Mock Version: 1.4.14
Mock Version: 1.4.14
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/f31-build-52252-27621/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 0x15580c17f0>timeout=345600uid=986gid=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=1548979200
Wrote: /builddir/build/SRPMS/percolator-3.02.01-2.fc31.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/f31-build-52252-27621/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 0x15580c17f0>timeout=345600uid=986gid=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=1548979200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.7NlXZR
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-02-01
+ /usr/bin/gzip -dc /builddir/build/SOURCES/percolator-rel-3-02-01.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-02-01
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ tar -xvf /builddir/build/SOURCES/yeast-01.sqt.tar.gz
+ 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
BUILDSTDERR: ++ jobs -p
+ exit 0
yeast-01.shuffled2.sqt
yeast-01.shuffled.sqt
yeast-01.sqt
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.aU0PcW
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ mkdir -p percolator
+ pushd percolator
+ 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
+ /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 ..
BUILDSTDERR: CMake Warning:
BUILDSTDERR:   Manually-specified variables were not used by the project:
BUILDSTDERR:     CMAKE_Fortran_FLAGS_RELEASE
BUILDSTDERR:     CMAKE_SKIP_INSTALL_RPATH
BUILDSTDERR:     INCLUDE_INSTALL_DIR
BUILDSTDERR:     LIB_INSTALL_DIR
BUILDSTDERR:     LIB_SUFFIX
BUILDSTDERR:     SHARE_INSTALL_PREFIX
BUILDSTDERR:     SYSCONF_INSTALL_DIR
+ 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
~/build/BUILD/percolator-rel-3-02-01/percolator ~/build/BUILD/percolator-rel-3-02-01
-- The C compiler identification is GNU 9.1.1
-- The CXX compiler identification is GNU 9.1.1
-- 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
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- Configuring done
-- Generating done
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-02-01/percolator
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-02-01 -B/builddir/build/BUILD/percolator-rel-3-02-01/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src/fido /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido/CMakeFiles/fido.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido/CMakeFiles/fido.dir/depend.internal".
Scanning dependencies of target fido
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/depend.internal".
Scanning dependencies of target picked_protein
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/perclibrary.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/perclibrary.dir/depend.internal".
Scanning dependencies of target perclibrary
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[  4%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[  1%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.h:5,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicGroupBigraph.h:8,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicGroupBigraph.cpp:4:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
CXX_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-3-02-01/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[  8%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[  7%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/MyException.cpp
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[  2%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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=In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.h:5,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.cpp:4:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Database.cpp: In member function 'void PercolatorCrux::Database::print(FILE*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Database.cpp:206:12: warning: unused variable 'protein' [-Wunused-variable]
BUILDSTDERR:   206 |   Protein* protein = NULL;
BUILDSTDERR:       |            ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
BUILDSTDERR:   106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
BUILDSTDERR:       |                                 ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
BUILDSTDERR:   102 |   DOMImplementation& dom_impl_;
BUILDSTDERR:       |                      ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:   144 | parser_impl::parser_impl() : clean_(true),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
BUILDSTDERR:   178 |       size_t n(s.size());
BUILDSTDERR:       |              ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   170 |     int i(1);
BUILDSTDERR:       |         ^
/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-3-02-01/src/fido/BasicBigraph.cpp
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator/src/percolator_in.cxx
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/picked_protein/Database.cpp
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BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein  -O2In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.h:5,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicGroupBigraph.h:8,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/GroupPowerBigraph.h:7,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/GroupPowerBigraph.cpp:4:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
 -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-3-02-01/src/parser.cxx
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Option.cpp
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/fido/GroupPowerBigraph.cpp
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BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fsta/builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Peptide.cpp:375:13: warning: 'bool equal_peptides(char*, PercolatorCrux::Peptide*)' defined but not used [-Wunused-function]
BUILDSTDERR:   375 | static bool equal_peptides(
BUILDSTDERR:       |             ^~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/picked_protein/Peptide.cpp
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/picked_protein/PeptideConstraint.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/picked_protein/PeptideSrc.cpp
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[ 26%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/BaseSpline.cpp
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[ 23%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/fido/Set.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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[ 28%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/picked_protein/PickedProteinCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/srcIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/DescriptionOfCorrect.cpp:23:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::shuffle(PercolatorCrux::DECOY_TYPE_T)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:529:9: warning: enumeration value 'PEPTIDE_REVERSE_DECOYS' not handled in switch [-Wswitch]
BUILDSTDERR:   529 |   switch(decoy_type){
BUILDSTDERR:       |         ^
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:12:
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'char* PercolatorCrux::Protein::getId()' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:571:10:
BUILDSTDERR: /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=]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp: In member function 'char* PercolatorCrux::Protein::getId()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:567:25: note: length computed here
BUILDSTDERR:   567 |   int id_length = strlen(id_) +1; // +\0
BUILDSTDERR:       |                   ~~~~~~^~~~~
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:12:
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'void PercolatorCrux::Protein::setId(const char*)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:600:12:
BUILDSTDERR: /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=]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::setId(const char*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:596:25: note: length computed here
BUILDSTDERR:   596 |   int id_length = strlen(id) +1; // +\0
BUILDSTDERR:       |                   ~~~~~~^~~~
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:12:
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'void PercolatorCrux::Protein::setSequence(const char*)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:648:12:
BUILDSTDERR: /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=]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::setSequence(const char*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:644:40: note: length computed here
BUILDSTDERR:   644 |   unsigned int sequence_length = strlen(sequence) +1; // +\0
BUILDSTDERR:       |                                  ~~~~~~^~~~~~~~~~
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:12:
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'char* PercolatorCrux::Protein::getAnnotation()' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:684:17:
BUILDSTDERR: /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=]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp: In member function 'char* PercolatorCrux::Protein::getAnnotation()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:681:33: note: length computed here
BUILDSTDERR:   681 |   int annotation_length = strlen(annotation_) +1; // +\0
BUILDSTDERR:       |                           ~~~~~~^~~~~~~~~~~~~
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:12:
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'virtual char* PercolatorCrux::Protein::getSequence(int)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:618:17,
BUILDSTDERR:     inlined from 'void PercolatorCrux::Protein::print(FILE*)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:130:31:
BUILDSTDERR: /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=]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::print(FILE*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:615:40: note: length computed here
BUILDSTDERR:   615 |   unsigned int sequence_length = strlen(sequence_) +1-offset; // +\0
BUILDSTDERR:       |                                  ~~~~~~^~~~~~~~~~~
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:12:
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'virtual char* PercolatorCrux::Protein::getSequence(int)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:618:17,
BUILDSTDERR:     inlined from 'static void PercolatorCrux::Protein::copy(PercolatorCrux::Protein*, PercolatorCrux::Protein*)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:245:36:
BUILDSTDERR: /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=]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp: In static member function 'static void PercolatorCrux::Protein::copy(PercolatorCrux::Protein*, PercolatorCrux::Protein*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Protein.cpp:615:40: note: length computed here
BUILDSTDERR:   615 |   unsigned int sequence_length = strlen(sequence_) +1-offset; // +\0
BUILDSTDERR:       |                                  ~~~~~~^~~~~~~~~~~
/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-3-02-01/src/DescriptionOfCorrect.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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[ 33%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/picked_protein/Protein.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/picked_protein/ProteinPeptideIterator.cpp
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BUILDSTDERR: /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/pickedIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:21:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    26 | PSMDescriptionDOC::PSMDescriptionDOC() :
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:21:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~
_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
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/PSMDescription.cpp
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator/src/percolator_out.cxx
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[ 49%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUIIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.h:36,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp: In member function 'int SetHandler::getNumFeatures(const string&, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp:160:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   160 |   double a = reader.readDouble();
BUILDSTDERR:       |          ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp: In member function 'void SetHandler::readPSMs(std::istream&, std::string&, bool, bool&, std::vector<OptionalField>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp:292:18: warning: unused variable 'targetIdx' [-Wunused-variable]
BUILDSTDERR:   292 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
BUILDSTDERR:       |                  ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp:292:34: warning: unused variable 'decoyIdx' [-Wunused-variable]
BUILDSTDERR:   292 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
BUILDSTDERR:       |                                  ^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp: In member function 'int SetHandler::readAndScoreTab(std::istream&, std::vector<double>&, Scores&, SanityCheck*&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.cpp:488:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   488 |   if (hasDefaultValues && init_values.size() > numFeatures) {
BUILDSTDERR:       |                           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
LD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/svm.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/SetHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
BUILDSTDERR: make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolatorIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.h:36,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.h:29,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.h: In constructor 'XMLInterface::XMLInterface(const string&, bool, bool, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.h:99:8: warning: 'XMLInterface::reportUniquePeptides_' will be initialized after [-Wreorder]
BUILDSTDERR:    99 |   bool reportUniquePeptides_;
BUILDSTDERR:       |        ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.h:93:8: warning:   'bool XMLInterface::printDecoys_' [-Wreorder]
BUILDSTDERR:    93 |   bool printDecoys_, printExpMass_;
BUILDSTDERR:       |        ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.cpp:58:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    58 | XMLInterface::XMLInterface(const std::string& outputFN,
BUILDSTDERR:       | ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.cpp: In member function 'int XMLInterface::readAndScorePin(std::istream&, std::vector<double>&, Scores&, const string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.cpp:257:26: warning: unused variable 'numFeatures' [-Wunused-variable]
BUILDSTDERR:   257 |       const unsigned int numFeatures = FeatureNames::getNumFeatures();
BUILDSTDERR:       |                          ^~~~~~~~~~~
'
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/XMLInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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/BUIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.h:28,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp: In member function 'int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:109:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
BUILDSTDERR:   109 |     for (int set = 0; set < numFolds_; ++set) {
BUILDSTDERR:       |                       ~~~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:113:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
BUILDSTDERR:   113 |     for (int set = 0; set < numFolds_; ++set) {
BUILDSTDERR:       |                       ~~~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp: In member function 'int CrossValidation::doStep(bool, Normalizer*, double)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:231:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
BUILDSTDERR:   231 |   for (int set = 0; set < numFolds_; ++set) {
BUILDSTDERR:       |                     ~~~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:237:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
BUILDSTDERR:   237 |     for (int set = 0; set < numFolds_; ++set) {
BUILDSTDERR:       |                       ~~~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:247:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
BUILDSTDERR:   247 |     for (int set = 0; set < numFolds_; ++set) {
BUILDSTDERR:       |                       ~~~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:279:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
BUILDSTDERR:   279 |     for (int set = 1; set < numFolds_; ++set) {
BUILDSTDERR:       |                       ~~~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp: In member function 'void CrossValidation::postIterationProcessing(Scores&, SanityCheck*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/CrossValidation.cpp:464:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
BUILDSTDERR:   464 |     for (int set = 0; set < numFolds_; ++set) {
BUILDSTDERR:       |                       ~~~~^~~~~~~~~~~
ILD/percolator-rel-3-02-01/src/Normalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/UniNormalizer.cpp
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[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/CrossValidation.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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/redhatIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/SanityCheck.cpp:21:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/SanityCheck.cpp:24:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SanityCheck.h: In constructor 'SanityCheck::SanityCheck()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SanityCheck.h:87:8: warning: 'SanityCheck::concatenatedSearch_' will be initialized after [-Wreorder]
BUILDSTDERR:    87 |   bool concatenatedSearch_;
BUILDSTDERR:       |        ^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SanityCheck.h:72:10: warning:   'double SanityCheck::test_fdr_' [-Wreorder]
BUILDSTDERR:    72 |   double test_fdr_, initial_train_fdr_;
BUILDSTDERR:       |          ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    31 | SanityCheck::SanityCheck() :
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.cpp: In member function 'void DataSet::print_features()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.cpp:62:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
BUILDSTDERR:    62 |   for (int i = 0; i < getSize(); i++) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~~
-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-3-02-01/src/SanityCheck.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/DataSet.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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 -In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.h:36,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/Caller.h:36,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/Caller.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
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-3-02-01/src/LogisticRegression.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Caller.cpp
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[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/SqtSanityCheck.cpp:17:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
ong -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-3-02-01/src/ProteinFDRestimator.cpp
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[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
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[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-/builddir/build/BUILD/percolator-rel-3-02-01/src/PosteriorEstimator.cpp: In static member function 'static void PosteriorEstimator::getQValuesFromPEP(const std::vector<double>&, std::vector<double>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PosteriorEstimator.cpp:468:14: warning: unused variable 'queue' [-Wunused-variable]
BUILDSTDERR:   468 |  int nP = 1, queue = 0;
BUILDSTDERR:       |              ^~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:34,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h: In constructor 'ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:238:16: warning: 'ProteinProbEstimator::absenceRatio_' will be initialized after [-Wreorder]
BUILDSTDERR:   238 |   double pi0_, absenceRatio_;
BUILDSTDERR:       |                ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:238:10: warning:   'double ProteinProbEstimator::pi0_' [-Wreorder]
BUILDSTDERR:   238 |   double pi0_, absenceRatio_;
BUILDSTDERR:       |          ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:242:16: warning: 'ProteinProbEstimator::numberTargetProteins_' will be initialized after [-Wreorder]
BUILDSTDERR:   242 |   unsigned int numberTargetProteins_;
BUILDSTDERR:       |                ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:237:8: warning:   'bool ProteinProbEstimator::usePi0_' [-Wreorder]
BUILDSTDERR:   237 |   bool usePi0_;
BUILDSTDERR:       |        ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:243:15: warning: 'ProteinProbEstimator::decoyPattern_' will be initialized after [-Wreorder]
BUILDSTDERR:   243 |   std::string decoyPattern_;
BUILDSTDERR:       |               ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:240:10: warning:   'double ProteinProbEstimator::fdr_' [-Wreorder]
BUILDSTDERR:   240 |   double fdr_;
BUILDSTDERR:       |          ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~~~~
02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/PosteriorEstimator.cpp
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BUILDSTDERR: [ 78%] Building CXX object srIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.cpp:32:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.cpp: In member function 'void Scores::fillFeatures(SetHandler&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.cpp:290:29: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
BUILDSTDERR:   290 |   if (totalNumberOfTargets_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
BUILDSTDERR:       |       ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.cpp:293:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
BUILDSTDERR:   293 |   if (totalNumberOfDecoys_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
BUILDSTDERR:       |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
c/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
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BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/EludeModel.cpp:34:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
01/src/Scores.cpp
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/MyException.cpp
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BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-protecIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.h: In constructor 'ProteinScoreHolder::ProteinScoreHolder(std::string, bool, ProteinScoreHolder::Peptide, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.h:108:8: warning: 'ProteinScoreHolder::isDecoy_' will be initialized after [-Wreorder]
BUILDSTDERR:   108 |   bool isDecoy_;
BUILDSTDERR:       |        ^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.h:106:7: warning:   'int ProteinScoreHolder::groupId_' [-Wreorder]
BUILDSTDERR:   106 |   int groupId_;
BUILDSTDERR:       |       ^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/ProteinScoreHolder.cpp
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[ 89%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/FeatureMemoryPool.cpp
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[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-seIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:34,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.h:20,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.h: In constructor 'FidoInterface::FidoInterface(double, double, double, bool, bool, bool, unsigned int, double, double, double, double, bool, std::string, bool, double)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.h:110:10: warning: 'FidoInterface::mseThreshold_' will be initialized after [-Wreorder]
BUILDSTDERR:   110 |   double mseThreshold_;
BUILDSTDERR:       |          ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.h:106:8: warning:   'bool FidoInterface::doGridSearch_' [-Wreorder]
BUILDSTDERR:   106 |   bool doGridSearch_;
BUILDSTDERR:       |        ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp:76:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
BUILDSTDERR:       | ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp: In member function 'double FidoInterface::estimatePriors(Scores&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp:132:10: warning: variable 'prior' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   132 |   double prior, prior2, prior3, prior4;
BUILDSTDERR:       |          ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp:556:12: warning: unused variable 'prob' [-Wunused-variable]
BUILDSTDERR:   556 |     double prob = probabilities[k];
BUILDSTDERR:       |            ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp:558:14: warning: unused variable 'fpChange' [-Wunused-variable]
BUILDSTDERR:   558 |     unsigned fpChange = proteinNames[k].size() - tpChange;
BUILDSTDERR:       |              ^~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:34,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h:26,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h: In constructor 'PickedProteinInterface::PickedProteinInterface(const string&, double, bool, bool, bool, double, bool, std::string&, double)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h:84:10: warning: 'PickedProteinInterface::maxPeptidePval_' will be initialized after [-Wreorder]
BUILDSTDERR:    84 |   double maxPeptidePval_;
BUILDSTDERR:       |          ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h:82:8: warning:   'bool PickedProteinInterface::reportFragmentProteins_' [-Wreorder]
BUILDSTDERR:    82 |   bool reportFragmentProteins_, reportDuplicateProteins_;
BUILDSTDERR:       |        ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h:82:33: warning: 'PickedProteinInterface::reportDuplicateProteins_' will be initialized after [-Wreorder]
BUILDSTDERR:    82 |   bool reportFragmentProteins_, reportDuplicateProteins_;
BUILDSTDERR:       |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h:80:26: warning:   'ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_' [-Wreorder]
BUILDSTDERR:    80 |   ProteinInferenceMethod protInferenceMethod_;
BUILDSTDERR:       |                          ^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp: In member function 'virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:165:36: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
BUILDSTDERR:   165 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
BUILDSTDERR:       |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp: In member function 'virtual void PickedProteinInterface::computeProbabilities(const string&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:319:13: warning: unused variable 'significantPeptides' [-Wunused-variable]
BUILDSTDERR:   319 |         int significantPeptides = 0;
BUILDSTDERR:       |             ^~~~~~~~~~~~~~~~~~~
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[ 88%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/PickedProteinInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 91%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a  CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/EludeModel.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
/usr/bin/ranlib libperclibrary.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 94%] Built target perclibrary
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
/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-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src/qvality /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality/CMakeFiles/qvality.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality/CMakeFiles/qvality.dir/depend.internal".
Scanning dependencies of target qvality
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/percolator.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/percolator.dir/depend.internal".
Scanning dependencies of target percolator
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
[ 95%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/qvality/qvality_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 98%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.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/qvality.dir/qvality_main.cpp.o  -o qvality  -L/builddir/build/BUILD/percolator-rel-3-02-01/percolator/src ../libperclibrary.a ../fido/libfido.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 98%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 97%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src && /usr/bin/c++  -DXML_SUPPORT -I/builddir/build/BUILD/percolatoIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/DataSet.h:31,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/SetHandler.h:36,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/Caller.h:36,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/main.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
+ popd
+ mkdir -p fido
+ pushd fido
+ 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
+ /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
BUILDSTDERR: CMake Warning:
BUILDSTDERR:   Manually-specified variables were not used by the project:
BUILDSTDERR:     CMAKE_C_FLAGS_RELEASE
BUILDSTDERR:     CMAKE_EXE_LINKER_FLAGS_RELEASE
BUILDSTDERR:     CMAKE_Fortran_FLAGS_RELEASE
BUILDSTDERR:     CMAKE_SKIP_INSTALL_RPATH
BUILDSTDERR:     CMAKE_SKIP_RPATH
BUILDSTDERR:     INCLUDE_INSTALL_DIR
BUILDSTDERR:     LIB_INSTALL_DIR
BUILDSTDERR:     LIB_SUFFIX
BUILDSTDERR:     SHARE_INSTALL_PREFIX
BUILDSTDERR:     SYSCONF_INSTALL_DIR
BUILDSTDERR:     TARGET_ARCH
BUILDSTDERR:     TokyoCabinet_INCLUDE_DIR
BUILDSTDERR:     TokyoCabinet_LIBRARY
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
r-rel-3-02-01/percolator/src -I/builddir/build/BUILD/percolator-rel-3-02-01/src/. -I/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[100%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/percolator/CMakeFiles 0
~/build/BUILD/percolator-rel-3-02-01
~/build/BUILD/percolator-rel-3-02-01/fido ~/build/BUILD/percolator-rel-3-02-01
-- The C compiler identification is GNU 9.1.1
-- The CXX compiler identification is GNU 9.1.1
-- 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
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-02-01/fido
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-02-01/src/fido -B/builddir/build/BUILD/percolator-rel-3-02-01/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/fido'
cd /builddir/build/BUILD/percolator-rel-3-02-01/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/fido /builddir/build/BUILD/percolator-rel-3-02-01/src/fido /builddir/build/BUILD/percolator-rel-3-02-01/fido /builddir/build/BUILD/percolator-rel-3-02-01/fido /builddir/build/BUILD/percolator-rel-3-02-01/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/fido/CMakeFiles/fido.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/fido/CMakeFiles/fido.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/fido/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/fido/CMakeFiles/fido.dir/depend.internal".
Scanning dependencies of target fido
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
/usr/bin/make -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
[ 25%] 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-3-02-01/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/fido/Set.cpp
BUILDSTDERR: make[2]: Leaving directory '/builddir/buIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.h:5,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicGroupBigraph.h:8,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicGroupBigraph.cpp:4:
BUILDSTDERR: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: ../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: ../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: ../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: ../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.h:5,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.cpp:4:
BUILDSTDERR: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: ../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: ../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: ../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: ../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.h:5,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicGroupBigraph.h:8,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/GroupPowerBigraph.h:7,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/GroupPowerBigraph.cpp:4:
BUILDSTDERR: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
BUILDSTDERR: ../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: ../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
BUILDSTDERR:       |   ^~~~~~~~~~~
BUILDSTDERR: ../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
BUILDSTDERR: ../src/Scores.h:53:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
BUILDSTDERR:    53 |   int label;
BUILDSTDERR:       |       ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    52 |   PSMDescription* pPSM;
BUILDSTDERR:       |                   ^~~~
BUILDSTDERR: ../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:       |   ^~~~~~~~~~~
ild/BUILD/percolator-rel-3-02-01/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/fido/Vector.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
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[ 50%] 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-3-02-01/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
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[ 12%] 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-3-02-01/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
BUILDSTDERR: make[2]: Entering directory '/builddir/build/BUILD/percolator+ popd
+ mkdir -p converters
+ 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
+ /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
BUILDSTDERR: CMake Warning:
BUILDSTDERR:   Manually-specified variables were not used by the project:
BUILDSTDERR:     CMAKE_Fortran_FLAGS_RELEASE
BUILDSTDERR:     CMAKE_SKIP_INSTALL_RPATH
BUILDSTDERR:     INCLUDE_INSTALL_DIR
BUILDSTDERR:     LIB_INSTALL_DIR
BUILDSTDERR:     LIB_SUFFIX
BUILDSTDERR:     SHARE_INSTALL_PREFIX
BUILDSTDERR:     SYSCONF_INSTALL_DIR
+ 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
-rel-3-02-01/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-3-02-01/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/fido/CMakeFiles 0
~/build/BUILD/percolator-rel-3-02-01
~/build/BUILD/percolator-rel-3-02-01/converters ~/build/BUILD/percolator-rel-3-02-01
-- The C compiler identification is GNU 9.1.1
-- The CXX compiler identification is GNU 9.1.1
-- 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-3-02-01/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
-- Boost version: 1.66.0
-- Found the following Boost libraries:
--   filesystem
--   system
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
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cd /builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/converters/MSToolkit/RAMP/ramp_base64.cpp
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[  3%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/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-annobi/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1698:13: warning: variable 'err' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1698 |         int err;
BUILDSTDERR:       |             ^~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:34:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:188:16: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:   188 |         (void) ramp_fgets(buf, sizeof(buf) - 1, result);
BUILDSTDERR:       |                ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:343:3: note: in expansion of macro 'ramp_fread'
BUILDSTDERR:   343 |   ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
BUILDSTDERR:       |   ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:509:18: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:   509 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
BUILDSTDERR:       |                  ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:541:18: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:   541 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
BUILDSTDERR:       |                  ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:575:16: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:   575 |         (void) ramp_fgets(buf, SIZE_BUF, pFI);
BUILDSTDERR:       |                ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:967:18: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:   967 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |                  ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:984:18: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:   984 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |                  ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1056:10: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1056 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |          ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1058:12: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1058 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |            ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1479:11: note: in expansion of macro 'ramp_fread'
BUILDSTDERR:  1479 |           ramp_fread(pData + partial, (int)(peaksLen - partial), pFI);
BUILDSTDERR:       |           ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1571:14: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1571 |       (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
BUILDSTDERR:       |              ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1573:16: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1573 |         (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
BUILDSTDERR:       |                ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1626:18: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1626 |           (void) ramp_fgets(buf, sizeof(buf) - 1 , pFI);
BUILDSTDERR:       |                  ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1658:9: note: in expansion of macro 'ramp_fread'
BUILDSTDERR:  1658 |         ramp_fread(pData + partial, peaksLen - partial, pFI);
BUILDSTDERR:       |         ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1792:10: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1792 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |          ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1795:12: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1795 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |            ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1816:12: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1816 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |            ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1926:10: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1926 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |          ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1933:13: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1933 |      (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |             ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
BUILDSTDERR:       |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1989:14: note: in expansion of macro 'ramp_fgets'
BUILDSTDERR:  1989 |       (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
BUILDSTDERR:       |              ^~~~~~~~~~
BUILDSTDERR: In file included from /usr/include/stdio.h:867,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.h:28,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:34:
BUILDSTDERR: In function 'int fprintf(FILE*, const char*, ...)',
BUILDSTDERR:     inlined from 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1602:20:
BUILDSTDERR: /usr/include/bits/stdio2.h:100:24: warning: '%.*s' directive argument is null [-Wformat-overflow=]
BUILDSTDERR:   100 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
BUILDSTDERR:       |          ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR:   101 |    __va_arg_pack ());
BUILDSTDERR:       |    ~~~~~~~~~~~~~~~~~    
BUILDSTDERR: In function 'int fprintf(FILE*, const char*, ...)',
BUILDSTDERR:     inlined from 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:1616:20:
BUILDSTDERR: /usr/include/bits/stdio2.h:100:24: warning: '%.*s' directive argument is null [-Wformat-overflow=]
BUILDSTDERR:   100 |   return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt,
BUILDSTDERR:       |          ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR:   101 |    __va_arg_pack ());
BUILDSTDERR:       |    ~~~~~~~~~~~~~~~~~    
BUILDSTDERR: In file included from /usr/include/string.h:494,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.h:123,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:34:
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'int rampSelfTest(char*)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12:
BUILDSTDERR: /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]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: In function 'char* strncpy(char*, const char*, size_t)',
BUILDSTDERR:     inlined from 'int rampSelfTest(char*)' at /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12:
BUILDSTDERR: /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]
BUILDSTDERR:   106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
BUILDSTDERR:       |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
n-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-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp
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cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit/RAMP && /usr/bin/cmake -E cmake_link_script CMakeFiles/RAMP.dir/link.txt --verbose=1
/usr/bin/ar qc libRAMP.a  CMakeFiles/RAMP.dir/ramp_base64.cpp.o CMakeFiles/RAMP.dir/ramp.cpp.o
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/converters/percolator_in.cxx
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[ 18%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Option.cpp.o
BUILDSTDERR: /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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/buil/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In function 'LazyMatrix* flip_lazy_matrix(LazyMatrix&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:21:23: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:    21 |  for ( uint j = 0 ; j < lm.rows() ; j++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:22:24: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:    22 |   for ( uint i = 0 ; i < lm.cols() ; i++ ) {
BUILDSTDERR:       |                      ~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor 'LazyMatrix::LazyMatrix(const self&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
BUILDSTDERR:    56 |      *data_copies++;
BUILDSTDERR:       |      ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::copy_m_flip(const self&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:67:28: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
BUILDSTDERR:    67 |       for ( uint i = 0 ; i < x.nrows ; i++ ) {
BUILDSTDERR:       |                          ~~^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   101 |           for ( int i = 0 ; i < m.size() ; i++ ) {
BUILDSTDERR:       |                             ~~^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(LazyMatrix::value_type, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   115 |    for ( int i = 0 ; i < m.size() ; i++ ) {
BUILDSTDERR:       |                      ~~^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::_get_row_retain(std::vector<float>&, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable 'b' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   179 |              std::vector<float>::iterator b = this->m[i]->begin();
BUILDSTDERR:       |                                           ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::add_val(float)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:313:24: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   313 |   for ( uint i = 0 ; i < nrows ; i++ ) {
BUILDSTDERR:       |                      ~~^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::mult_val(float)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:322:24: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   322 |   for ( uint i = 0 ; i < nrows ; i++ ) {
BUILDSTDERR:       |                      ~~^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::div_val(float)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:331:24: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   331 |   for ( uint i = 0 ; i < nrows ; i++ ) {
BUILDSTDERR:       |                      ~~^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_min_val(float)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:339:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   339 |     for ( uint i = 0 ; i < nrows ; i++ ) {
BUILDSTDERR:       |                        ~~^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_max_val(float)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:351:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   351 |     for ( uint i = 0 ; i < nrows ; i++ ) {
BUILDSTDERR:       |                        ~~^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::column_shift(int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:369:23: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   369 |   for ( uint i = 0 ;i < rows() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:370:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   370 |     for ( uint j = 0 ; j < cols() ; j++ ) {
BUILDSTDERR:       |                        ~~^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:373:21: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   373 |       if ( dest_idx >= cols() ) break;
BUILDSTDERR:       |            ~~~~~~~~~^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::linear_shift(int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:389:25: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   389 |     for ( uint i = 0; i < shift ; i++ ) {
BUILDSTDERR:       |                       ~~^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:393:29: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   393 |     for ( uint i = shift; i < nrows; i++ ) {
BUILDSTDERR:       |                           ~~^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp:412:39: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
BUILDSTDERR:   412 |     for ( uint i = nrows - offset ; i < nrows; i++ ) {
BUILDSTDERR:       |                                     ~~^~~~~~~
d/BUILD/percolator-rel-3-02-01/src/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Option.cpp
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/converters/percolator_out.cxx
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Enzyme.cpp
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[ 25%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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-switch/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSObject.cpp: In copy constructor 'MSObject::MSObject(const MSObject&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    21 |   for(i=0;i<m.vSpectrum->size();i++){
BUILDSTDERR:       |           ~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSObject.cpp: In member function 'MSObject& MSObject::operator=(const MSObject&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    36 |     for(i=0;i<m.vSpectrum->size();i++){
BUILDSTDERR:       |             ~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::appendFile(Spectrum&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   916 |    for(int i=0; i<chgs.size(); i++)
BUILDSTDERR:       |                 ~^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:750:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   750 |   int err;
BUILDSTDERR:       |       ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:756:9: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   756 |   uLong sizeM;
BUILDSTDERR:       |         ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:757:9: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   757 |   uLong sizeI;
BUILDSTDERR:       |         ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::executeSqlStmt(Spectrum&, char*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable 'charge' [-Wunused-variable]
BUILDSTDERR:  1187 |   int charge=-1;
BUILDSTDERR:       |       ^~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeCompressSpec(FILE*, Spectrum&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:1610:6: warning: variable 'err' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1610 |  int err;
BUILDSTDERR:       |      ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:1616:8: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1616 |  uLong sizeM;
BUILDSTDERR:       |        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:1617:8: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1617 |  uLong sizeI;
BUILDSTDERR:       |        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'int MSReader::openFile(const char*, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   101 |       fread(&iFType,4,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   102 |       fread(&iVersion,4,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   103 |    fread(&header,sizeof(MSHeader),1,fileIn);
BUILDSTDERR:       |    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::readFile(const char*, bool, Spectrum&, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   189 |          fread(&i,4,1,fileIn);
BUILDSTDERR:       |          ~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   191 |          fread(&i,4,1,fileIn);
BUILDSTDERR:       |          ~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   207 |       fread(&z.z,4,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   208 |       fread(&z.mz,8,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   213 |       fread(&ez.z,4,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   214 |       fread(&ez.mh,8,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   215 |       fread(&ez.pRTime,4,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   216 |       fread(&ez.pArea,4,1,fileIn);
BUILDSTDERR:       |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   239 |        fread(&p.mz,8,1,fileIn);
BUILDSTDERR:       |        ~~~~~^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   240 |        fread(&p.intensity,4,1,fileIn);
BUILDSTDERR:       |        ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   280 |        fgets(tstr,256,fileIn);
BUILDSTDERR:       |        ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   285 |        fgets(tstr,256,fileIn);
BUILDSTDERR:       |        ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   297 |         fgets(tstr,256,fileIn);
BUILDSTDERR:       |         ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   347 |          fgets(tstr,256,fileIn);
BUILDSTDERR:       |          ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   374 |          fgets(tstr,256,fileIn);
BUILDSTDERR:       |          ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:377:13: warning: ignoring res -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-3-02-01/src/converters/MSToolkit/MSObject.cpp
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[ 27%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Globals.cpp.o
/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Globals.cpp
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[ 30%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/MassHandler.cpp.o
/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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[ 29%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONeturn value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:   377 |        fgets(tstr,256,fileIn);
BUILDSTDERR:       |        ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   400 |            fgets(tstr,256,fileIn);
BUILDSTDERR:       |            ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   405 |        fscanf(fileIn,"%lf %f\n",&p.mz,&p.intensity);
BUILDSTDERR:       |        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   411 |         fgets(tstr,256,fileIn);
BUILDSTDERR:       |         ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readCompressSpec(FILE*, MSScanInfo&, Spectrum&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1669 |  fread(&i,4,1,fileIn);
BUILDSTDERR:       |  ~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1671 |  fread(&i,4,1,fileIn);
BUILDSTDERR:       |  ~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1677 |  fread(compr,mzLen,1,fileIn);
BUILDSTDERR:       |  ~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1684 |  fread(compr,intensityLen,1,fileIn);
BUILDSTDERR:       |  ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readSpecHeader(FILE*, MSScanInfo&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1882 |   fread(&ms.scanNumber[0],4,1,fileIn);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1884 |   fread(&ms.scanNumber[1],4,1,fileIn);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1885 |   fread(&ms.mz,8,1,fileIn);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1886 |   fread(&ms.rTime,4,1,fileIn);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1889 |     fread(&ms.BPI,4,1,fileIn);
BUILDSTDERR:       |     ~~~~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1890 |     fread(&ms.BPM,8,1,fileIn);
BUILDSTDERR:       |     ~~~~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1891 |     fread(&ms.convA,8,1,fileIn);
BUILDSTDERR:       |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1892 |     fread(&ms.convB,8,1,fileIn);
BUILDSTDERR:       |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1893 |     fread(&ms.TIC,8,1,fileIn);
BUILDSTDERR:       |     ~~~~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1894 |     fread(&ms.IIT,4,1,fileIn);
BUILDSTDERR:       |     ~~~~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1897 |   fread(&ms.numZStates,4,1,fileIn);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1899 |   if(iVersion>=3) fread(&ms.numEZStates,4,1,fileIn);
BUILDSTDERR:       |                   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1902 |   fread(&ms.numDataPoints,4,1,fileIn);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp: In member function 'MSFileFormat MSReader::checkFileFormat(const char*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1952 |   fread(&i,4,1,f);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1953 |   fread(&iVersion,4,1,f);
BUILDSTDERR:       |   ~~~~~^~~~~~~~~~~~~~~~~
S -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-3-02-01/src/converters/MSToolkit/MSReader.cpp
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/serializer.cxx
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cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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/MSSingleScan.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSSingleScan.cpp
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[ 38%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percola/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSTAllRT.cpp: In function 'int main(int, char**)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    51 |   for ( int i = 0 ; i < rts.size() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSTAllRT.cpp:26:15: warning: variable 'ff' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:    26 |  MSFileFormat ff;
BUILDSTDERR:       |               ^~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
BUILDSTDERR:   106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
BUILDSTDERR:       |                                 ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
BUILDSTDERR:   102 |   DOMImplementation& dom_impl_;
BUILDSTDERR:       |                      ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:   144 | parser_impl::parser_impl() : clean_(true),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
BUILDSTDERR:   178 |       size_t n(s.size());
BUILDSTDERR:       |              ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
BUILDSTDERR:   170 |     int i(1);
BUILDSTDERR:       |         ^
tor-rel-3-02-01/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-3-02-01/src/converters/MSToolkit/MSTAllRT.cpp
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/usr/bin/cmake -P CMakeFiles/perclibrary_part.dir/cmake_clean_target.cmake
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BUILDSTDERR: /usr/bin/ar qc libperclibrary_part.a  CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Option.cpp.o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Enzyme.cpp.o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Globals.cpp.o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/MassHandler.cpp.o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/serializer.cxx.o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx.o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Logger.cpp.o CMakeFil/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/Spectrum.cpp: In member function 'Spectrum& Spectrum::operator=(const Spectrum&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    81 |     for(i=0;i<s.vPeaks->size();i++){
BUILDSTDERR:       |             ~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    85 |     for(i=0;i<s.vEZ->size();i++){
BUILDSTDERR:       |             ~^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    89 |     for(i=0;i<s.vZ->size();i++){
BUILDSTDERR:       |             ~^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/Spectrum.cpp: In member function 'bool Spectrum::getRawFilter(char*, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   282 |   if(sz<strlen(rawFilter)) {
BUILDSTDERR:       |      ~~^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/Spectrum.cpp: In member function 'float Spectrum::getTotalIntensity()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   389 |   for(int i=0; i<vPeaks->size(); i++)
BUILDSTDERR:       |                ~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::setPeaks(std::vector<Peak_T>)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   428 |   for(int i=0; i<peaks.size(); i++)
BUILDSTDERR:       |                ~^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::printMe()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   453 |   for(int i=0; i<vPeaks->size(); i++)
BUILDSTDERR:       |                ~^~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSWarper.cpp:17:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   517 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   519 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   600 |    int a = 3;
BUILDSTDERR:       |        ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   703 |     int a  = 3;
BUILDSTDERR:       |         ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSWarper.cpp: In function 'int main(int, char**)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    87 |   for ( int f_idx = 0; f_idx < ms1_file_names.size() ; f_idx++ ) {
BUILDSTDERR:       |                        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSWarper.cpp:17:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: At global scope:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   812 | static int test_msmat_time_interp( msmat * msmat_f );
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   813 | static int test_msmat_sg_test( msmat * msmat_fh);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   815 | static msmat * test_msmat(int argc, char ** argv);
BUILDSTDERR:       |                ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   818 | static void output_bp_chrom( msmat & m , char * fname);
BUILDSTDERR:       |             ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
BUILDSTDERR:       |                 ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   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 );
BUILDSTDERR:       |                ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:48,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSWarper.cpp:17:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
BUILDSTDERR:    69 | const static char * valid_fields[] = {
BUILDSTDERR:       |                     ^~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:17:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   517 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   519 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   600 |    int a = 3;
BUILDSTDERR:       |        ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   703 |     int a  = 3;
BUILDSTDERR:       |         ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor(float)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    37 |        for ( int i = 0 ; i < precursors.size() ; i++ )
BUILDSTDERR:       |                          ~~^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor_idx(int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    48 |         for ( int i = 0 ; i < ti.size() ; i++ ) {
BUILDSTDERR:       |                           ~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In constructor 'transition_manager::transition_manager(std::vector<transition_info>)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    57 |       for ( int  i = 0 ; i < transitions.size() ; i++ ) {
BUILDSTDERR:       |                          ~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::init_transitions_from_labels()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    86 |    for ( int i = 0 ; i < labels.size() ; i++ ) {
BUILDSTDERR:       |                      ~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_input(std::ifstream&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   119 |      for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
BUILDSTDERR:       |                             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   120 |          for ( int c_idx = 0 ; c_idx < this->get_num_rts() ; c_idx++ ) {
BUILDSTDERR:       |                                ~~~~~~^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:117:10: warning: unused variable 'num_chroms' [-Wunused-variable]
BUILDSTDERR:   117 |      int num_chroms = this->get_num_mzs();
BUILDSTDERR:       |          ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:118:10: warning: unused variable 'num_rts' [-Wunused-variable]
BUILDSTDERR:   118 |      int num_rts = this->get_num_rts();
BUILDSTDERR:       |          ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_dist_set(int, std::vector<int>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   228 |     for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
BUILDSTDERR:       |                       ~~^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom_set(int, std::vector<std::pair<int, int> >&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   247 |     for ( int i = 1 ; i < retain_range.size() ; i++ ) {
BUILDSTDERR:       |                       ~~^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   255 |     for ( int i = 0 ; i < delete_range.size() ; i++ ) {
BUILDSTDERR:       |                       ~~^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:237:9: warning: unused variable 'set_idx' [-Wunused-variable]
BUILDSTDERR:   237 |     int set_idx = 0;
BUILDSTDERR:       |         ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom(int, int, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   266 |   for ( int i = stop_scan_idx + 1 ; i < get_num_rts() ; i++ ) {
BUILDSTDERR:       |                                     ~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::check_size_from_position() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   283 |   if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
BUILDSTDERR:       |        ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::rt_to_rtidx(float) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   417 |      if ( iter_delt == rts.size() - 1 )
BUILDSTDERR:       |           ~~~~~~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::calc_bp_chrom()':
/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkies/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/MyException.cpp.o
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cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/converters/MSToolkit/Spectrum.cpp
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[ 45%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/converters/MSToolkit/MSWarper.cpp
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[ 56%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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/inclt/msmat.cpp:680:28: warning: variable 'scan_length' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   680 |   int scan_idx, num_scans, scan_length;
BUILDSTDERR:       |                            ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::time_interpolate(double, msmat&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1068:14: warning: variable 'dim' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1068 |   matrix_dim dim = get_data_dim();
BUILDSTDERR:       |              ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_median() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1278 |   for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1279 |     for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
BUILDSTDERR:       |                       ~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_avg(int) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1294 |     if ( i < 0 || i >= get_num_rts()  ) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_twomat_num(const msmat&, double, double, int) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1325 |                                      for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
BUILDSTDERR:       |                                                               ~~~~~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1327 |                                        if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
BUILDSTDERR:       |                                                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_mat_denom(double, int) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1350 |     if ( i < 0 || i >= get_num_rts() ) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::correlation_w_shift(const msmat&, int) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1368:17: warning: unused variable 'self' [-Wunused-variable]
BUILDSTDERR:  1368 |   const msmat & self = *this;
BUILDSTDERR:       |                 ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1422:9: warning: unused variable 'foo' [-Wunused-variable]
BUILDSTDERR:  1422 |     int foo = 5;
BUILDSTDERR:       |         ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_chrom(int, std::vector<float>&) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1498:11: warning: unused variable 'volatile_this' [-Wunused-variable]
BUILDSTDERR:  1498 |   msmat * volatile_this;
BUILDSTDERR:       |           ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::scan_scramble()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1555 |   for ( int i = 0 ; i < get_num_rts() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1561 |   for ( int i = 0 ; i < scram_cmds.size() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In function 'msmat* test_msmat(int, char**)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1605:19: warning: variable 'ti_file' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1605 |   FILE * o_file, *ti_file, *sg_file;
BUILDSTDERR:       |                   ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1605:29: warning: variable 'sg_file' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:  1605 |   FILE * o_file, *ti_file, *sg_file;
BUILDSTDERR:       |                             ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1746 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1762 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_avg(int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1828 |     new_cnt < mzs.size() ;
BUILDSTDERR:       |     ~~~~~~~~^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_avg(int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1858 |     new_cnt < rts.size() ;
BUILDSTDERR:       |     ~~~~~~~~^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_sample(int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1880 |     new_cnt < mzs.size() ;
BUILDSTDERR:       |     ~~~~~~~~^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_sample(int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1898 |     new_cnt < rts.size() ;
BUILDSTDERR:       |     ~~~~~~~~^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'bool msmat::equals_data(const msmat&, double) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1921 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::sum_abs_diffs(const msmat&) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1944 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1941:10: warning: unused variable 'nrows' [-Wunused-variable]
BUILDSTDERR:  1941 |   size_t nrows = get_num_rows();
BUILDSTDERR:       |          ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_output(std::ostream&, int, int, int, int, bool, char)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  2004 |     for ( int i = 0 ; i < rts_slice.size() - 1 ; i++ ) {
BUILDSTDERR:       |                       ~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  2010 |   for ( int i = 0 ; i < mzs_slice.size() ; i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  2019 |     for ( int j = 0 ; j < out_chrom.size() - 1 ; j++ ) {
BUILDSTDERR:       |                       ~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1990:13: warning: unused variable 'num_mzs' [-Wunused-variable]
BUILDSTDERR:  1990 |   const int num_mzs = get_num_mzs();
BUILDSTDERR:       |             ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_scan_interp(float, std::vector<float>&) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  2071 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_chroms::get_scan_interp(float, std::vector<float>&) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  2095 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
BUILDSTDERR:       |                     ~~^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp: In member function 'void ttest_score_matrix::unmask_search(msmat::mz_type, msmat::rt_type, msmat::rt_type)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:2109:7: warning: unused variable 'start_rt_idx' [-Wunused-variable]
BUILDSTDERR:  2109 |   int start_rt_idx = this->rt_to_rtidx(start_rt);
BUILDSTDERR:       |       ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:2110:7: warning: unused variable 'stop_rt_idx' [-Wunused-variable]
BUILDSTDERR:  2110 |   int stop_rt_idx = this->rt_to_rtidx(stop_rt);
BUILDSTDERR:       |       ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:17:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: At global scope:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   812 | static int test_msmat_time_interp( msmat * msmat_f );
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   813 | static int test_msmat_sg_test( msmat * msmat_fh);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1740 | msmat * msmat_from_thevoid
BUILDSTDERR:       |         ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1713:6: warning: 'void output_bp_chrom(msmat&, char*)' defined but not used [-Wunused-function]
BUILDSTDERR:  1713 | void output_bp_chrom( msmat & m, char * fname  ) {
BUILDSTDERR:       |      ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:1582:9: warning: 'msmat* test_msmat(int, char**)' defined but not used [-Wunused-function]
BUILDSTDERR:  1582 | msmat * test_msmat ( int argc , char ** argv ) {
BUILDSTDERR:       |         ^~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:48,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:17:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
BUILDSTDERR:    69 | const static char * valid_fields[] = {
BUILDSTDERR:       |                     ^~~~~~~~~~~~
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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/gaml_tandem1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/converters/gaml_tandem1.0.cxx
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[ 54%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o
BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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 -gre/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rankties(std::vector<float>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable 'start_idx' [-Wunused-variable]
BUILDSTDERR:   261 |     int start_idx = -1;
BUILDSTDERR:       |         ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable 'stop_idx' [-Wunused-variable]
BUILDSTDERR:   262 |     int stop_idx = -1;
BUILDSTDERR:       |         ^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rank_by_pos_ties(const std::vector<std::pair<float, int> >&, std::vector<float>&, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   354 |       if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[i].first == last_val) ) {
BUILDSTDERR:       |              ~~^~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable 'last_rank' [-Wunused-variable]
BUILDSTDERR:   346 |     int last_rank = -1;
BUILDSTDERR:       |         ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   944 |     if (cumulative_area.size() == idx)
BUILDSTDERR:       |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&, const std::vector<float>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   990 |     if (cumulative_area.size() == idx)
BUILDSTDERR:       |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::tryptic_digester_proto(std::string, std::vector<std::__cxx11::basic_string<char> >&, int)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp:1121:10: warning: unused variable 'last_tryp' [-Wunused-variable]
BUILDSTDERR:  1121 |     bool last_tryp = false;
BUILDSTDERR:       |          ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp: In function 'std::vector<std::pair<std::set<int>, std::set<int> > > crawutils::permute_two_groups(IdxGroupType, IdxGroupType)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp:1214:8: warning: unused variable 'g2_len' [-Wunused-variable]
BUILDSTDERR:  1214 |    int g2_len = g2.size();
BUILDSTDERR:       |        ^~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_base.cpp:16:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
BUILDSTDERR:    69 | const static char * valid_fields[] = {
BUILDSTDERR:       |                     ^~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:20:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   517 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   519 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   600 |    int a = 3;
BUILDSTDERR:       |        ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   703 |     int a  = 3;
BUILDSTDERR:       |         ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'int msmat_header_parser::read_header(msmat*, FILE*, bool, int*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:92:14: warning: unused variable 'should_be_semi' [-Wunused-variable]
BUILDSTDERR:    92 |         char should_be_semi = (char)fgetc(header_fh);
BUILDSTDERR:       |              ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:343:22: warning: unused variable 'key_fields_len' [-Wunused-variable]
BUILDSTDERR:   343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
BUILDSTDERR:       |                      ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:343:38: warning: unused variable 'key_last_loc' [-Wunused-variable]
BUILDSTDERR:   343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
BUILDSTDERR:       |                                      ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:343:52: warning: unused variable 'key_data_len' [-Wunused-variable]
BUILDSTDERR:   343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
BUILDSTDERR:       |                                                    ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:344:8: warning: unused variable 'key_len_data' [-Wunused-variable]
BUILDSTDERR:   344 |   char key_len_data[128], val_len_data[128];
BUILDSTDERR:       |        ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:344:27: warning: unused variable 'val_len_data' [-Wunused-variable]
BUILDSTDERR:   344 |   char key_len_data[128], val_len_data[128];
BUILDSTDERR:       |                           ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:367:7: warning: unused variable 'key_data_idx' [-Wunused-variable]
BUILDSTDERR:   367 |   int key_data_idx;
BUILDSTDERR:       |       ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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> >&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:431:9: warning: unused variable 'num_elements' [-Wunused-variable]
BUILDSTDERR:   431 |     int num_elements = s.size();
BUILDSTDERR:       |         ^~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp:20:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: At global scope:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   812 | static int test_msmat_time_interp( msmat * msmat_f );
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   813 | static int test_msmat_sg_test( msmat * msmat_fh);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   815 | static msmat * test_msmat(int argc, char ** argv);
BUILDSTDERR:       |                ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   818 | static void output_bp_chrom( msmat & m , char * fname);
BUILDSTDERR:       |             ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
BUILDSTDERR:       |                 ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   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 );
BUILDSTDERR:       |                ^~~~~~~~~~~~~~~~~~
cord-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-3-02-01/src/converters/MSToolkit/crawutils.cpp
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[ 61%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/converters/MSToolkit/msmat_base.cpp
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cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp
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BUILDSTDERR: /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Reader.cpp: In member function 'void Reader::translateFileToXML(const string&, bool, unsigned int, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Reader.cpp:319:32: warning: 'tcd' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   319 |         tmpDirs[lineNumber_par]=tcd;
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_test.cpp:4:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   517 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:   519 |   }
BUILDSTDERR:       |   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:600:8: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   600 |    int a = 3;
BUILDSTDERR:       |        ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
BUILDSTDERR:   703 |     int a  = 3;
BUILDSTDERR:       |         ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_test.cpp: In function 'int main(int, char**)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable 'm' [-Wunused-variable]
BUILDSTDERR:    13 |   msmat  * m;
BUILDSTDERR:       |            ^
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_test.cpp:4:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H: At global scope:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   812 | static int test_msmat_time_interp( msmat * msmat_f );
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   813 | static int test_msmat_sg_test( msmat * msmat_fh);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
BUILDSTDERR:       |            ^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   815 | static msmat * test_msmat(int argc, char ** argv);
BUILDSTDERR:       |                ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   818 | static void output_bp_chrom( msmat & m , char * fname);
BUILDSTDERR:       |             ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
BUILDSTDERR:   819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
BUILDSTDERR:       |                 ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   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 );
BUILDSTDERR:       |                ^~~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.H:48,
BUILDSTDERR:                  from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_test.cpp:4:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
BUILDSTDERR:    69 | const static char * valid_fields[] = {
BUILDSTDERR:       |                     ^~~~~~~~~~~~
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BUILDSTDERR: cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/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-/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MzidentmlReader.cpp: In member function 'virtual void MzidentmlReader::getMaxMinCharge(const string&, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MzidentmlReader.cpp:86:30: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
BUILDSTDERR:    86 |   } catch (ifstream::failure e) {
BUILDSTDERR:       |                              ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MzidentmlReader.cpp:94:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=]
BUILDSTDERR:    94 |   } catch (MyException e) {
BUILDSTDERR:       |                        ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
BUILDSTDERR:    97 |   } catch (std::exception e) {
BUILDSTDERR:       |                           ^
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/converters/MzidentmlReader.cpp
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BUILDSTDERR: /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/per/builddir/build/BUILD/percolator-rel-3-02-01/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&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/SequestReader.cpp:170:12: warning: unused variable 'PI' [-Wunused-variable]
BUILDSTDERR:   170 |     double PI = boost::lexical_cast<double>(item.calculatedPI().get());
BUILDSTDERR:       |            ^~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/SequestReader.cpp:175:14: warning: unused variable 'peptide_length' [-Wunused-variable]
BUILDSTDERR:   175 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
BUILDSTDERR:       |              ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MsgfplusReader.cpp:334:13: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
BUILDSTDERR:   334 |             else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
BUILDSTDERR:       |             ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MsgfplusReader.cpp:334:90: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
BUILDSTDERR:   334 |             else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
BUILDSTDERR:       |                                                                                          ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MsgfplusReader.cpp:272:14: warning: unused variable 'peptide_length' [-Wunused-variable]
BUILDSTDERR:   272 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
BUILDSTDERR:       |              ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MsgfplusReader.cpp:292:12: warning: variable 'SpecEValue' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   292 |     double SpecEValue = 0.0;
BUILDSTDERR:       |            ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/TandemReader.cpp:479:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
BUILDSTDERR:   479 |     f_seq.push_back( charge == c ? 1.0 : 0.0);
BUILDSTDERR:       |                      ~~~~~~~^~~~
colator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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/SequestReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/SequestReader.cpp
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/usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/converters/TandemReader.cpp
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BUILDSTDERR: make[2]: Entering directory '/bui/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/FragSpectrumScanDatabase.cpp: In member function 'std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    80 |     if (it->first <= peptideSeq.length()) {
BUILDSTDERR:       |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function 'virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable 'valueSize' [-Wunused-variable]
BUILDSTDERR:   165 |   size_t valueSize(buf.size ());
BUILDSTDERR:       |          ^~~~~~~~~
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BUILDSTDERR: /usr/bin/c++  -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-02-01/converters -I/builddir/build/BUILD/percolator-rel-3-02-01/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 -speIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Interface.cpp:18:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Interface.h: In constructor 'Interface::Interface()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Interface.h:50:7: warning: 'Interface::xmlOutput' will be initialized after [-Wreorder]
BUILDSTDERR:    50 |  bool xmlOutput;
BUILDSTDERR:       |       ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Interface.h:47:14: warning:   'std::string Interface::outputFN' [-Wreorder]
BUILDSTDERR:    47 |  std::string outputFN;
BUILDSTDERR:       |              ^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Interface.cpp:21:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
BUILDSTDERR:       | ^~~~~~~~~
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+ mkdir -p elude
+ pushd elude
+ 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
+ /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
ection -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/tandem2pin.dir/Tandem2Pin.cpp.o  -o tandem2pin  -L/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c -Wl,-Bstatic -lboost_filesystem -lboost_system -Wl,-Bdynamic -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[100%] Linking CXX executable msgf2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/msgf2pin.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/msgf2pin.dir/Msgfplus2Pin.cpp.o  -o msgf2pin  -L/builddir/build/BUILD/percolator-rel-3-02-01/src/converters/../../src libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c -Wl,-Bstatic -lboost_filesystem -lboost_system -Wl,-Bdynamic -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles 0
~/build/BUILD/percolator-rel-3-02-01
~/build/BUILD/percolator-rel-3-02-01/elude ~/build/BUILD/percolator-rel-3-02-01
-- The C compiler identification is GNU 9.1.1
-- The CXX compiler identification is GNU 9.1.1
-- 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:
BUILDSTDERR: --CMake Warning:
BUILDSTDERR:   Manually-specified variables were not used by the project:
BUILDSTDERR:     CMAKE_Fortran_FLAGS_RELEASE
BUILDSTDERR:     CMAKE_SKIP_INSTALL_RPATH
BUILDSTDERR:     CMAKE_USE_RELATIVE_PATHS
BUILDSTDERR:     INCLUDE_INSTALL_DIR
BUILDSTDERR:     LIB_INSTALL_DIR
BUILDSTDERR:     LIB_SUFFIX
BUILDSTDERR:     SHARE_INSTALL_PREFIX
BUILDSTDERR:     SYSCONF_INSTALL_DIR
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp:27:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
BUILDSTDERR:    57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
BUILDSTDERR:       |                                                                 ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:    57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
BUILDSTDERR:       |                                                                   ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp: In member function 'virtual int LibSVRModel::LoadModel(FILE*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp:284:1: warning: control reaches end of non-void function [-Wreturn-type]
BUILDSTDERR:   284 | }
BUILDSTDERR:       | ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp: In member function 'int LibSVRModel::CalibrateLinearModel(const std::vector<PSMDescription*>&, const int&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   205 |   svr_parameters_.p = best_e;
BUILDSTDERR:       |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   204 |   svr_parameters_.C = best_c;
BUILDSTDERR:       |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp: In member function 'int LibSVRModel::CalibrateRBFModel(const std::vector<PSMDescription*>&, const int&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   242 |   svr_parameters_.gamma = best_g;
BUILDSTDERR:       |   ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   241 |   svr_parameters_.p = best_e;
BUILDSTDERR:       |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized in this function [-Wmaybe-uninitialized]
BUILDSTDERR:   240 |   svr_parameters_.C = best_c;
BUILDSTDERR:       |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
 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-3-02-01/src/elude_tool/../..
-- CMAKE_PREFIX_PATH = /usr
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = riscv64
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Boost version: 1.66.0
-- Configuring done
-- Generating done
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-02-01/elude
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-02-01/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/elude'
cd /builddir/build/BUILD/percolator-rel-3-02-01/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/eludelibrary.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/eludelibrary.dir/depend.internal".
Scanning dependencies of target eludelibrary
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 13%] Building CXX object CMakeFiles/eludelibrary.dir/EludeMain.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/elude_tool/EludeMain.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 17%] Building CXX object CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o
BUILDSTDERR: /usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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-declaratio/builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibsvmWrapper.cpp: In function 'svm_model* libsvm_wrapper::LoadModel(FILE*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibsvmWrapper.cpp:172:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   172 |   int ret;
BUILDSTDERR:       |       ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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*>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   332 |     if (!remove_from_test && (initial_train_size != train_psms.size())) {
BUILDSTDERR:       |                               ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<PSMDescription*> DataManager::RemoveNonEnzymatic(const Enzyme*, std::vector<PSMDescription*>&, const string&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/DataManager.cpp:352:7: warning: unused variable 'initial_size' [-Wunused-variable]
BUILDSTDERR:   352 |   int initial_size = psms.size();
BUILDSTDERR:       |       ^~~~~~~~~~~~
ns -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-3-02-01/src/elude_tool/LibSVRModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
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/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/elude_tool/LibsvmWrapper.cpp
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/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/elude_tool/DataManager.cpp
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[  4%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o
BUILDSTDERR: /usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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.di/builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionFeatures.cpp: In static member function 'static double RetentionFeatures::IndexN(const string&, const std::map<std::__cxx11::basic_string<char>, double>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionFeatures.cpp:304:21: warning: unused variable 'len' [-Wunused-variable]
BUILDSTDERR:   304 |   int end_position, len = peptide.size();
BUILDSTDERR:       |                     ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:17:1: warning: "/*" within comment [-Wcomment]
BUILDSTDERR:    17 | /*
BUILDSTDERR:       |  
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:27:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
BUILDSTDERR:    57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
BUILDSTDERR:       |                                                                 ^
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
BUILDSTDERR:    57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
BUILDSTDERR:       |                                                                   ^
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:24:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.h: In constructor 'RetentionModel::RetentionModel(Normalizer*)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.h:99:16: warning: 'RetentionModel::the_normalizer_' will be initialized after [-Wreorder]
BUILDSTDERR:    99 |    Normalizer *the_normalizer_;
BUILDSTDERR:       |                ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.h:95:14: warning:   'SVRModel* RetentionModel::svr_model_' [-Wreorder]
BUILDSTDERR:    95 |    SVRModel *svr_model_;
BUILDSTDERR:       |              ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:30:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    30 | RetentionModel::RetentionModel(Normalizer *norm) : the_normalizer_(norm),
BUILDSTDERR:       | ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp: In destructor 'RetentionModel::~RetentionModel()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:36:12: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
BUILDSTDERR:    36 |     delete svr_model_;
BUILDSTDERR:       |            ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp: In member function 'void RetentionModel::PrintSub()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    62 |   for(int i = 0; i < vsub_.size(); ++i)
BUILDSTDERR:       |                  ~~^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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*>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:187:12: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
BUILDSTDERR:   187 |     delete svr_model_;
BUILDSTDERR:       |            ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::SaveModelToFile(const string&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   291 |   if (vsub_.size() !=  number_features) {
BUILDSTDERR:       |       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::LoadModelFromFile(const string&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:356:12: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
BUILDSTDERR:   356 |     delete svr_model_;
BUILDSTDERR:       |            ^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:363:24: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:   363 |   int number_features, ret;
BUILDSTDERR:       |                        ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::setData(std::vector<double>&, std::vector<double>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    48 |   for (int i = 0; i < x.size(); ++i) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::fillResiduals(std::pair<double, double>)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:    84 |   for (int i = 0; i < data.size(); ++i) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::runLTS()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   168 |         for (int i = 1; i < Q.size(); ++i)
BUILDSTDERR:       |                         ~~^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   177 |   for (int j = 0; j < best10Subsets.size(); ++j) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printVector(std::vector<dataPoint>)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   209 |   for (int i = 0; i < v.size(); ++i) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printDataPoints()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   220 |   for (int i = h; i < data.size(); ++i) {
BUILDSTDERR:       |                   ~~^~~~~~~~~~~~~
r/RetentionFeatures.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionFeatures.cpp
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BUILDSTDERR: /usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/../..In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:30:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
BUILDSTDERR:   167 |    bool remove_non_enzymatic_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
BUILDSTDERR:   143 |    bool context_format_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:30:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
BUILDSTDERR:   189 |    RetentionModel *rt_model_;
BUILDSTDERR:       |                    ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
BUILDSTDERR:   173 |    bool ignore_ptms_;
BUILDSTDERR:       |         ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:30:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
BUILDSTDERR:   196 |    bool supress_print_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
BUILDSTDERR:   175 |    bool only_hydrophobicity_index_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   519 |       while (found != string::npos) {
BUILDSTDERR:       |              ~~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
BUILDSTDERR:   639 |     int ret = 1;
BUILDSTDERR:       |         ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
BUILDSTDERR:   940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
BUILDSTDERR:       |          ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const string&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
BUILDSTDERR:       |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
BUILDSTDERR:       |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
BUILDSTDERR:       |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/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-3-02-01/src/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Enzyme.cpp
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/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescription.cpp
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[ 73%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Globals.cpp.o
BUILDSTDERR: /usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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-uIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:21:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    26 | PSMDescriptionDOC::PSMDescriptionDOC() :
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:21:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
BUILDSTDERR:    92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
BUILDSTDERR:       |                          ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
BUILDSTDERR:       | ^~~~~~~~~~~~~~~~~
nwind-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-3-02-01/src/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Globals.cpp
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/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/src/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Option.cpp
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BUILDSTDERR: /usr/bin/ar qc libeludelibrary.a  CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o CMakeFiles/eludelibrary.dir/DataManager.cpp.o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/svm.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Normalizer.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/UniNormalizer.cpp.o CIn file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:30:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
BUILDSTDERR:   167 |    bool remove_non_enzymatic_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
BUILDSTDERR:   143 |    bool context_format_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:30:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
BUILDSTDERR:   189 |    RetentionModel *rt_model_;
BUILDSTDERR:       |                    ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
BUILDSTDERR:   173 |    bool ignore_ptms_;
BUILDSTDERR:       |         ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: In file included from /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:30:
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
BUILDSTDERR:   196 |    bool supress_print_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
BUILDSTDERR:   175 |    bool only_hydrophobicity_index_;
BUILDSTDERR:       |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
BUILDSTDERR:       | ^~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:   519 |       while (found != string::npos) {
BUILDSTDERR:       |              ~~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
BUILDSTDERR:   639 |     int ret = 1;
BUILDSTDERR:       |         ^~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
BUILDSTDERR:   940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
BUILDSTDERR:       |          ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const string&)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
BUILDSTDERR:       |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
BUILDSTDERR:       |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/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]
BUILDSTDERR:  1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
BUILDSTDERR:       |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
MakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/StdvNormalizer.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Option.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Enzyme.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescription.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Globals.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Logger.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/MyException.cpp.o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/PseudoRandom.cpp.o
/usr/bin/ranlib libeludelibrary.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 91%] Built target eludelibrary
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
cd /builddir/build/BUILD/percolator-rel-3-02-01/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/elude.dir/DependInfo.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/elude.dir/depend.internal".
Dependee "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/elude.dir/depend.internal".
Scanning dependencies of target elude
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 95%] Building CXX object CMakeFiles/elude.dir/EludeCaller.cpp.o
/usr/bin/c++   -I/builddir/build/BUILD/percolator-rel-3-02-01/elude -I/builddir/build/BUILD/percolator-rel-3-02-01/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/elude.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/EludeCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[100%] Linking CXX executable elude
/usr/bin/cmake -E cmake_link_script CMakeFiles/elude.dir/link.txt --verbose=1
BUILDSTDERR: /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-declar+ popd
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
ations -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  -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/elude.dir/EludeCaller.cpp.o  -o elude  -L/builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/../../src libeludelibrary.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles 0
~/build/BUILD/percolator-rel-3-02-01
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.IbSC0U
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64
+ cd percolator-rel-3-02-01
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-02-01 -B/builddir/build/BUILD/percolator-rel-3-02-01/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-02-01/percolator/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/make -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Nothing to be done for 'src/picked_protein/CMakeFiles/picked_protein.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 17%] Built target picked_protein
/usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/make -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src/fido /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 94%] Built target fido
/usr/bin/make -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
BUILDSTDERR: make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolat+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64 'INSTALL=/usr/bin/install -p' -C converters
or'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01 /builddir/build/BUILD/percolator-rel-3-02-01/src/qvality /builddir/build/BUILD/percolator-rel-3-02-01/percolator /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/percolator'
make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[100%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/percolator/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/qvality
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-02-01/src/converters -B/builddir/build/BUILD/percolator-rel-3-02-01/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 23%] Built target perclibrary_part
/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-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 29%] Built target RAMP
/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-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 32%] 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-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles/converters.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 61%] Built target converters
/usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 89%] Built target MSToolkit
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 92%] Built target sqt2pin
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/make -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 96%] 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-3-02-01/converters'
cd /builddir/build/BUILD/percolator-rel-3-02-01/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/src/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: make[2]: Nothing to be done for 'CMakeFiles/tandem2+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64 'INSTALL=/usr/bin/install -p' -C elude
pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/converters/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-02-01/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
cd /builddir/build/BUILD/percolator-rel-3-02-01/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/make -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[2]: Nothing to be done for 'CMakeFiles/eludelibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/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-3-02-01/elude'
cd /builddir/build/BUILD/percolator-rel-3-02-01/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/make -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[2]: Nothing to be done for 'CMakeFiles/elude.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[100%] Built target elude
BUILDSTDERR: make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/+ mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
BUILDSTDERR: ++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./elude/libeludelibrary.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.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-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/lib64/percolator
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 3.02.01-2.fc31 --unique-debug-suffix -3.02.01-2.fc31.riscv64 --unique-debug-src-base percolator-3.02.01-2.fc31.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-02-01
BUILDSTDERR: 6007 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 0
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-2.fc31.riscv64/elude/Globals.h is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-2.fc31.riscv64/src/serializer.cxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-2.fc31.riscv64/src/parser.cxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-2.fc31.riscv64/src/parser.hxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-2.fc31.riscv64/src/serializer.hxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-2.fc31.riscv64/percolator/src/Globals.h is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-2.fc31.riscv64/converters/Globals.h is executable but has empty or no shebang, removing executable bit
elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-02-01/elude/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/elude
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Jupiter_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Luna_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/yeast_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Luna_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Luna_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/yeast_40.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Jupiter_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Jupiter_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Jupiter_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Luna_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/yeast_20.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Jupiter_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/Luna_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/elude/models/tfa.model
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/elude
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/qvality
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/percolator
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/elude
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/qvality
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/percolator
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/sqt2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/sqt2pin
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/tandem2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/bin/tandem2pin
original debug info size: 80104kB, size after compression: 68688kB
/usr/lib/rpm/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.2WjlMV
Processing files: percolator-3.02.01-2.fc31.riscv64
Provides: percolator = 3.02.01-2.fc31 percolator(riscv-64) = 3.02.01-2.fc31
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-3.02.01-2.fc31.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.nRTPbV
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/doc/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/doc/percolator-data
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.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-3.02.01-2.fc31.riscv64/usr/share/doc/percolator-data
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.F1t0SU
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-data
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-data
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-data
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Provides: percolator-data = 3.02.01-2.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.02.01-2.fc31.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.osL4AV
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/doc/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/doc/percolator-static
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.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-3.02.01-2.fc31.riscv64/usr/share/doc/percolator-static
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.WEpEKV
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-static
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-static
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64/usr/share/licenses/percolator-static
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Provides: percolator-static = 3.02.01-2.fc31 percolator-static(riscv-64) = 3.02.01-2.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.02.01-2.fc31.riscv64
Provides: percolator-debugsource = 3.02.01-2.fc31 percolator-debugsource(riscv-64) = 3.02.01-2.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.02.01-2.fc31.riscv64
Provides: debuginfo(build-id) = 0c6e08df2c6b0a3392b767eb5b197a912df79eab debuginfo(build-id) = 1237d8b226820ba8146db013aebed0f92f0533d8 debuginfo(build-id) = 4202cb08247fe86bcfd3ddf4075b6d8c87cd4336 debuginfo(build-id) = 45a3e6387adaf3ed1fc4a95657014d2c06234e85 debuginfo(build-id) = e52f6c1e9307c8b3d6c193f6b10da74e17406a1d debuginfo(build-id) = fd374c456a9dcbd8f1d033eb04f3815e995615b3 percolator-debuginfo = 3.02.01-2.fc31 percolator-debuginfo(riscv-64) = 3.02.01-2.fc31
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(riscv-64) = 3.02.01-2.fc31
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64
Wrote: /builddir/build/RPMS/percolator-debugsource-3.02.01-2.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-3.02.01-2.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.02.01-2.fc31.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.02.01-2.fc31.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.02.01-2.fc31.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.GWrw0V
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.02.01-2.fc31.riscv64
+ RPM_EC=0
BUILDSTDERR: ++ jobs -p
+ exit 0
Child return code was: 0