Mock Version: 1.4.21
Mock Version: 1.4.21
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/f33-build-128756-40527/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x3fb933d700>timeout=432000uid=987gid=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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1580256000
Wrote: /builddir/build/SRPMS/percolator-3.04-2.fc33.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/f33-build-128756-40527/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x3fb933d700>timeout=432000uid=987gid=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;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
setting SOURCE_DATE_EPOCH=1580256000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SU07kb
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-04
+ /usr/bin/gzip -dc /builddir/build/SOURCES/percolator-rel-3-04.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-04
+ /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
+ sed -e 's|${ELUDE_MODELS_PATH}..|${ELUDE_MODELS_PATH}|g' -i src/elude_tool/CMakeLists.txt
+ sed -e 's|${CMAKE_INSTALL_PREFIX}/share/elude/models/|${CMAKE_INSTALL_PREFIX}/share/elude|g' -i src/elude_tool/CMakeLists.txt
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.FbQzOc
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-04
+ mkdir -p percolator
+ pushd percolator
~/build/BUILD/percolator-rel-3-04/percolator ~/build/BUILD/percolator-rel-3-04
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ /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_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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -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 -fPIC -pie -Wl,-z,now -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 10.0.1
-- The CXX compiler identification is GNU 10.0.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- 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<Variable>=<Value>
-- 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: 3.2.2
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:
    CMAKE_Fortran_FLAGS_RELEASE
    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-3-04/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-3-04 -B/builddir/build/BUILD/percolator-rel-3-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-04/percolator/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/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/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.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-3-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04 /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-04/percolator /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/depend.internal".
Scanning dependencies of target picked_protein
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04 /builddir/build/BUILD/percolator-rel-3-04/src/fido /builddir/build/BUILD/percolator-rel-3-04/percolator /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
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Scanning dependencies of target fido
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04 /builddir/build/BUILD/percolator-rel-3-04/src /builddir/build/BUILD/percolator-rel-3-04/percolator /builddir/build/BUILD/percolator-rel-3-04/percolator/src /builddir/build/BUILD/percolator-rel-3-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/CMakeFiles/perclibrary.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/percolator/src/CMakeFiles/perclibrary.dir/depend.internal".
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
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[  1%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Globals.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/MyException.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Database.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Database.cpp: In member function 'void PercolatorCrux::Database::print(FILE*)':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Database.cpp:206:12: warning: unused variable 'protein' [-Wunused-variable]
  206 |   Protein* protein = NULL;
      |            ^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[  8%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 11%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Peptide.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Peptide.cpp:375:13: warning: 'bool equal_peptides(char*, PercolatorCrux::Peptide*)' defined but not used [-Wunused-function]
  375 | static bool equal_peptides(
      |             ^~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 13%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/PeptideConstraint.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/PeptideSrc.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[  4%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/fido.dir/BasicBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
[ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/PickedProteinCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/PickedProteinCaller.cpp: In member function 'bool PickedProteinCaller::getProteinFragmentsAndDuplicates(std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/PickedProteinCaller.cpp:365:8: warning: unused variable 'success' [-Wunused-variable]
  365 |   bool success = true;
      |        ^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[  5%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-04/percolator/src/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 20%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::shuffle(PercolatorCrux::DECOY_TYPE_T)':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:529:9: warning: enumeration value 'PEPTIDE_REVERSE_DECOYS' not handled in switch [-Wswitch]
  529 |   switch(decoy_type){
      |         ^
In file included from /usr/include/string.h:495,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'char* PercolatorCrux::Protein::getId()' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:571:10:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp: In member function 'char* PercolatorCrux::Protein::getId()':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:567:25: note: length computed here
  567 |   int id_length = strlen(id_) +1; // +\0
      |                   ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'void PercolatorCrux::Protein::setId(const char*)' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:600:12:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::setId(const char*)':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:596:25: note: length computed here
  596 |   int id_length = strlen(id) +1; // +\0
      |                   ~~~~~~^~~~
In file included from /usr/include/string.h:495,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'void PercolatorCrux::Protein::setSequence(const char*)' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:648:12:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::setSequence(const char*)':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:644:40: note: length computed here
  644 |   unsigned int sequence_length = strlen(sequence) +1; // +\0
      |                                  ~~~~~~^~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'char* PercolatorCrux::Protein::getAnnotation()' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:684:17:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp: In member function 'char* PercolatorCrux::Protein::getAnnotation()':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:681:33: note: length computed here
  681 |   int annotation_length = strlen(annotation_) +1; // +\0
      |                           ~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'virtual char* PercolatorCrux::Protein::getSequence(int)' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:618:17,
    inlined from 'void PercolatorCrux::Protein::print(FILE*)' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:130:31:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::print(FILE*)':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:615:40: note: length computed here
  615 |   unsigned int sequence_length = strlen(sequence_) +1-offset; // +\0
      |                                  ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:12:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'virtual char* PercolatorCrux::Protein::getSequence(int)' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:618:17,
    inlined from 'static void PercolatorCrux::Protein::copy(PercolatorCrux::Protein*, PercolatorCrux::Protein*)' at /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:245:36:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp: In static member function 'static void PercolatorCrux::Protein::copy(PercolatorCrux::Protein*, PercolatorCrux::Protein*)':
/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/Protein.cpp:615:40: note: length computed here
  615 |   unsigned int sequence_length = strlen(sequence_) +1-offset; // +\0
      |                                  ~~~~~~^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 21%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/picked_protein/ProteinPeptideIterator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 24%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 24%] Built target picked_protein
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 18%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
[ 23%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const string&, bool, std::string, std::string, std::string, std::string, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
  170 |     int i(1);
      |         ^
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[ 26%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-04/src/serializer.cxx
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[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/DescriptionOfCorrect.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/DescriptionOfCorrect.cpp:23:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
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[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/MassHandler.cpp
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[ 28%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/BaseSpline.cpp
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[ 33%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/fido.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Numerical.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/fido.dir/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Random.cpp
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[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PSMDescription.cpp
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[ 27%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
[ 37%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/fido.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Set.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
   26 | PSMDescriptionDOC::PSMDescriptionDOC() :
      | ^~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
      | ^~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/ResultHolder.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 40%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/fido.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Vector.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 46%] Linking CXX static library libfido.a
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido && /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a  CMakeFiles/fido.dir/BasicBigraph.cpp.o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o CMakeFiles/fido.dir/Numerical.cpp.o CMakeFiles/fido.dir/Random.cpp.o CMakeFiles/fido.dir/Set.cpp.o CMakeFiles/fido.dir/Vector.cpp.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 46%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/StdvNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-04/percolator/src/percolator_out.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/SetHandler.cpp: In member function 'int SetHandler::getNumFeatures(const string&, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp:158:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
  158 |   double a = reader.readDouble();
      |          ^
/builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp: In member function 'void SetHandler::readPSMs(std::istream&, std::string&, bool, bool&, std::vector<OptionalField>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp:290:18: warning: unused variable 'targetIdx' [-Wunused-variable]
  290 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
      |                  ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp:290:34: warning: unused variable 'decoyIdx' [-Wunused-variable]
  290 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
      |                                  ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp: In member function 'int SetHandler::readAndScoreTab(std::istream&, std::vector<double>&, Scores&, SanityCheck*&)':
/builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.cpp:486:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  486 |   if (hasDefaultValues && init_values.size() > numFeatures) {
      |                           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.h:29,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.h: In constructor 'XMLInterface::XMLInterface(const string&, bool, bool, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.h:99:8: warning: 'XMLInterface::reportUniquePeptides_' will be initialized after [-Wreorder]
   99 |   bool reportUniquePeptides_;
      |        ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.h:93:8: warning:   'bool XMLInterface::printDecoys_' [-Wreorder]
   93 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.cpp:58:1: warning:   when initialized here [-Wreorder]
   58 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.cpp: In member function 'int XMLInterface::readAndScorePin(std::istream&, std::vector<double>&, Scores&, const string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)':
/builddir/build/BUILD/percolator-rel-3-04/src/XMLInterface.cpp:257:26: warning: unused variable 'numFeatures' [-Wunused-variable]
  257 |       const unsigned int numFeatures = FeatureNames::getNumFeatures();
      |                          ^~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/svm.cpp
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[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Globals.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Enzyme.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Normalizer.cpp
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[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/UniNormalizer.cpp
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[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/SanityCheck.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-rel-3-04/src/SanityCheck.h: In constructor 'SanityCheck::SanityCheck()':
/builddir/build/BUILD/percolator-rel-3-04/src/SanityCheck.h:87:8: warning: 'SanityCheck::concatenatedSearch_' will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/SanityCheck.h:72:10: warning:   'double SanityCheck::test_fdr_' [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.h:28,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/CrossValidation.cpp: In member function 'int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)':
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:110:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  110 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:114:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  114 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp: In member function 'int CrossValidation::doStep(bool, Normalizer*, double)':
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:232:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  232 |   for (int set = 0; set < numFolds_; ++set) {
      |                     ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:238:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  238 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:248:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  248 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:280:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  280 |     for (int set = 1; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp: In member function 'void CrossValidation::postIterationProcessing(Scores&, SanityCheck*)':
/builddir/build/BUILD/percolator-rel-3-04/src/CrossValidation.cpp:470:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  470 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
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[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/FeatureNames.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/DataSet.cpp: In member function 'void DataSet::print_features()':
/builddir/build/BUILD/percolator-rel-3-04/src/DataSet.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   69 |   for (int i = 0; i < getSize(); i++) {
      |                   ~~^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/LogisticRegression.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Caller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Caller.cpp: In member function 'bool Caller::parseOptions(int, char**)':
/builddir/build/BUILD/percolator-rel-3-04/src/Caller.cpp:682:7: warning: label 'std' defined but not used [-Wunused-label]
  682 |       std:cerr << "Error: the --static option requires the --init-weights "
      |       ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PosteriorEstimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/builddir/build/BUILD/percolator-rel-3-04/src/PosteriorEstimator.cpp: In static member function 'static void PosteriorEstimator::getQValuesFromPEP(const std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/PosteriorEstimator.cpp:468:14: warning: unused variable 'queue' [-Wunused-variable]
  468 |  int nP = 1, queue = 0;
      |              ^~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/SqtSanityCheck.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:34,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h: In constructor 'ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)':
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:238:16: warning: 'ProteinProbEstimator::absenceRatio_' will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:238:10: warning:   'double ProteinProbEstimator::pi0_' [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:242:16: warning: 'ProteinProbEstimator::numberTargetProteins_' will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:237:8: warning:   'bool ProteinProbEstimator::usePi0_' [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:243:15: warning: 'ProteinProbEstimator::decoyPattern_' will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:240:10: warning:   'double ProteinProbEstimator::fdr_' [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
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[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/ssl.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PackedVector.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Scores.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/Scores.cpp:32:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.cpp: In member function 'void Scores::fillFeatures(SetHandler&)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.cpp:292:29: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  292 |   if (totalNumberOfTargets_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
      |       ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.cpp:295:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  295 |   if (totalNumberOfDecoys_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PackedMatrix.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Logger.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/EludeModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/EludeModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/EludeModel.cpp:34:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
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[ 84%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/MyException.cpp
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/ProteinScoreHolder.cpp
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In file included from /builddir/build/BUILD/percolator-rel-3-04/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinScoreHolder.h: In constructor 'ProteinScoreHolder::ProteinScoreHolder(std::string, bool, ProteinScoreHolder::Peptide, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinScoreHolder.h:108:8: warning: 'ProteinScoreHolder::isDecoy_' will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinScoreHolder.h:106:7: warning:   'int ProteinScoreHolder::groupId_' [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/Matrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/Matrix.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 85%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:34,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.h:20,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.h: In constructor 'FidoInterface::FidoInterface(double, double, double, bool, bool, bool, unsigned int, double, double, double, double, bool, std::string, bool, double)':
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.h:110:10: warning: 'FidoInterface::mseThreshold_' will be initialized after [-Wreorder]
  110 |   double mseThreshold_;
      |          ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.h:106:8: warning:   'bool FidoInterface::doGridSearch_' [-Wreorder]
  106 |   bool doGridSearch_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp:76:1: warning:   when initialized here [-Wreorder]
   76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
      | ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp: In member function 'double FidoInterface::estimatePriors(Scores&)':
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp:132:10: warning: variable 'prior' set but not used [-Wunused-but-set-variable]
  132 |   double prior, prior2, prior3, prior4;
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp: In member function 'void FidoInterface::getEstimated_and_Empirical_FDR(const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, const std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp:556:12: warning: unused variable 'prob' [-Wunused-variable]
  556 |     double prob = probabilities[k];
      |            ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/FidoInterface.cpp:558:14: warning: unused variable 'fpChange' [-Wunused-variable]
  558 |     unsigned fpChange = proteinNames[k].size() - tpChange;
      |              ^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 88%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/ProteinProbEstimator.h:34,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.h: In constructor 'PickedProteinInterface::PickedProteinInterface(const string&, double, bool, bool, bool, double, bool, std::string&, double)':
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.h:86:10: warning: 'PickedProteinInterface::maxPeptidePval_' will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.h:85:8: warning:   'bool PickedProteinInterface::reportFragmentProteins_' [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.h:85:33: warning: 'PickedProteinInterface::reportDuplicateProteins_' will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.h:83:26: warning:   'ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_' [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp: In member function 'virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)':
/builddir/build/BUILD/percolator-rel-3-04/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()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp: In member function 'virtual void PickedProteinInterface::computeProbabilities(const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/PickedProteinInterface.cpp:344:13: warning: unused variable 'significantPeptides' [-Wunused-variable]
  344 |         int significantPeptides = 0;
      |             ^~~~~~~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-04/percolator/src -I/builddir/build/BUILD/percolator-rel-3-04/src/. -I/builddir/build/BUILD/percolator-rel-3-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-04/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/main.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
[100%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-rel-3-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
/usr/bin/c++  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -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 -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o  -o percolator  libperclibrary.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -lstdc++ 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-04
+ mkdir -p fido
+ pushd fido
~/build/BUILD/percolator-rel-3-04/fido ~/build/BUILD/percolator-rel-3-04
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ /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_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 '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -pie -Wl,-z,now' -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=riscv64 ../src/fido
-- The C compiler identification is GNU 10.0.1
-- The CXX compiler identification is GNU 10.0.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
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_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-3-04/fido
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-04/src/fido -B/builddir/build/BUILD/percolator-rel-3-04/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-04/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-3-04/fido'
cd /builddir/build/BUILD/percolator-rel-3-04/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/fido /builddir/build/BUILD/percolator-rel-3-04/src/fido /builddir/build/BUILD/percolator-rel-3-04/fido /builddir/build/BUILD/percolator-rel-3-04/fido /builddir/build/BUILD/percolator-rel-3-04/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-04/fido/CMakeFiles/fido.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/fido/CMakeFiles/fido.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-04/fido/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/fido/CMakeFiles/fido.dir/depend.internal".
Scanning dependencies of target fido
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
/usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
[ 50%] Building CXX object CMakeFiles/fido.dir/Numerical.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
[ 62%] Building CXX object CMakeFiles/fido.dir/Random.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/Random.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
[ 75%] Building CXX object CMakeFiles/fido.dir/Set.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/Set.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Set.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
[ 37%] Building CXX object CMakeFiles/fido.dir/BasicGroupBigraph.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/BasicGroupBigraph.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   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:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
../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-3-04/fido'
[ 87%] Building CXX object CMakeFiles/fido.dir/Vector.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/Vector.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/Vector.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
[ 37%] Building CXX object CMakeFiles/fido.dir/GroupPowerBigraph.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/GroupPowerBigraph.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/GroupPowerBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   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:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
../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-3-04/fido'
[ 12%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/fido/BasicBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   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:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   53 |   int label;
      |       ^~~~~
../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   52 |   PSMDescription* pPSM;
      |                   ^~~~
../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-3-04/fido'
[100%] Linking CXX static library libfido.a
/usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a  CMakeFiles/fido.dir/BasicBigraph.o CMakeFiles/fido.dir/BasicGroupBigraph.o CMakeFiles/fido.dir/GroupPowerBigraph.o CMakeFiles/fido.dir/Numerical.o CMakeFiles/fido.dir/Random.o CMakeFiles/fido.dir/Set.o CMakeFiles/fido.dir/Vector.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/fido/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-04
+ mkdir -p converters
~/build/BUILD/percolator-rel-3-04/converters ~/build/BUILD/percolator-rel-3-04
+ pushd converters
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ /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_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_CXX_FLAGS_RELEASE:STRING=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -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 -fPIC -pie -Wl,-z,now -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=riscv64 ../src/converters
-- The C compiler identification is GNU 10.0.1
-- The CXX compiler identification is GNU 10.0.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- 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-CONVERTERS:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- 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-3-04/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: 3.2.2
-- Package CodeSynthesis XSD found: /usr/include
-- 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/include (found suitable version "1.69.0", minimum required is "1.46.0") found components: filesystem system 
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Generating classes from xsd-schema using CodeSynthesis
-- Generating /builddir/build/BUILD/percolator-rel-3-04/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-04/converters/gaml_tandem1.0.hxx
-- SQL Lite 3 found: /usr/include
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
-- ZLIB found: /usr/include, /usr/lib64/libz.so
-- Using FragSpectrumScanDatabaseTokyodb.cpp
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:
    CMAKE_Fortran_FLAGS_RELEASE
    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-3-04/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-3-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/depend.internal".
Scanning dependencies of target generate_perc_xsdfiles
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend.internal".
Scanning dependencies of target RAMP
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
/usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
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make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/perclibrary_part.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/perclibrary_part.dir/depend.internal".
Scanning dependencies of target perclibrary_part
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
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cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/converters.dir/DependInfo.cmake --color=
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Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/converters.dir/depend.internal".
Scanning dependencies of target converters
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[  5%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/RAMP.dir/ramp_base64.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp_base64.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[  7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/RAMP.dir/ramp.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:34:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:188:16: note: in expansion of macro 'ramp_fgets'
  188 |         (void) ramp_fgets(buf, sizeof(buf) - 1, result);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:343:3: note: in expansion of macro 'ramp_fread'
  343 |   ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
      |   ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:509:18: note: in expansion of macro 'ramp_fgets'
  509 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:541:18: note: in expansion of macro 'ramp_fgets'
  541 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:575:16: note: in expansion of macro 'ramp_fgets'
  575 |         (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:967:18: note: in expansion of macro 'ramp_fgets'
  967 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:984:18: note: in expansion of macro 'ramp_fgets'
  984 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1056:10: note: in expansion of macro 'ramp_fgets'
 1056 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1058:12: note: in expansion of macro 'ramp_fgets'
 1058 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1479:11: note: in expansion of macro 'ramp_fread'
 1479 |           ramp_fread(pData + partial, (int)(peaksLen - partial), pFI);
      |           ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1571:14: note: in expansion of macro 'ramp_fgets'
 1571 |       (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
      |              ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1573:16: note: in expansion of macro 'ramp_fgets'
 1573 |         (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1626:18: note: in expansion of macro 'ramp_fgets'
 1626 |           (void) ramp_fgets(buf, sizeof(buf) - 1 , pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1658:9: note: in expansion of macro 'ramp_fread'
 1658 |         ramp_fread(pData + partial, peaksLen - partial, pFI);
      |         ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1792:10: note: in expansion of macro 'ramp_fgets'
 1792 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1795:12: note: in expansion of macro 'ramp_fgets'
 1795 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1816:12: note: in expansion of macro 'ramp_fgets'
 1816 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1926:10: note: in expansion of macro 'ramp_fgets'
 1926 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1933:13: note: in expansion of macro 'ramp_fgets'
 1933 |      (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |             ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1989:14: note: in expansion of macro 'ramp_fgets'
 1989 |       (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |              ^~~~~~~~~~
In file included from /usr/include/stdio.h:871,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:28,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:34:
In function 'int fprintf(FILE*, const char*, ...)',
    inlined from 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)' at /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1602:20:
/usr/include/bits/stdio2.h:100:24: warning: '%.*s' directive argument is null [-Wformat-overflow=]
  100 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  101 |    __va_arg_pack ());
      |    ~~~~~~~~~~~~~~~~~    
In function 'int fprintf(FILE*, const char*, ...)',
    inlined from 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)' at /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:1616:20:
/usr/include/bits/stdio2.h:100:24: warning: '%.*s' directive argument is null [-Wformat-overflow=]
  100 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
      |          ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  101 |    __va_arg_pack ());
      |    ~~~~~~~~~~~~~~~~~    
In file included from /usr/include/string.h:495,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.h:123,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:34:
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'int rampSelfTest(char*)' at /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 256 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
    inlined from 'int rampSelfTest(char*)' at /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12:
/usr/include/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound 256 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/builddir/build/BUILD/percolator-rel-3-04/src/converters/Reader.cpp: In member function 'void Reader::translateFileToXML(const string&, bool, unsigned int, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/Reader.cpp:319:32: warning: 'tcd' may be used uninitialized in this function [-Wmaybe-uninitialized]
  319 |         tmpDirs[lineNumber_par]=tcd;
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/converters.dir/MzidentmlReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MzidentmlReader.cpp
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/builddir/build/BUILD/percolator-rel-3-04/src/converters/MzidentmlReader.cpp: In member function 'virtual void MzidentmlReader::getMaxMinCharge(const string&, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MzidentmlReader.cpp:86:30: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
   86 |   } catch (ifstream::failure e) {
      |                              ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MzidentmlReader.cpp:94:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=]
   94 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
   97 |   } catch (std::exception e) {
      |                           ^
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/builddir/build/BUILD/percolator-rel-3-04/src/converters/SequestReader.cpp: In member function 'virtual void SequestReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/SequestReader.cpp:169:12: warning: unused variable 'PI' [-Wunused-variable]
  169 |     double PI = boost::lexical_cast<double>(item.calculatedPI().get());
      |            ^~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/SequestReader.cpp:174:14: warning: unused variable 'peptide_length' [-Wunused-variable]
  174 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
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Dependee "/builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/depend.internal".
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Scanning dependencies of target MSToolkit
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const string&, bool, std::string, std::string, std::string, std::string, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-04/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
  170 |     int i(1);
      |         ^
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cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/MSObject.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSObject.cpp
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/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSObject.cpp: In copy constructor 'MSObject::MSObject(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSObject.cpp:21:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   21 |   for(i=0;i<m.vSpectrum->size();i++){
      |           ~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSObject.cpp: In member function 'MSObject& MSObject::operator=(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSObject.cpp:36:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   36 |     for(i=0;i<m.vSpectrum->size();i++){
      |             ~^~~~~~~~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp
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/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In function 'LazyMatrix* flip_lazy_matrix(LazyMatrix&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:21:23: 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-3-04/src/converters/MSToolkit/LazyMatrix.cpp:22:24: 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-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor 'LazyMatrix::LazyMatrix(const self&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
   56 |      *data_copies++;
      |      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::copy_m_flip(const self&)':
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:101:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  101 |           for ( int i = 0 ; i < m.size() ; i++ ) {
      |                             ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(LazyMatrix::value_type, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:115:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  115 |    for ( int i = 0 ; i < m.size() ; i++ ) {
      |                      ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::_get_row_retain(std::vector<float>&, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable 'b' set but not used [-Wunused-but-set-variable]
  179 |              std::vector<float>::iterator b = this->m[i]->begin();
      |                                           ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::add_val(float)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:313:24: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  313 |   for ( uint i = 0 ; i < nrows ; i++ ) {
      |                      ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::mult_val(float)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:322:24: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  322 |   for ( uint i = 0 ; i < nrows ; i++ ) {
      |                      ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::div_val(float)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:331:24: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  331 |   for ( uint i = 0 ; i < nrows ; i++ ) {
      |                      ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_min_val(float)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:339:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  339 |     for ( uint i = 0 ; i < nrows ; i++ ) {
      |                        ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_max_val(float)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:351:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  351 |     for ( uint i = 0 ; i < nrows ; i++ ) {
      |                        ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::column_shift(int)':
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/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-3-04/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-3-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::linear_shift(int)':
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/converters/MSToolkit/LazyMatrix.cpp:393:29: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  393 |     for ( uint i = shift; i < nrows; i++ ) {
      |                           ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/LazyMatrix.cpp:412:39: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  412 |     for ( uint i = nrows - offset ; i < nrows; i++ ) {
      |                                     ~~^~~~~~~
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 56%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/MSReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::appendFile(Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:916:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  916 |    for(int i=0; i<chgs.size(); i++)
      |                 ~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:750:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  750 |   int err;
      |       ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:756:9: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
  756 |   uLong sizeM;
      |         ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:757:9: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
  757 |   uLong sizeI;
      |         ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::executeSqlStmt(Spectrum&, char*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable 'charge' [-Wunused-variable]
 1187 |   int charge=-1;
      |       ^~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeCompressSpec(FILE*, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1610:6: warning: variable 'err' set but not used [-Wunused-but-set-variable]
 1610 |  int err;
      |      ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1616:8: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
 1616 |  uLong sizeM;
      |        ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1617:8: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
 1617 |  uLong sizeI;
      |        ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'int MSReader::openFile(const char*, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:101:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  101 |       fread(&iFType,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:102:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  102 |       fread(&iVersion,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:103:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  103 |    fread(&header,sizeof(MSHeader),1,fileIn);
      |    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::readFile(const char*, bool, Spectrum&, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:189:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  189 |          fread(&i,4,1,fileIn);
      |          ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:191:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  191 |          fread(&i,4,1,fileIn);
      |          ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:207:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  207 |       fread(&z.z,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:208:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  208 |       fread(&z.mz,8,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:213:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  213 |       fread(&ez.z,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:214:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  214 |       fread(&ez.mh,8,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:215:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  215 |       fread(&ez.pRTime,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:216:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  216 |       fread(&ez.pArea,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:239:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  239 |        fread(&p.mz,8,1,fileIn);
      |        ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:240:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  240 |        fread(&p.intensity,4,1,fileIn);
      |        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:280:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  280 |        fgets(tstr,256,fileIn);
      |        ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:285:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  285 |        fgets(tstr,256,fileIn);
      |        ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:297:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  297 |         fgets(tstr,256,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:347:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  347 |          fgets(tstr,256,fileIn);
      |          ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:374:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  374 |          fgets(tstr,256,fileIn);
      |          ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:377:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  377 |        fgets(tstr,256,fileIn);
      |        ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:400:17: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  400 |            fgets(tstr,256,fileIn);
      |            ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:405:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
  405 |        fscanf(fileIn,"%lf %f\n",&p.mz,&p.intensity);
      |        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:411:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  411 |         fgets(tstr,256,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readCompressSpec(FILE*, MSScanInfo&, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1669:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1669 |  fread(&i,4,1,fileIn);
      |  ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1671:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1671 |  fread(&i,4,1,fileIn);
      |  ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1677:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1677 |  fread(compr,mzLen,1,fileIn);
      |  ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1684:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1684 |  fread(compr,intensityLen,1,fileIn);
      |  ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readSpecHeader(FILE*, MSScanInfo&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1882:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1882 |   fread(&ms.scanNumber[0],4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1884:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1884 |   fread(&ms.scanNumber[1],4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1885:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1885 |   fread(&ms.mz,8,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1886:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1886 |   fread(&ms.rTime,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1889:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1889 |     fread(&ms.BPI,4,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1890:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1890 |     fread(&ms.BPM,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1891:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1891 |     fread(&ms.convA,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1892:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1892 |     fread(&ms.convB,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1893:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1893 |     fread(&ms.TIC,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1894:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1894 |     fread(&ms.IIT,4,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1897:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1897 |   fread(&ms.numZStates,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1899:24: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1899 |   if(iVersion>=3) fread(&ms.numEZStates,4,1,fileIn);
      |                   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1902:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1902 |   fread(&ms.numDataPoints,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp: In member function 'MSFileFormat MSReader::checkFileFormat(const char*)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1952:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1952 |   fread(&i,4,1,f);
      |   ~~~~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSReader.cpp:1953:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1953 |   fread(&iVersion,4,1,f);
      |   ~~~~~^~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 60%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSTAllRT.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSTAllRT.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSTAllRT.cpp:51:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   51 |   for ( int i = 0 ; i < rts.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSTAllRT.cpp:26:15: warning: variable 'ff' set but not used [-Wunused-but-set-variable]
   26 |  MSFileFormat ff;
      |               ^~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 61%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 32%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o
/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/converters.dir/MsgfplusReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MsgfplusReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/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<FragSpectrumScanDatabase>, const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MsgfplusReader.cpp:333:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  333 |             else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |             ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MsgfplusReader.cpp:333:90: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  333 |             else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                                                                                          ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MsgfplusReader.cpp:272:14: warning: unused variable 'peptide_length' [-Wunused-variable]
  272 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MsgfplusReader.cpp:291:12: warning: variable 'SpecEValue' set but not used [-Wunused-but-set-variable]
  291 |     double SpecEValue = 0.0;
      |            ^~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 65%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp: In member function 'Spectrum& Spectrum::operator=(const Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp:81:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   81 |     for(i=0;i<s.vPeaks->size();i++){
      |             ~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp:85:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<EZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   85 |     for(i=0;i<s.vEZ->size();i++){
      |             ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp:89:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   89 |     for(i=0;i<s.vZ->size();i++){
      |             ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp: In member function 'bool Spectrum::getRawFilter(char*, int)':
/builddir/build/BUILD/percolator-rel-3-04/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<strlen(rawFilter)) {
      |      ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp: In member function 'float Spectrum::getTotalIntensity()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp:389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  389 |   for(int i=0; i<vPeaks->size(); i++)
      |                ~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::setPeaks(std::vector<Peak_T>)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp:428:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  428 |   for(int i=0; i<peaks.size(); i++)
      |                ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::printMe()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/Spectrum.cpp:453:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  453 |   for(int i=0; i<vPeaks->size(); i++)
      |                ~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 41%] Building CXX object CMakeFiles/converters.dir/TandemReader.cpp.o
/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/TandemReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/TandemReader.cpp: In member function 'void TandemReader::createPSM(const domain_type&, double, unsigned int, double, double, bool, boost::shared_ptr<FragSpectrumScanDatabase>, const peptideProteinMapType&, const string&, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/TandemReader.cpp:491:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  491 |     f_seq.push_back( charge == c ? 1.0 : 0.0);
      |                      ~~~~~~~^~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 63%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSWarper.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
  600 |    int a = 3;
      |        ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSWarper.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSWarper.cpp:87:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<const char*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   87 |   for ( int f_idx = 0; f_idx < ms1_file_names.size() ; f_idx++ ) {
      |                        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
[ 67%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o
/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/FragSpectrumScanDatabase.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/FragSpectrumScanDatabase.cpp: In member function 'std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/FragSpectrumScanDatabase.cpp:80:19: warning: comparison of integer expressions of different signedness: 'const int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   80 |     if (it->first <= peptideSeq.length()) {
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 72%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o
/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function 'virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable 'valueSize' [-Wunused-variable]
  165 |   size_t valueSize(buf.size ());
      |          ^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 69%] Building CXX object CMakeFiles/converters.dir/Interface.cpp.o
/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/Interface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/Interface.h: In constructor 'Interface::Interface()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/Interface.h:50:7: warning: 'Interface::xmlOutput' will be initialized after [-Wreorder]
   50 |  bool xmlOutput;
      |       ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/Interface.h:47:14: warning:   'std::string Interface::outputFN' [-Wreorder]
   47 |  std::string outputFN;
      |              ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/Interface.cpp:21:1: warning:   when initialized here [-Wreorder]
   21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
      | ^~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_base.cpp
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In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_base.cpp:16:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/msmat.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp
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In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:17:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
  600 |    int a = 3;
      |        ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor(float)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:37:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   37 |        for ( int i = 0 ; i < precursors.size() ; i++ )
      |                          ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor_idx(int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:48:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   48 |         for ( int i = 0 ; i < ti.size() ; i++ ) {
      |                           ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In constructor 'transition_manager::transition_manager(std::vector<transition_info>)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:57:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   57 |       for ( int  i = 0 ; i < transitions.size() ; i++ ) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::init_transitions_from_labels()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   86 |    for ( int i = 0 ; i < labels.size() ; i++ ) {
      |                      ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_input(std::ifstream&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:119:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  119 |      for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
      |                             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:120:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  120 |          for ( int c_idx = 0 ; c_idx < this->get_num_rts() ; c_idx++ ) {
      |                                ~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:117:10: warning: unused variable 'num_chroms' [-Wunused-variable]
  117 |      int num_chroms = this->get_num_mzs();
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:118:10: warning: unused variable 'num_rts' [-Wunused-variable]
  118 |      int num_rts = this->get_num_rts();
      |          ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_dist_set(int, std::vector<int>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:228:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  228 |     for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom_set(int, std::vector<std::pair<int, int> >&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:247:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  247 |     for ( int i = 1 ; i < retain_range.size() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:255:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     for ( int i = 0 ; i < delete_range.size() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:237:9: warning: unused variable 'set_idx' [-Wunused-variable]
  237 |     int set_idx = 0;
      |         ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom(int, int, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:266:39: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  266 |   for ( int i = stop_scan_idx + 1 ; i < get_num_rts() ; i++ ) {
      |                                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::check_size_from_position() const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:283:30: warning: comparison of integer expressions of different signedness: 'off64_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  283 |   if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
      |        ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::rt_to_rtidx(float) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:417:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  417 |      if ( iter_delt == rts.size() - 1 )
      |           ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::calc_bp_chrom()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:680:28: warning: variable 'scan_length' set but not used [-Wunused-but-set-variable]
  680 |   int scan_idx, num_scans, scan_length;
      |                            ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::time_interpolate(double, msmat&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1068:14: warning: variable 'dim' set but not used [-Wunused-but-set-variable]
 1068 |   matrix_dim dim = get_data_dim();
      |              ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_median() const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1278:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1278 |   for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1279:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1279 |     for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_avg(int) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1294:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1294 |     if ( i < 0 || i >= get_num_rts()  ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_twomat_num(const msmat&, double, double, int) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1325:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1325 |                                      for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
      |                                                               ~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1327:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1327 |                                        if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
      |                                                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_mat_denom(double, int) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1350:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1350 |     if ( i < 0 || i >= get_num_rts() ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::correlation_w_shift(const msmat&, int) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1368:17: warning: unused variable 'self' [-Wunused-variable]
 1368 |   const msmat & self = *this;
      |                 ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1422:9: warning: unused variable 'foo' [-Wunused-variable]
 1422 |     int foo = 5;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_chrom(int, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1498:11: warning: unused variable 'volatile_this' [-Wunused-variable]
 1498 |   msmat * volatile_this;
      |           ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::scan_scramble()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1555:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1555 |   for ( int i = 0 ; i < get_num_rts() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1561:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1561 |   for ( int i = 0 ; i < scram_cmds.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In function 'msmat* test_msmat(int, char**)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1605:19: warning: variable 'ti_file' set but not used [-Wunused-but-set-variable]
 1605 |   FILE * o_file, *ti_file, *sg_file;
      |                   ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1605:29: warning: variable 'sg_file' set but not used [-Wunused-but-set-variable]
 1605 |   FILE * o_file, *ti_file, *sg_file;
      |                             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In function 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1746:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1746 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1762:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1762 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1828:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1828 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1858:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1858 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1880:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1880 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1898:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1898 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'bool msmat::equals_data(const msmat&, double) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1921:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1921 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::sum_abs_diffs(const msmat&) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1944:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1944 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1941:10: warning: unused variable 'nrows' [-Wunused-variable]
 1941 |   size_t nrows = get_num_rows();
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/converters/MSToolkit/msmat.cpp:2004:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2004 |     for ( int i = 0 ; i < rts_slice.size() - 1 ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:2010:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2010 |   for ( int i = 0 ; i < mzs_slice.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:2019:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2019 |     for ( int j = 0 ; j < out_chrom.size() - 1 ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1990:13: warning: unused variable 'num_mzs' [-Wunused-variable]
 1990 |   const int num_mzs = get_num_mzs();
      |             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:2071:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2071 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
      |                     ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_chroms::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:2095:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2095 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
      |                     ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/src/converters/MSToolkit/msmat.cpp:2109:7: warning: unused variable 'start_rt_idx' [-Wunused-variable]
 2109 |   int start_rt_idx = this->rt_to_rtidx(start_rt);
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:2110:7: warning: unused variable 'stop_rt_idx' [-Wunused-variable]
 2110 |   int stop_rt_idx = this->rt_to_rtidx(stop_rt);
      |       ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:17:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1740:9: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' defined but not used [-Wunused-function]
 1740 | msmat * msmat_from_thevoid
      |         ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1713:6: warning: 'void output_bp_chrom(msmat&, char*)' defined but not used [-Wunused-function]
 1713 | void output_bp_chrom( msmat & m, char * fname  ) {
      |      ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:1582:9: warning: 'msmat* test_msmat(int, char**)' defined but not used [-Wunused-function]
 1582 | msmat * test_msmat ( int argc , char ** argv ) {
      |         ^~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.cpp:17:
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
[ 87%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_test.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_test.cpp:4:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
  600 |    int a = 3;
      |        ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_test.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable 'm' [-Wunused-variable]
   13 |   msmat  * m;
      |            ^
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_test.cpp:4:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_test.cpp:4:
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
[ 85%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
  600 |    int a = 3;
      |        ^
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/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-3-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char>, float>&, const char*, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:22: warning: unused variable 'key_fields_len' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:38: warning: unused variable 'key_last_loc' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                      ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:52: warning: unused variable 'key_data_len' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                                    ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/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-3-04/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-3-04/src/converters/MSToolkit/msmat_header_parser.cpp:367:7: warning: unused variable 'key_data_idx' [-Wunused-variable]
  367 |   int key_data_idx;
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::write_header_field_string_list(FILE*, const char*, const std::vector<std::__cxx11::basic_string<char> >&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp:431:9: warning: unused variable 'num_elements' [-Wunused-variable]
  431 |     int num_elements = s.size();
      |         ^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 70%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rankties(std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable 'start_idx' [-Wunused-variable]
  261 |     int start_idx = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable 'stop_idx' [-Wunused-variable]
  262 |     int stop_idx = -1;
      |         ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rank_by_pos_ties(const std::vector<std::pair<float, int> >&, std::vector<float>&, bool)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:354:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<float, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  354 |       if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[i].first == last_val) ) {
      |              ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable 'last_rank' [-Wunused-variable]
  346 |     int last_rank = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:944:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  944 |     if (cumulative_area.size() == idx)
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&, const std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:990:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  990 |     if (cumulative_area.size() == idx)
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::tryptic_digester_proto(std::string, std::vector<std::__cxx11::basic_string<char> >&, int)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:1121:10: warning: unused variable 'last_tryp' [-Wunused-variable]
 1121 |     bool last_tryp = false;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp: In function 'std::vector<std::pair<std::set<int>, std::set<int> > > crawutils::permute_two_groups(IdxGroupType, IdxGroupType)':
/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/crawutils.cpp:1214:8: warning: unused variable 'g2_len' [-Wunused-variable]
 1214 |    int g2_len = g2.size();
      |        ^~~~~~
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-04/converters -I/builddir/build/BUILD/percolator-rel-3-04/src/converters  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/converters/Sqt2Pin.cpp
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/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-04
+ mkdir -p elude
+ pushd elude
~/build/BUILD/percolator-rel-3-04/elude ~/build/BUILD/percolator-rel-3-04
+ CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FFLAGS
+ FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ /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_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_CXX_FLAGS_RELEASE:STRING=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -pie -Wl,-z,now -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_PREFIX_PATH:STRING=/usr -DBoost_USE_STATIC_LIBS:BOOL=OFF -DCMAKE_USE_RELATIVE_PATHS:BOOL=ON -DTARGET_ARCH=riscv64 ../src/elude_tool
-- The C compiler identification is GNU 10.0.1
-- The CXX compiler identification is GNU 10.0.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- 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 ELUDE:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../..
-- CMAKE_PREFIX_PATH = /usr
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = riscv64
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Found Boost: /usr/include (found version "1.69.0")  
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_SKIP_INSTALL_RPATH
    CMAKE_USE_RELATIVE_PATHS
    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-3-04/elude
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-04/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
cd /builddir/build/BUILD/percolator-rel-3-04/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool /builddir/build/BUILD/percolator-rel-3-04/elude /builddir/build/BUILD/percolator-rel-3-04/elude /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/eludelibrary.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/eludelibrary.dir/depend.internal".
Scanning dependencies of target eludelibrary
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[ 17%] Building CXX object CMakeFiles/eludelibrary.dir/EludeMain.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-04/elude -I/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../../src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeMain.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[  8%] Building CXX object CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-04/elude -I/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../../src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                 ^
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                   ^
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp: In member function 'virtual int LibSVRModel::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp:284:1: warning: control reaches end of non-void function [-Wreturn-type]
  284 | }
      | ^
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp: In member function 'int LibSVRModel::CalibrateLinearModel(const std::vector<PSMDescription*>&, const int&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized in this function [-Wmaybe-uninitialized]
  205 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized in this function [-Wmaybe-uninitialized]
  204 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp: In member function 'int LibSVRModel::CalibrateRBFModel(const std::vector<PSMDescription*>&, const int&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized in this function [-Wmaybe-uninitialized]
  242 |   svr_parameters_.gamma = best_g;
      |   ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized in this function [-Wmaybe-uninitialized]
  241 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized in this function [-Wmaybe-uninitialized]
  240 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[ 21%] Building CXX object CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-04/elude -I/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../../src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibsvmWrapper.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibsvmWrapper.cpp: In function 'svm_model* libsvm_wrapper::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibsvmWrapper.cpp:172:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
  172 |   int ret;
      |       ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[  4%] Building CXX object CMakeFiles/eludelibrary.dir/DataManager.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-04/elude -I/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../../src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/eludelibrary.dir/DataManager.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/DataManager.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<std::pair<PSMDescription*, std::__cxx11::basic_string<char> > > DataManager::RemoveInSourceFragments(const Enzyme*, const double&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/DataManager.cpp:332:50: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PSMDescription*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  332 |     if (!remove_from_test && (initial_train_size != train_psms.size())) {
      |                               ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<PSMDescription*> DataManager::RemoveNonEnzymatic(const Enzyme*, std::vector<PSMDescription*>&, const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/DataManager.cpp:352:7: warning: unused variable 'initial_size' [-Wunused-variable]
  352 |   int initial_size = psms.size();
      |       ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[ 13%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-04/elude -I/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../../src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionFeatures.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionFeatures.cpp: In static member function 'static double RetentionFeatures::IndexN(const string&, const std::map<std::__cxx11::basic_string<char>, double>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionFeatures.cpp:304:21: warning: unused variable 'len' [-Wunused-variable]
  304 |   int end_position, len = peptide.size();
      |                     ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[ 26%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-04/elude -I/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../../src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:17:1: warning: "/*" within comment [-Wcomment]
   17 | /*
      |  
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                 ^
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                   ^
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:24:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.h: In constructor 'RetentionModel::RetentionModel(Normalizer*)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.h:99:16: warning: 'RetentionModel::the_normalizer_' will be initialized after [-Wreorder]
   99 |    Normalizer *the_normalizer_;
      |                ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.h:95:14: warning:   'SVRModel* RetentionModel::svr_model_' [-Wreorder]
   95 |    SVRModel *svr_model_;
      |              ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | RetentionModel::RetentionModel(Normalizer *norm) : the_normalizer_(norm),
      | ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp: In destructor 'RetentionModel::~RetentionModel()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:36:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
   36 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp: In member function 'void RetentionModel::PrintSub()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   62 |   for(int i = 0; i < vsub_.size(); ++i)
      |                  ~~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::TrainRetentionModel(const std::set<std::__cxx11::basic_string<char> >&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:187:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  187 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::SaveModelToFile(const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:291:20: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  291 |   if (vsub_.size() !=  number_features) {
      |       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::LoadModelFromFile(const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:356:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  356 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/RetentionModel.cpp:363:24: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
  363 |   int number_features, ret;
      |                        ^~~
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make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::setData(std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp:48:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   48 |   for (int i = 0; i < x.size(); ++i) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::fillResiduals(std::pair<double, double>)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   84 |   for (int i = 0; i < data.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::runLTS()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp:168:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  168 |         for (int i = 1; i < Q.size(); ++i)
      |                         ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp:177:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<dataPoint> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  177 |   for (int j = 0; j < best10Subsets.size(); ++j) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printVector(std::vector<dataPoint>)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp:209:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  209 |   for (int i = 0; i < v.size(); ++i) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printDataPoints()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/LTSRegression.cpp:220:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  220 |   for (int i = h; i < data.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
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In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
  167 |    bool remove_non_enzymatic_;
      |         ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
  143 |    bool context_format_;
      |         ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
  189 |    RetentionModel *rt_model_;
      |                    ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
  173 |    bool ignore_ptms_;
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
  196 |    bool supress_print_;
      |         ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
  175 |    bool only_hydrophobicity_index_;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
  519 |       while (found != string::npos) {
      |              ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
  639 |     int ret = 1;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
  940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-04/elude -I/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/../../src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -fopenmp -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -fPIC -pie -Wl,-z,now -I../src -I/usr/include/tirpc -O3 -DNDEBUG   -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp
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In file included from /builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
   26 | PSMDescriptionDOC::PSMDescriptionDOC() :
      | ^~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
      | ^~~~~~~~~~~~~~~~~
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make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
  167 |    bool remove_non_enzymatic_;
      |         ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
  143 |    bool context_format_;
      |         ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
  189 |    RetentionModel *rt_model_;
      |                    ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
  173 |    bool ignore_ptms_;
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
  196 |    bool supress_print_;
      |         ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
  175 |    bool only_hydrophobicity_index_;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
  519 |       while (found != string::npos) {
      |              ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
  639 |     int ret = 1;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
  940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const string&)':
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 82%] Built target perclibrary
/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-3-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04 /builddir/build/BUILD/percolator-rel-3-04/src/fido /builddir/build/BUILD/percolator-rel-3-04/percolator /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 94%] 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-3-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04 /builddir/build/BUILD/percolator-rel-3-04/src /builddir/build/BUILD/percolator-rel-3-04/percolator /builddir/build/BUILD/percolator-rel-3-04/percolator/src /builddir/build/BUILD/percolator-rel-3-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[ 97%] 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-3-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04 /builddir/build/BUILD/percolator-rel-3-04/src/qvality /builddir/build/BUILD/percolator-rel-3-04/percolator /builddir/build/BUILD/percolator-rel-3-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/percolator'
make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
[100%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/percolator/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/qvality
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 23%] 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-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 27%] 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-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/converters.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 56%] 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-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 61%] 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-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/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-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 92%] Built target msgf2pin
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[ 96%] Built target tandem2pin
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/src/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
[100%] Built target sqt2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/converters/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/converters'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64 'INSTALL=/usr/bin/install -p' -C elude
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-04/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-04/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
cd /builddir/build/BUILD/percolator-rel-3-04/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool /builddir/build/BUILD/percolator-rel-3-04/elude /builddir/build/BUILD/percolator-rel-3-04/elude /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
make[2]: Nothing to be done for 'CMakeFiles/eludelibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[ 91%] Built target eludelibrary
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
cd /builddir/build/BUILD/percolator-rel-3-04/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool /builddir/build/BUILD/percolator-rel-3-04/src/elude_tool /builddir/build/BUILD/percolator-rel-3-04/elude /builddir/build/BUILD/percolator-rel-3-04/elude /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
make[2]: Nothing to be done for 'CMakeFiles/elude.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-04/elude/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/elude
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Luna_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/yeast_40.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Luna_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Jupiter_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Luna_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Jupiter_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/yeast_20.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Luna_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Jupiter_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Jupiter_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Luna_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/tfa.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/yeast_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/elude/models/Jupiter_240.model
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-04/elude'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.04-2.fc33.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-3.04-2.fc33.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./elude/libeludelibrary.a /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.04-2.fc33.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-3.04-2.fc33.riscv64/usr/lib64/percolator
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 3.04-2.fc33 --unique-debug-suffix -3.04-2.fc33.riscv64 --unique-debug-src-base percolator-3.04-2.fc33.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-04
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/elude
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/msgf2pin
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/percolator
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/qvality
extracting debug info from /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/elude
extracting debug info from /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/percolator
extracting debug info from /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/qvality
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/sqt2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/sqt2pin
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/tandem2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/bin/tandem2pin
original debug info size: 79400kB, size after compression: 63804kB
/usr/lib/rpm/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
6020 blocks
+ /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/redhat/brp-python-bytecompile /usr/bin/python 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
*** WARNING: ./usr/src/debug/percolator-3.04-2.fc33.riscv64/converters/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.04-2.fc33.riscv64/src/parser.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.04-2.fc33.riscv64/src/serializer.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.04-2.fc33.riscv64/src/parser.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.04-2.fc33.riscv64/src/serializer.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.04-2.fc33.riscv64/elude/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.04-2.fc33.riscv64/percolator/src/Globals.h is executable but has no shebang, removing executable bit
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.l3eQ9a
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-04
+ mkdir -p test
+ cd test
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt
Pin-converter version 3.04.0, Build Date Jan 29 2020 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 
Reading ../yeast-01.sqt
Reading ../yeast-01.shuffled.sqt
+ ../percolator/src/percolator -X pout.xml pin.tab
Percolator version 3.04.0, Build Date Jan 29 2020 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 Fri Mar 27 15:13:11 2020
 on 
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 20.4943 cpu seconds or 20 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 4335 cpu seconds or 1675 seconds wall clock time.
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.04-2.fc33.riscv64
Provides: percolator = 3.04-2.fc33 percolator(riscv-64) = 3.04-2.fc33
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) libdl.so.2()(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(GOMP_4.5)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libpthread.so.0()(64bit) libpthread.so.0(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_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(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_3.4.5)(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)
Processing files: percolator-data-3.04-2.fc33.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.i2YoLa
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-data
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-data
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.XwWHob
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-data
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-data
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.04-2.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.04-2.fc33.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FHfyUb
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-static
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-static
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.DFnOId
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-static
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-static
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.04-2.fc33 percolator-static(riscv-64) = 3.04-2.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.04-2.fc33.riscv64
Provides: percolator-debugsource = 3.04-2.fc33 percolator-debugsource(riscv-64) = 3.04-2.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.04-2.fc33.riscv64
Provides: debuginfo(build-id) = 041d39946911af54c43f047530cd4419677d03d5 debuginfo(build-id) = 3cc2793df8741fec2767b9aeea931d23dafcfd2e debuginfo(build-id) = 6e91a8c5dcd3180190f304391f0a33b1cdfa4bd3 debuginfo(build-id) = 73820f24ad3a00ba22826e81d8f7481c7f64d8c0 debuginfo(build-id) = 8d7cd45b7d0d6e7847558fa8e53d062402a5dac4 debuginfo(build-id) = c0ac394dab7be2ae9ddf4685ef6ecc5d429d03a0 percolator-debuginfo = 3.04-2.fc33 percolator-debuginfo(riscv-64) = 3.04-2.fc33
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(riscv-64) = 3.04-2.fc33
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64
Wrote: /builddir/build/RPMS/percolator-debugsource-3.04-2.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-3.04-2.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.04-2.fc33.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.04-2.fc33.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.04-2.fc33.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.jgMOHb
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-04
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.04-2.fc33.riscv64
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0