%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int k = 0; k < s.size(); k++) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 191 | for (int k = 0; k < s.size(); k++) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 200 | for (int k = 0; k < associatedProteinsBySection.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 211 | for (int j = 0; j ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 9 | for (int k = 0; k < rhs.size(); k++) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array::operator==(const Array&) const [with T = int]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable::searchList(const std::__cxx11::list&, const D&) const [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable::add(const D&) [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 267 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 47 | for (int k = 0; k < groups.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 58 | for (int k = 0; k < groups.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 79 | for (int k=0; k&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 90 | for (int k=0; k BasicGroupBigraph::probabilityE(const Model&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int k=0; k&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 168 | for (int k=0; k BasicGroupBigraph::eCorrection(const Model&, const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int k=0; k BasicGroupBigraph::probabilityRGivenN(const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 289 | for (int k=0; k BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 322 | for ( int k=0; k ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 9 | for (int k = 0; k < rhs.size(); k++) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array::operator==(const Array&) const [with T = int]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable::searchList(const std::__cxx11::list&, const D&) const [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable::add(const D&) [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 267 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array GroupPowerBigraph::proteinProbs()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 10 | for (int k = 0; k < subgraphs_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 22 | for (int k = 0; k < subgraphs_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int k = 0; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector&, std::map, long unsigned int>&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | for (; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector > >&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 77 | for (int k = 0; k < groupProtNames_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector > >&, std::vector&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 94 | for (int k=0; k GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 128 | for (int k = 0; k < preResult.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 188 | for (int k = 0; k < subBasic.size(); k++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array > GroupPowerBigraph::peptideNames() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 202 | for (int k = 0; k < subgraphs_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair > >, Array > GroupPowerBigraph::getDescendingProteinsAndWeights() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 210 | for (int k = 0; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 222 | for (int k = 0; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 24%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In static member function ‘static bool PercolatorCrux::Protein::readRawSequence(FILE*, char*, unsigned int, char*, unsigned int*)’, inlined from ‘bool PercolatorCrux::Protein::parseProteinFastaFile(FILE*)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23: /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 505 | raw_sequence[i_seq] = '\0'; | ~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp: In member function ‘bool PercolatorCrux::Protein::parseProteinFastaFile(FILE*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object ‘buffer’ of size 40000 355 | static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in. | ^~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/ProteinPeptideIterator.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 30%] Linking CXX static library libpicked_protein.a cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1 /usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o /usr/bin/ranlib libpicked_protein.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 27%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/Random.cpp.o -MF CMakeFiles/fido.dir/Random.cpp.o.d -o CMakeFiles/fido.dir/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array&, double, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 65 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 142 | for (int k=0; k gp_; // (new XMLGrammarPoolImpl (mm)); | ^~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:102:22: warning: ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder] 102 | DOMImplementation& dom_impl_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning: when initialized here [-Wreorder] 144 | parser_impl::parser_impl() : clean_(true), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable] 178 | size_t n(s.size()); | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable] 170 | int i(1); | ^ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 31%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/fido/CMakeFiles/fido.dir/Vector.cpp.o -MF CMakeFiles/fido.dir/Vector.cpp.o.d -o CMakeFiles/fido.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:4: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array&, const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 382 | for (int k=0; k& operator*=(Array&, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 392 | for (int k=0; k operator-(const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 530 | for (int k=0; k(n))*sizeof(type)) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:2128:22: note: in expansion of macro ‘Malloc’ 2128 | model->sv_coef = Malloc(double*, static_cast(nr_class - 1)); | ^~~~~~ In file included from /usr/include/c++/13/bits/std_abs.h:38, from /usr/include/c++/13/cmath:49, from /usr/include/c++/13/math.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:1: /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable] 91 | bool hasScannr = false, hasRt = false, hasDm = false; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::unnormalizeweight(const std::vector&, std::vector&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:40:10: warning: unused variable ‘sum’ [-Wunused-variable] 40 | double sum = 0; | ^~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::normalizeweight(const std::vector&, std::vector&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:49:10: warning: unused variable ‘sum’ [-Wunused-variable] 49 | double sum = 0; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Normalizer.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:28, from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39, from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:29: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:100:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder] 100 | bool trainBestPositive_; | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:89:16: warning: ‘unsigned int CrossValidation::numThreads_’ [-Wreorder] 89 | unsigned int numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:32:1: warning: when initialized here [-Wreorder] 32 | CrossValidation::CrossValidation(bool quickValidation, | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:110:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 110 | for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(Normalizer*, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:296:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 296 | for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){ | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::mergeCpCnPairs(double, options&, std::vector >&, const std::vector&, const std::vector&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:370:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 370 | for (set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:410:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 410 | for (set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:441:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare] 441 | for (set = 0; set < numFolds_; ++set) { | ~~~~^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:21: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:24: /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder] 87 | bool concatenatedSearch_; | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:72:10: warning: ‘double SanityCheck::test_fdr_’ [-Wreorder] 72 | double test_fdr_, initial_train_fdr_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:31:1: warning: when initialized here [-Wreorder] 31 | SanityCheck::SanityCheck() : | ^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/UniNormalizer.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:30, from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder] 119 | bool reportPepXML_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:111:8: warning: ‘bool XMLInterface::printDecoys_’ [-Wreorder] 111 | bool printDecoys_, printExpMass_; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:58:1: warning: when initialized here [-Wreorder] 58 | XMLInterface::XMLInterface(const std::string& outputFN, | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘int XMLInterface::readAndScorePin(std::istream&, std::vector&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:258:26: warning: unused variable ‘numFeatures’ [-Wunused-variable] 258 | const unsigned int numFeatures = FeatureNames::getNumFeatures(); | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘void XMLInterface::writePepXML_PSMs(Scores&, double, std::string)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:641:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 641 | if (sh->q < selectionFdr_) | ^~ /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:643:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 643 | index++; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/FeatureNames.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h: In constructor ‘Caller::Caller()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:111:27: warning: ‘Caller::analytics_’ will be initialized after [-Wreorder] 111 | skipNormalizeScores_, analytics_; | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:97:8: warning: ‘bool Caller::xmlPrintDecoys_’ [-Wreorder] 97 | bool xmlPrintDecoys_, xmlPrintExpMass_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning: when initialized here [-Wreorder] 36 | Caller::Caller() : | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:110:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder] 110 | bool reportEachIteration_, quickValidation_, trainBestPositive_, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:108:59: warning: ‘unsigned int Caller::numThreads_’ [-Wreorder] 108 | unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning: when initialized here [-Wreorder] 36 | Caller::Caller() : | ^~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinFDRestimator.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PseudoRandom.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:10: warning: ‘double ProteinProbEstimator::pi0_’ [-Wreorder] 238 | double pi0_, absenceRatio_; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder] 242 | unsigned int numberTargetProteins_; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:237:8: warning: ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder] 237 | bool usePi0_; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder] 243 | std::string decoyPattern_; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:240:10: warning: ‘double ProteinProbEstimator::fdr_’ [-Wreorder] 240 | double fdr_; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning: when initialized here [-Wreorder] 25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio, | ^~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/SqtSanityCheck.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SqtSanityCheck.cpp:17: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.cpp:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ssl.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.h:11, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.cpp:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.cpp:37: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder] 108 | bool isDecoy_; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:106:7: warning: ‘int ProteinScoreHolder::groupId_’ [-Wreorder] 106 | int groupId_; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:20:1: warning: when initialized here [-Wreorder] 20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide, | ^~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Matrix.cpp.o -MF CMakeFiles/perclibrary.dir/Matrix.cpp.o.d -o CMakeFiles/perclibrary.dir/Matrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:4: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp: In member function ‘const Matrix& Matrix::operator=(const Array >&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:10:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 10 | for (int k=0; k > operator-(const Array >&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 519 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:27, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder] 86 | double maxPeptidePval_; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:8: warning: ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder] 85 | bool reportFragmentProteins_, reportDuplicateProteins_; | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:83:26: warning: ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder] 83 | ProteinInferenceMethod protInferenceMethod_; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning: when initialized here [-Wreorder] 22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase, | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:165:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 165 | if (total_non_enzymatic_flanks > peptideScores.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:35: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map&, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:163:16: warning: unused variable ‘native_id’ [-Wunused-variable] 163 | unsigned int native_id = scan - 1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:167:10: warning: unused variable ‘RT’ [-Wunused-variable] 167 | double RT = pPSM->getRetentionTime(); | ^~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 82%] Linking CXX static library libperclibrary.a cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1 /usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o /usr/bin/ranlib libperclibrary.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 84%] Built target perclibrary make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend /usr/bin/make -f 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/builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator 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-I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 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-I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 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-I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 88%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/main.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/src/main.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 87%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp:24: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’: /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 65 | if (n > 0) | ^ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’: /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:140:9: warning: unused variable ‘numInit’ [-Wunused-variable] 140 | int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm, | ^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36, from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14, from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23, from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25, from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33, from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 95%] Linking CXX executable percolator cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o -o percolator libperclibrary.a blas/libblas.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -ltirpc -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [100%] Built target percolator make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [100%] Linking CXX executable gtest_unit cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit ../../../src/libperclibrary.a ../../../src/blas/libblas.a ../../../src/fido/libfido.a -lpthread /usr/lib64/libgtest_main.so.1.14.0 /usr/lib64/libgtest.so.1.14.0 make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [100%] Built target gtest_unit make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0 + popd ~/build/BUILD/percolator-rel-3-06-04 + mkdir -p fido + pushd fido ~/build/BUILD/percolator-rel-3-06-04/fido ~/build/BUILD/percolator-rel-3-06-04 + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc' -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=riscv64 ../src/fido -- The C compiler identification is GNU 13.2.1 -- The CXX compiler identification is GNU 13.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (3.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_EXE_LINKER_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH CMAKE_SKIP_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR TARGET_ARCH TokyoCabinet_INCLUDE_DIR TokyoCabinet_LIBRARY -- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/fido + /usr/bin/make -O -j4 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -B/builddir/build/BUILD/percolator-rel-3-06-04/fido --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/fido//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' cd /builddir/build/BUILD/percolator-rel-3-06-04/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' /usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' [ 50%] Building CXX object CMakeFiles/fido.dir/Numerical.o /usr/bin/g++ -I/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Numerical.o -MF CMakeFiles/fido.dir/Numerical.o.d -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Numerical.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' [ 62%] Building CXX object CMakeFiles/fido.dir/Random.o /usr/bin/g++ -I/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Random.o -MF CMakeFiles/fido.dir/Random.o.d -o CMakeFiles/fido.dir/Random.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array&, double, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 65 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 142 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array&, const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 382 | for (int k=0; k& operator*=(Array&, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 392 | for (int k=0; k operator-(const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 530 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8: ../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: ../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ ../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ ../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: ../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ ../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ ../src/Scores.h: At global scope: ../src/Scores.h:84:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 84 | struct lexicOrderProb : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:11: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:107:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 107 | struct OrderScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:117:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 117 | struct OrderScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:129:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 129 | struct OrderScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:138:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 138 | struct UniqueScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:144:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct UniqueScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:150:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 150 | struct UniqueScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 47 | for (int k = 0; k < groups.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 58 | for (int k = 0; k < groups.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 79 | for (int k=0; k&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 90 | for (int k=0; k BasicGroupBigraph::probabilityE(const Model&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 100 | for (int k=0; k&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 168 | for (int k=0; k BasicGroupBigraph::eCorrection(const Model&, const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 252 | for (int k=0; k BasicGroupBigraph::probabilityRGivenN(const Array&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 289 | for (int k=0; k BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 322 | for ( int k=0; k ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 9 | for (int k = 0; k < rhs.size(); k++) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array::operator==(const Array&) const [with T = int]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable::searchList(const std::__cxx11::list&, const D&) const [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable::add(const D&) [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 267 | for (int k=0; k Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8: ../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: ../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ ../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ ../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: ../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ ../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ ../src/Scores.h: At global scope: ../src/Scores.h:84:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 84 | struct lexicOrderProb : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:11: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:107:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 107 | struct OrderScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:117:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 117 | struct OrderScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:129:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 129 | struct OrderScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:138:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 138 | struct UniqueScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:144:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct UniqueScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:150:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 150 | struct UniqueScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array GroupPowerBigraph::proteinProbs()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 10 | for (int k = 0; k < subgraphs_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 22 | for (int k = 0; k < subgraphs_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 34 | for (int k = 0; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector&, std::map, long unsigned int>&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 48 | for (; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector > >&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 77 | for (int k = 0; k < groupProtNames_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector > >&, std::vector&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 94 | for (int k=0; k GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 128 | for (int k = 0; k < preResult.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 188 | for (int k = 0; k < subBasic.size(); k++) { | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array > GroupPowerBigraph::peptideNames() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 202 | for (int k = 0; k < subgraphs_.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair > >, Array > GroupPowerBigraph::getDescendingProteinsAndWeights() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 210 | for (int k = 0; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 222 | for (int k = 0; k < sorted.size(); k++) { | ~~^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' [ 50%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o /usr/bin/g++ -I/src -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicBigraph.o -MF CMakeFiles/fido.dir/BasicBigraph.o.d -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4: ../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’: ../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ ../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:56:3: warning: when initialized here [-Wreorder] 56 | ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {} | ^~~~~~~~~~~ ../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’: ../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder] 54 | int label; | ^~~~~ ../src/Scores.h:53:19: warning: ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder] 53 | PSMDescription* pPSM; | ^~~~ ../src/Scores.h:57:3: warning: when initialized here [-Wreorder] 57 | ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) : | ^~~~~~~~~~~ ../src/Scores.h: At global scope: ../src/Scores.h:84:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 84 | struct lexicOrderProb : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:4: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:107:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 107 | struct OrderScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:117:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 117 | struct OrderScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:129:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 129 | struct OrderScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:138:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 138 | struct UniqueScanMassCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:144:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct UniqueScanMassLabelCharge : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Scores.h:150:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 150 | struct UniqueScanLabel : public binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array Array::operator[](const Array&) const [with T = int]’ was hidden [-Woverloaded-virtual=] 139 | Array Array::operator [](const Array & rhs) const | ^~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7, from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 52 | T & Array::operator [] (std::size_t k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=] 45 | const T & Array::operator [] (std::size_t k) const | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=] 38 | T & Array::operator [] (int k) | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note: by ‘Set::operator[]’ 31 | const int & operator [](int k) const { | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 185 | for (int k = 0; k < s.size(); k++) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 191 | for (int k = 0; k < s.size(); k++) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsignedmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido' int’} [-Wsign-compare] 200 | for (int k = 0; k < associatedProteinsBySection.size(); k++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 211 | for (int j = 0; j ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 9 | for (int k = 0; k < rhs.size(); k++) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array::operator==(const Array&) const [with T = int]’: /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23: required from ‘int HashTable::searchList(const std::__cxx11::list&, const D&) const [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8: required from ‘bool HashTable::add(const D&) [with D = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16: required from ‘static Array ReplicateIndexer::replicates(unsigned int (*)(const T&), const Array&) [with T = Set]’ /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56: required from here /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 267 | for (int k=0; k= -- Indicate the type of XML serialization scheme : -DSERIALIZE="Boost" or -DSERIALIZE="TokyoCabinet" or -DSERIALIZE="LevelDB". By setting up the variable SERIALIZE to either Boost or TokyoCabinet or LevelDB you will choose the serialization scheme that will be used to build Converters. Boost serialization option will be used as default if no option is given. -- CMAKE_INSTALL_PREFIX = /usr -- CMAKE_BUILD_TYPE = Release -- XML_SUPPORT = ON -- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../.. -- CMAKE_PREFIX_PATH = ../ -- TARGET_ARCH = riscv64 -- TOOL CHAIN FILE = -- SERIALIZE = TokyoCabinet -- PROFILING = -- Using Tokyo Cabinet Serialization scheme -- ------------------------------------------------------------------------------- -- -- Architecture: -- Checking packages.. -- Found Xerces-C: /usr/lib64/libxerces-c.so -- : /usr/include -- Version: 3.2.3 -- Package CodeSynthesis XSD found: /usr/include -- Executable: /usr/bin/xsdcxx -- Found TokyoCabinet: /usr/lib64/libtokyocabinet.so -- Package Tokyo Cabinet found : /usr/include -- Found BZip2: /usr/lib64/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so - found -- Bzip2 found -- Found Boost: /usr/lib64/cmake/Boost-1.81.0/BoostConfig.cmake (found suitable version "1.81.0", minimum required is "1.46.0") found components: filesystem system -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- RPC found, will include headers from: /usr/include/tirpc -- and libraries from : /usr/lib64/libtirpc.so -- Generating classes from xsd-schema using CodeSynthesis -- Generating /builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.hxx -- SQL Lite 3 found: /usr/include -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.13") -- ZLIB found: /usr/include, /usr/lib64/libz.so -- Using FragSpectrumScanDatabaseTokyodb.cpp -- Configuring done (10.3s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/converters + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../src/xml/percolator_in.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../src/xml/percolator_out.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns ../src/xml/mzIdentML1.1.0.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/gaml_tandem1.0.xsd + xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/tandem2011.12.01.1.xsd + /usr/bin/make -O -j4 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/converters//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'. make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 8%] Built target generate_perc_xsdfiles make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 8%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o -MF CMakeFiles/RAMP.dir/ramp_base64.cpp.o.d -o CMakeFiles/RAMP.dir/ramp_base64.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp_base64.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 8%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o -MF CMakeFiles/RAMP.dir/ramp.cpp.o.d -o CMakeFiles/RAMP.dir/ramp.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1698:13: warning: variable ‘err’ set but not used [-Wunused-but-set-variable] 1698 | int err; | ^~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.h:134, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:34: In function ‘const char* strchr(const char*, int)’, inlined from ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35: /usr/include/string.h:241:27: warning: ‘char* __builtin_strchr(const char*, int)’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’: cc1plus: note: source object is likely at address zero In function ‘const char* strchr(const char*, int)’, inlined from ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35: /usr/include/string.h:241:27: warning: ‘char* __builtin_strchr(const char*, int)’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread] 241 | return __builtin_strchr (__s, __c); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~ In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’: cc1plus: note: source object is likely at address zero /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘int rampSelfTest(char*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 256 equals destination size [-Wstringop-truncation] 2050 | strncpy(buf, filename, sizeof(buf)); | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 256 equals destination size [-Wstringop-truncation] 2054 | strncpy(buf, filename, sizeof(buf)); | ^ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 14%] Linking CXX static library libRAMP.a cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -P CMakeFiles/RAMP.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -E cmake_link_script CMakeFiles/RAMP.dir/link.txt --verbose=1 /usr/bin/ar qc libRAMP.a CMakeFiles/RAMP.dir/ramp_base64.cpp.o CMakeFiles/RAMP.dir/ramp.cpp.o /usr/bin/ranlib libRAMP.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 14%] Built target RAMP make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 12%] Building CXX object CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -MF CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o.d -o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 8%] Building CXX object CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/percolator_in.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 19%] Building CXX object CMakeFiles/converters.dir/Reader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/Reader.cpp.o -MF CMakeFiles/converters.dir/Reader.cpp.o.d -o CMakeFiles/converters.dir/Reader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Reader.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 17%] Building CXX object CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -MF CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o.d -o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/tandem2011.12.01.1.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 23%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 25%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 26%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 16%] Building CXX object CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o -MF CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/percolator_out.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 28%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 21%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 33%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 30%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:106:33: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder] 106 | std::auto_ptr gp_; // (new XMLGrammarPoolImpl (mm)); | ^~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:102:22: warning: ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder] 102 | DOMImplementation& dom_impl_; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning: when initialized here [-Wreorder] 144 | parser_impl::parser_impl() : clean_(true), | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable] 178 | size_t n(s.size()); | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable] 170 | int i(1); | ^ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 35%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 37%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 41%] Linking CXX static library libperclibrary_part.a /usr/bin/cmake -P CMakeFiles/perclibrary_part.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary_part.dir/link.txt --verbose=1 /usr/bin/ar qc libperclibrary_part.a CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o" /usr/bin/ranlib libperclibrary_part.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 44%] Built target perclibrary_part make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 46%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -MF CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSConvertFile.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 48%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o -MF CMakeFiles/MSToolkit.dir/MSObject.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSObject.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSObject.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 39%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -MF CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o.d -o CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.H:28, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:16: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In function ‘LazyMatrix* flip_lazy_matrix(LazyMatrix&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:21:30: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 21 | for ( uint j = 0 ; j < lm.rows() ; j++ ) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:22:38: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 22 | for ( uint i = 0 ; i < lm.cols() ; i++ ) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In constructor ‘LazyMatrix::LazyMatrix(int, int, sparse_level, FILE*, off_t)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:39:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 39 | for ( std::size_t i = 0 ; i < nrows ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:44:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 44 | for ( std::size_t i = 0 ; i < nrows; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor ‘LazyMatrix::LazyMatrix(const self&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value] 56 | *data_copies++; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::copy_m_flip(const self&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:67:28: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare] 67 | for ( uint i = 0 ; i < x.nrows ; i++ ) { | ~~^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::set_col(std::vector&, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:150:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 150 | for ( std::size_t i = 0 ; i < nrows ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::_get_row_retain(std::vector&, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable ‘b’ set but not used [-Wunused-but-set-variable] 179 | std::vector::iterator b = this->m[static_cast(i)]->begin(); | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_cols(int, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:290:72: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 290 | for ( std::size_t i = static_cast(start_idx); i < stop_idx ; i++ ) { | ~~^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_start_cols(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:298:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 298 | for ( std::size_t i = 0 ; i < rows() ; i++ ) { | ~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_stop_cols(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:305:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 305 | for ( std::size_t i =0 ; i < rows() ; i++ ) { | ~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::column_shift(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:369:23: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 369 | for ( uint i = 0 ;i < rows() ; i++ ) { | ~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:370:26: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 370 | for ( uint j = 0 ; j < cols() ; j++ ) { | ~~^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:373:21: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 373 | if ( dest_idx >= cols() ) break; | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::linear_shift(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:389:25: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 389 | for ( uint i = 0; i < shift ; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:393:62: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 393 | for ( std::size_t i = static_cast(shift); i < nrows; i++ ) { | ~~^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:409:31: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 409 | for ( uint i = offset ; i < nrows - static_cast(offset); i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:412:76: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 412 | for ( uint i = static_cast(nrows - static_cast(offset)) ; i < nrows; i++ ) { | ~~^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o -MF CMakeFiles/MSToolkit.dir/MSReader.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeFile(const char*, bool, MSObject&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:509:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 509 | for(unsigned int j=0;j&, const std::vector&, std::vector >&, bool)’ declared ‘static’ but never defined [-Wunused-function] 814 | static msmat * msmat_from_thevoid ( const std::vector & mzs, const std::vector & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true ); | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 64%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -MF CMakeFiles/MSToolkit.dir/Spectrum.cpp.o.d -o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp: In member function ‘bool Spectrum::getRawFilter(char*, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp:282:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 282 | if(sz, const std::string&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp:169:12: warning: unused variable ‘PI’ [-Wunused-variable] 169 | double PI = boost::lexical_cast(item.calculatedPI().get()); | ^~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp:174:14: warning: unused variable ‘peptide_length’ [-Wunused-variable] 174 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks); | ^~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 69%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_base.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.cpp:16: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 62%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/MsgfplusReader.cpp.o -MF CMakeFiles/converters.dir/MsgfplusReader.cpp.o.d -o CMakeFiles/converters.dir/MsgfplusReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp: In member function ‘virtual void MsgfplusReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr, const std::string&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:332:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 332 | else StdevErrorTop7 = boost::lexical_cast(up.value().get().c_str()); break; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:332:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 332 | else StdevErrorTop7 = boost::lexical_cast(up.value().get().c_str()); break; | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:271:14: warning: unused variable ‘peptide_length’ [-Wunused-variable] 271 | unsigned peptide_length = peptideLength(peptideSeqWithFlanks); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:290:12: warning: variable ‘SpecEValue’ set but not used [-Wunused-but-set-variable] 290 | double SpecEValue = 0.0; | ^~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 73%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.H:20, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:19: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:20: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable] 594 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable] 697 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘int msmat_header_parser::read_header(msmat*, FILE*, bool, int*)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:92:14: warning: unused variable ‘should_be_semi’ [-Wunused-variable] 92 | char should_be_semi = (char)fgetc(header_fh); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘void msmat_header_parser::load_strmap_from_str(std::map, float>&, const char*, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:361:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 361 | for ( std::size_t i = c1_loc+1 ; i < key_last+1 ; i++ ) { | ~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:14: warning: unused variable ‘key_fields_len’ [-Wunused-variable] 343 | int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:30: warning: unused variable ‘key_last_loc’ [-Wunused-variable] 343 | int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:44: warning: unused variable ‘key_data_len’ [-Wunused-variable] 343 | int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:344:8: warning: unused variable ‘key_len_data’ [-Wunused-variable] 344 | char key_len_data[128], val_len_data[128]; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:344:27: warning: unused variable ‘val_len_data’ [-Wunused-variable] 344 | char key_len_data[128], val_len_data[128]; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:359:7: warning: unused variable ‘key_data_idx’ [-Wunused-variable] 359 | int key_data_idx; | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function] 806 | static int test_msmat_time_interp( msmat * msmat_f ); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function] 807 | static int test_msmat_sg_test( msmat * msmat_fh); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function] 808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function] 809 | static msmat * test_msmat(int argc, char ** argv); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function] 812 | static void output_bp_chrom( msmat & m , char * fname); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function] 813 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA ); | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)’ declared ‘static’ but never defined [-Wunused-function] 814 | static msmat * msmat_from_thevoid ( const std::vector & mzs, const std::vector & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true ); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘void msmat_header_parser::load_map_from_str(flt_map&, const char*, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 314 | delete k; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:306:48: note: returned from ‘void* operator new [](std::size_t)’ 306 | flt_map_type * k = new flt_map_type[num_items]; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 315 | delete v; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:307:48: note: returned from ‘void* operator new [](std::size_t)’ 307 | flt_map_type * v = new flt_map_type[num_items]; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member functionmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' ‘void msmat_header_parser::load_strmap_from_str(std::map, float>&, const char*, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:386:10: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 386 | delete values; | ^~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:381:37: note: returned from ‘void* operator new [](std::size_t)’ 381 | float * values = new float[val_len]; | ^ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 67%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:17: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable] 594 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable] 697 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In constructor ‘transition_manager::transition_manager(std::vector)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:47:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 47 | for ( int i = 0 ; i < transitions.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::init_transitions_from_labels()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:76:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | for ( int i = 0 ; i < labels.size() ; i++ ) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_input(std::ifstream&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:107:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 107 | for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::zero_chrom(int, int, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:185:70: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 185 | for ( std::size_t i = static_cast(start_scan_idx) ; i <= stop_scan_idx ; i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_dist_set(int, std::vector&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:216:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 216 | for ( int i = 0 ; i < this->get_num_rts() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_chrom_set(int, std::vector >&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:225:9: warning: unused variable ‘set_idx’ [-Wunused-variable] 225 | int set_idx = 0; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_chrom(int, int, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:251:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 251 | for ( std::size_t i = 0 ; i < start_scan_idx ; i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘int msmat::check_size_from_position() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:271:30: warning: comparison of integer expressions of different signedness: ‘off64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 271 | if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::calc_bp_chrom()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:668:36: warning: variable ‘scan_length’ set but not used [-Wunused-but-set-variable] 668 | std::size_t scan_idx, num_scans, scan_length; | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::pad_start_stop(int, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:775:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 775 | for ( int i = stop_mapped_coord+1 ; i < get_num_rts() ; i++ ) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::time_interpolate(double, msmat&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1056:14: warning: variable ‘dim’ set but not used [-Wunused-but-set-variable] 1056 | matrix_dim dim = get_data_dim(); | ^~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_median() const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1266:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1266 | for ( int i = 0 ; i < this->get_num_rows() ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1267:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1267 | for ( int j = 0 ; j < this->get_num_cols() ; j++ ) { | ~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_avg(int) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1282:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1282 | if ( i < 0 || i >= get_num_rts() ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_twomat_num(const msmat&, double, double, int) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1313:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1313 | for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) { | ~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1315:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1315 | if ( other_idx < 0 || other_idx >= other.get_num_rts() ) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_mat_denom(double, int) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1338:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1338 | if ( i < 0 || i >= get_num_rts() ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::correlation_w_shift(const msmat&, int) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1356:17: warning: unused variable ‘self’ [-Wunused-variable] 1356 | const msmat & self = *this; | ^~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1411:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1411 | for ( std::size_t i = 0; i < r_stop - r_start ; i++ ) { | ~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1410:9: warning: unused variable ‘foo’ [-Wunused-variable] 1410 | int foo = 5; | ^~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘virtual void msmat_scans::get_chrom(int, std::vector&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1486:11: warning: unused variable ‘volatile_this’ [-Wunused-variable] 1486 | msmat * volatile_this; | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In function ‘msmat* test_msmat(int, char**)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:19: warning: variable ‘ti_file’ set but not used [-Wunused-but-set-variable] 1593 | FILE * o_file, *ti_file, *sg_file; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:29: warning: variable ‘sg_file’ set but not used [-Wunused-but-set-variable] 1593 | FILE * o_file, *ti_file, *sg_file; | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_avg(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1816:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1816 | new_cnt < mzs.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1818:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1818 | for ( std::size_t i = 0 ; i < decimate_size ; i++ ) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_avg(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1846:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1846 | new_cnt < rts.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1848:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1848 | for ( std::size_t i = 0 ; i < decimate_size ; i++ ) { | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_sample(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1868:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1868 | new_cnt < mzs.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_sample(int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1886:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1886 | new_cnt < rts.size() ; | ~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘bool msmat::equals_data(const msmat&, double) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1909:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1909 | for ( int i = 0 ; i < get_num_rows() ; i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::sum_abs_diffs(const msmat&) const’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1932:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1932 | for ( int i = 0 ; i < get_num_rows() ; i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1929:10: warning: unused variable ‘nrows’ [-Wunused-variable] 1929 | size_t nrows = get_num_rows(); | ^~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_output(std::ostream&, int, int, int, int, bool, char)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1978:13: warning: unused variable ‘num_mzs’ [-Wunused-variable] 1978 | const int num_mzs = static_cast(get_num_mzs()); | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void ttest_score_matrix::unmask_search(msmat::mz_type, msmat::rt_type, msmat::rt_type)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:2097:7: warning: unused variable ‘start_rt_idx’ [-Wunused-variable] 2097 | int start_rt_idx = this->rt_to_rtidx(start_rt); | ^~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:2098:7: warning: unused variable ‘stop_rt_idx’ [-Wunused-variable] 2098 | int stop_rt_idx = this->rt_to_rtidx(stop_rt); | ^~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function] 806 | static int test_msmat_time_interp( msmat * msmat_f ); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function] 807 | static int test_msmat_sg_test( msmat * msmat_fh); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function] 808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1728:9: warning: ‘msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)’ defined but not used [-Wunused-function] 1728 | msmat * msmat_from_thevoid | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1701:6: warning: ‘void output_bp_chrom(msmat&, char*)’ defined but not used [-Wunused-function] 1701 | void output_bp_chrom( msmat & m, char * fname ) { | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1570:9: warning: ‘msmat* test_msmat(int, char**)’ defined but not used [-Wunused-function] 1570 | msmat * test_msmat ( int argc , char ** argv ) { | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 71%] Building CXX object CMakeFiles/converters.dir/TandemReader.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp: In member function ‘virtual void TandemReader::getMaxMinCharge(const std::string&, bool)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:248:24: warning: catching polymorphic type ‘class MyException’ by value [-Wcatch-value=] 248 | } catch (MyException e) { | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:251:27: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 251 | } catch (std::exception e) { | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp: In member function ‘void TandemReader::createPSM(const tandem_ns::peptide::domain_type&, double, unsigned int, double, double, bool, boost::shared_ptr, const peptideProteinMapType&, const std::string&, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:468:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 468 | f_seq.push_back( charge == c ? 1.0 : 0.0); | ~~~~~~~^~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 76%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_test.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:4: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable] 594 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable] 697 | int a = 3; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp: In function ‘int main(int, char**)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable ‘m’ [-Wunused-variable] 13 | msmat * m; | ^ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function] 806 | static int test_msmat_time_interp( msmat * msmat_f ); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function] 807 | static int test_msmat_sg_test( msmat * msmat_fh); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function] 808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function] 809 | static msmat * test_msmat(int argc, char ** argv); | ^~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function] 812 | static void output_bp_chrom( msmat & m , char * fname); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function] 813 | static msmat * msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA ); | ^~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector&, const std::vector&, std::vector >&, bool)’ declared ‘static’ but never defined [-Wunused-function] 814 | static msmat * msmat_from_thevoid ( const std::vector & mzs, const std::vector & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true ); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable] 69 | const static char * valid_fields[] = { | ^~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 75%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp: In member function ‘std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 81 | if (it->first <= peptideSeq.length()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 80%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function ‘virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable ‘valueSize’ [-Wunused-variable] 165 | size_t valueSize(buf.size ()); | ^~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 66%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o -MF CMakeFiles/MSToolkit.dir/crawutils.cpp.o.d -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38, from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:21: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rankties(std::vector&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable ‘start_idx’ [-Wunused-variable] 261 | int start_idx = -1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable ‘stop_idx’ [-Wunused-variable] 262 | int stop_idx = -1; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rank_by_pos_ties(const std::vector >&, std::vector&, bool)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:354:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 354 | if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[static_cast(i)].first == last_val) ) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable ‘last_rank’ [-Wunused-variable] 346 | int last_rank = -1; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_3(const std::vector&, const std::vector&, double, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:455:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 455 | for ( std::size_t i = 0 ; i < (int)s1.size(); i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_4(const std::vector&, const std::vector&, double, double)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:488:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 488 | for ( std::size_t i = 0 ; i < (int)s1.size(); i++ ) { | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘int crawutils::idx_of_centroid(const std::vector&, const std::vector&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:976:23: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 976 | for (idx = 1; idx < (int)y.size(); idx++) | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘int crawutils::tryptic_digester_proto(std::string, std::vector >&, int)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:1090:10: warning: unused variable ‘last_tryp’ [-Wunused-variable] 1090 | bool last_tryp = false; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawstats::pi0_from_StoreySplineFit(const std::vector >&)’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:1402:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1402 | for (std::size_t i = 1; i <= n - 1; i++) | ~~^~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 82%] Linking CXX static library libMSToolkit.a cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1 /usr/bin/ar qc libMSToolkit.a CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o /usr/bin/ranlib libMSToolkit.a make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 82%] Built target MSToolkit make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 78%] Building CXX object CMakeFiles/converters.dir/Interface.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/Interface.cpp.o -MF CMakeFiles/converters.dir/Interface.cpp.o.d -o CMakeFiles/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:18: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h: In constructor ‘Interface::Interface()’: /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:50:14: warning: ‘Interface::xmlOutput’ will be initialized after [-Wreorder] 50 | bool xmlOutput; | ^~~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:47:21: warning: ‘std::string Interface::outputFN’ [-Wreorder] 47 | std::string outputFN; | ^~~~~~~~ /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:21:1: warning: when initialized here [-Wreorder] 21 | Interface::Interface() : xmlOutput(false), outputFN("") { } | ^~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 83%] Linking CXX static library libconverters.a /usr/bin/cmake -P CMakeFiles/converters.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script 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CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 94%] Building CXX object CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -MF CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o.d -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Sqt2Pin.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 94%] Building CXX object CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -MF CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o.d -o CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Tandem2Pin.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 94%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -MF CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o.d -o CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Msgfplus2Pin.cpp make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 96%] Linking CXX executable sqt2pin /usr/bin/cmake -E cmake_link_script CMakeFiles/sqt2pin.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [100%] Built target sqt2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 98%] Linking CXX executable tandem2pin /usr/bin/cmake -E cmake_link_script CMakeFiles/tandem2pin.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [100%] Built target tandem2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [100%] Linking CXX executable msgf2pin /usr/bin/cmake -E cmake_link_script CMakeFiles/msgf2pin.dir/link.txt --verbose=1 /usr/bin/g++ -std=c++14 -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -ltirpc -rdynamic CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [100%] Built target msgf2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0 + popd ~/build/BUILD/percolator-rel-3-06-04 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Drduna + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 ++ dirname /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd percolator-rel-3-06-04 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 'INSTALL=/usr/bin/install -p' -C percolator make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/percolator//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 54%] Built target perclibrary /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Nothing to be done for 'src/picked_protein/CMakeFiles/picked_protein.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 68%] Built target picked_protein /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Nothing to be done for 'src/blas/CMakeFiles/blas.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 75%] Built target blas /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 84%] Built target fido /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 87%] Built target percolator /usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [ 89%] Built target qvality /usr/bin/make -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/make -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[2]: Nothing to be done for 'tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' [100%] Built target gtest_unit make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/bin/percolator -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/bin/qvality -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/./bin/gtest_unit make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator' + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 'INSTALL=/usr/bin/install -p' -C converters make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/converters//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 25%] Built target perclibrary_part /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 28%] Built target generate_perc_xsdfiles /usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 57%] Built target converters /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 62%] Built target RAMP /usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 89%] Built target MSToolkit /usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 92%] Built target msgf2pin /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [ 96%] Built target sqt2pin /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' [100%] Built target tandem2pin make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/bin/msgf2pin -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/bin/sqt2pin -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/bin/tandem2pin -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd -- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters' + mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator ++ find . -type f '(' -name '*.a' ')' + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + for i in `find . -type f \( -name "*.a" \)` + install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/lib64/percolator + rm -f /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/bin/gtest_unit + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 3.06.04-1.fc40 --unique-debug-suffix -3.06.04-1.fc40.riscv64 --unique-debug-src-base percolator-3.06.04-1.fc40.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-06-04 find-debuginfo: starting Extracting debug info from 5 files DWARF-compressing 5 files sepdebugcrcfix: Updated 5 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/percolator-3.06.04-1.fc40.riscv64 5448 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Z40Iw0 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd percolator-rel-3-06-04 + mkdir -p test ~/build/BUILD/percolator-rel-3-06-04/test ~/build/BUILD/percolator-rel-3-06-04 + pushd test + ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt Pin-converter version 3.06.4, Build Date Dec 8 2023 00:00:00 Copyright (c) 2013 Lukas Käll. All rights reserved. Written by Lukas Käll (lukas.kall@scilifelab.se) in the School of Biotechnology at KTH - Royal Institute of Technology, Stockholm. Issued command: ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt on unmatchedbuild05 Reading ../yeast-01.sqt Reading ../yeast-01.shuffled.sqt + ../percolator/src/percolator -X pout.xml pin.tab Protein decoy-prefix used is random_ All files have been read Percolator version 3.06.4, Build Date Dec 8 2023 00:00:00 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: ../percolator/src/percolator -X pout.xml pin.tab Started Mon Dec 18 09:43:12 2023 on unmatchedbuild05 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile pin.tab Features: lnrSp deltLCn deltCn Xcorr Sp IonFrac Mass PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM Found 139410 PSMs Separate target and decoy search inputs detected, using mix-max method. Train/test set contains 69705 positives and 69705 negatives, size ratio=1 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Found 7004 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 6.7251 cpu seconds or 6 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 10193 PSMs with q<0.01 Iteration 2: Estimated 11236 PSMs with q<0.01 Iteration 3: Estimated 11461 PSMs with q<0.01 Iteration 4: Estimated 11509 PSMs with q<0.01 Iteration 5: Estimated 11560 PSMs with q<0.01 Iteration 6: Estimated 11576 PSMs with q<0.01 Iteration 7: Estimated 11602 PSMs with q<0.01 Iteration 8: Estimated 11617 PSMs with q<0.01 Iteration 9: Estimated 11617 PSMs with q<0.01 Iteration 10: Estimated 11616 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.4835 -0.3200 -0.4134 lnrSp 0.1414 0.1989 0.1695 deltLCn 0.6622 0.6394 0.7524 deltCn 0.6588 0.6486 0.6804 Xcorr -0.0413 0.0625 -0.0978 Sp 0.0244 0.1588 0.2191 IonFrac 0.8867 0.6292 0.4141 Mass -0.7489 -0.3031 -0.0249 PepLen 0.1083 0.1800 0.1009 Charge1 0.0250 0.0242 0.0043 Charge2 -0.0471 -0.0610 -0.0250 Charge3 1.3220 1.2346 1.2522 enzN 1.3377 1.1510 1.1172 enzC -1.9073 -1.7718 -1.6438 enzInt -0.0159 -0.0088 0.1201 lnNumSP 0.0188 0.0011 0.0218 dM 0.0044 0.0139 0.0016 absdM -6.5792 -6.3779 -5.8394 m0 Found 11446 test set PSMs with q<0.01. Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. Selecting pi_0=0.86749 Calculating q values. New pi_0 estimate on final list yields 7371 target peptides with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 608.9886 cpu seconds or 257 seconds wall clock time. + popd ~/build/BUILD/percolator-rel-3-06-04 + pushd percolator ~/build/BUILD/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-rel-3-06-04 + /usr/bin/ctest --test-dir . --output-on-failure --force-new-ctest-process -j4 Test project /builddir/build/BUILD/percolator-rel-3-06-04/percolator Start 1: UnitTest_Percolator_RunAllTests 1/1 Test #1: UnitTest_Percolator_RunAllTests ... Passed 0.36 sec 100% tests passed, 0 tests failed out of 1 Total Test time (real) = 0.38 sec + popd ~/build/BUILD/percolator-rel-3-06-04 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: percolator-3.06.04-1.fc40.riscv64 Provides: percolator = 3.06.04-1.fc40 percolator(riscv-64) = 3.06.04-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.4)(64bit) libgcc_s.so.1(GCC_4.3.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.5)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtirpc.so.3()(64bit) libtirpc.so.3(TIRPC_0.3.0)(64bit) libtokyocabinet.so.9()(64bit) libxerces-c-3.2.so()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH) Obsoletes: fido-pi = 0:0 Processing files: percolator-data-3.06.04-1.fc40.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.3HZtes + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-06-04 + DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-data + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-data + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-data + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-data + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-data + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.YOMgMg + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-06-04 + LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-data + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-data + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-data + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-data + RPM_EC=0 ++ jobs -p + exit 0 Provides: percolator-data = 3.06.04-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: percolator-static-3.06.04-1.fc40.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.NliIxZ + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-06-04 + DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-static + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-static + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-static + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-static + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/doc/percolator-static + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.iIm3S1 + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-06-04 + LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-static + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-static + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-static + cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64/usr/share/licenses/percolator-static + RPM_EC=0 ++ jobs -p + exit 0 Provides: percolator-static = 3.06.04-1.fc40 percolator-static(riscv-64) = 3.06.04-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: percolator-debugsource-3.06.04-1.fc40.riscv64 Provides: percolator-debugsource = 3.06.04-1.fc40 percolator-debugsource(riscv-64) = 3.06.04-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: percolator-debuginfo-3.06.04-1.fc40.riscv64 Provides: debuginfo(build-id) = 18f25322633559d602066c681ac3d0fc6a8376a2 debuginfo(build-id) = 5a6da128b266c4f617b4f1504f65ea5a3c51eaf6 debuginfo(build-id) = 5fd27b1d7870c4d95cda64085ae62ee948466bb3 debuginfo(build-id) = dbb11c09e10cf2ad0b795728bb6c7e2d8cb7bda0 debuginfo(build-id) = fd435e860cc1e401ce4eee0566d956cdda51e2c0 percolator-debuginfo = 3.06.04-1.fc40 percolator-debuginfo(riscv-64) = 3.06.04-1.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: percolator-debugsource(riscv-64) = 3.06.04-1.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 Wrote: /builddir/build/RPMS/percolator-debugsource-3.06.04-1.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/percolator-data-3.06.04-1.fc40.noarch.rpm Wrote: /builddir/build/RPMS/percolator-3.06.04-1.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/percolator-debuginfo-3.06.04-1.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/percolator-static-3.06.04-1.fc40.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.soKq8a + umask 022 + cd /builddir/build/BUILD + cd percolator-rel-3-06-04 + /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.riscv64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.brsRXO + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS + rm -rf percolator-rel-3-06-04 percolator-rel-3-06-04.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0