Mock Version: 1.4.13
Mock Version: 1.4.13
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/percolator.spec'], chrootPath='/var/lib/mock/f29-build-33054-17808/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x20023f2400>timeout=432000uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=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': 'C.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
Wrote: /builddir/build/SRPMS/percolator-3.02.01-1.fc29.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/f29-build-33054-17808/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': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x20023f2400>timeout=432000uid=998gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=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': 'C.UTF-8'} and shell False
Building target platforms: riscv64
Building for target riscv64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.tXFP2o
+ 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
yeast-01.shuffled2.sqt
yeast-01.shuffled.sqt
yeast-01.sqt
+ find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.h' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.xx' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.txt' -exec chmod 0644 '{}' ';'
+ chmod a-x src/converters/MSToolkit/RAMP/README
+ mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README
+ mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt
+ cp -p /builddir/build/SOURCES/percolator-RAMP_license_lgpl-2.1.txt RAMP_license_lgpl-2.1.txt
+ sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt
+ sed -e 's|${ELUDE_MODELS_PATH}..|${ELUDE_MODELS_PATH}|g' -i src/elude_tool/CMakeLists.txt
+ sed -e 's|${CMAKE_INSTALL_PREFIX}/share/elude/models/|${CMAKE_INSTALL_PREFIX}/share/elude|g' -i src/elude_tool/CMakeLists.txt
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0ubMi9
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ mkdir -p percolator
~/build/BUILD/percolator-rel-3-02-01/percolator ~/build/BUILD/percolator-rel-3-02-01
+ 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 ..
-- The C compiler identification is GNU 8.2.1
-- The CXX compiler identification is GNU 8.2.1
-- 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
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
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-02-01/percolator
+ cd src
+ xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../../src/xml/percolator_out.xsd
+ cd ..
+ /usr/bin/make -O -j4
/usr/bin/cmake -H/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/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=
Scanning dependencies of target picked_protein
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'
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=
Scanning dependencies of target fido
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
/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 /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=
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'
[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.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/__/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/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
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'
[ 10%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.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/__/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'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 11%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.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/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Database.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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:    Protein* protein = NULL;
BUILDSTDERR:             ^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 13%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.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/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/Peptide.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
BUILDSTDERR: /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:  static bool equal_peptides(
BUILDSTDERR:              ^~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 14%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.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/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'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.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/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/PeptideSrc.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[  5%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.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/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/percolator_in.cxx
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[ 18%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.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/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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:    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:    DOMImplementation& dom_impl_;
BUILDSTDERR:                       ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
BUILDSTDERR:        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:      int i(1);
BUILDSTDERR:          ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 20%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.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/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/serializer.cxx
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[  2%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.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/BasicBigraph.cpp.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/percolator'
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: /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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 17%] 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
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 24%] 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'
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:    switch(decoy_type){
BUILDSTDERR:          ^
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[ 26%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.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/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/picked_protein/ProteinPeptideIterator.cpp
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[ 27%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
/usr/bin/ar qc libpicked_protein.a  CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
/usr/bin/ranlib libpicked_protein.a
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[ 23%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
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make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
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[ 31%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.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/Numerical.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/Numerical.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/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/MassHandler.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/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/Random.cpp
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[ 36%] 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
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[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.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/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'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 28%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.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/GroupPowerBigraph.cpp.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/percolator'
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: /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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.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/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
BUILDSTDERR:    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:    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:  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::__cxx11::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:    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:    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:  PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
BUILDSTDERR:  ^~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.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/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/ResultHolder.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/Vector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/Vector.cpp
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[ 39%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.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/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/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-02-01/percolator/src/fido && /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a  CMakeFiles/fido.dir/BasicBigraph.cpp.o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o CMakeFiles/fido.dir/Numerical.cpp.o CMakeFiles/fido.dir/Random.cpp.o CMakeFiles/fido.dir/Set.cpp.o CMakeFiles/fido.dir/Vector.cpp.o
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[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.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/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/StdvNormalizer.cpp
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[ 49%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.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/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/svm.cpp
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[ 44%] 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'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    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::__cxx11::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:      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:      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:    if (hasDefaultValues && init_values.size() > numFeatures) {
BUILDSTDERR:                            ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
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
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[ 43%] 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'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    bool reportUniquePeptides_;
BUILDSTDERR:         ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.h:93:8: warning:   'bool XMLInterface::printDecoys_' [-Wreorder]
BUILDSTDERR:    bool printDecoys_, printExpMass_;
BUILDSTDERR:         ^~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/XMLInterface.cpp:58:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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:        const unsigned int numFeatures = FeatureNames::getNumFeatures();
BUILDSTDERR:                           ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 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
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/BUILD/percolator-rel-3-02-01/src/Normalizer.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'
[ 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
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'
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.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/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'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    bool concatenatedSearch_;
BUILDSTDERR:         ^~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/SanityCheck.h:72:10: warning:   'double SanityCheck::test_fdr_' [-Wreorder]
BUILDSTDERR:    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:  SanityCheck::SanityCheck() :
BUILDSTDERR:  ^~~~~~~~~~~
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'
[ 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'
BUILDSTDERR: In 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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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 'unsigned int' [-Wsign-compare]
BUILDSTDERR:      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 'unsigned int' [-Wsign-compare]
BUILDSTDERR:      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 'unsigned int' [-Wsign-compare]
BUILDSTDERR:    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 'unsigned int' [-Wsign-compare]
BUILDSTDERR:      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 'unsigned int' [-Wsign-compare]
BUILDSTDERR:      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 'unsigned int' [-Wsign-compare]
BUILDSTDERR:      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 'unsigned int' [-Wsign-compare]
BUILDSTDERR:      for (int set = 0; set < numFolds_; ++set) {
BUILDSTDERR:                        ~~~~^~~~~~~~~~~
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'
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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    for (int i = 0; i < getSize(); i++) {
BUILDSTDERR:                    ~~^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.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/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/LogisticRegression.cpp
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[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
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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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.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/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinFDRestimator.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.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/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/PseudoRandom.cpp
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[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.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/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/PosteriorEstimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
BUILDSTDERR: /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:   int nP = 1, queue = 0;
BUILDSTDERR:               ^~~~~
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[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.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/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/SqtSanityCheck.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.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/ssl.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/ssl.cpp
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[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.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/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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::__cxx11::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:    double pi0_, absenceRatio_;
BUILDSTDERR:                 ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:238:10: warning:   'double ProteinProbEstimator::pi0_' [-Wreorder]
BUILDSTDERR:    double pi0_, absenceRatio_;
BUILDSTDERR:           ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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:    unsigned int numberTargetProteins_;
BUILDSTDERR:                 ^~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:237:8: warning:   'bool ProteinProbEstimator::usePi0_' [-Wreorder]
BUILDSTDERR:    bool usePi0_;
BUILDSTDERR:         ^~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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:    std::string decoyPattern_;
BUILDSTDERR:                ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.h:240:10: warning:   'double ProteinProbEstimator::fdr_' [-Wreorder]
BUILDSTDERR:    double fdr_;
BUILDSTDERR:           ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
BUILDSTDERR:  ^~~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 71%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.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/Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    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:    if (totalNumberOfDecoys_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
BUILDSTDERR:        ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.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/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/PackedMatrix.cpp
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[ 82%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.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/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Logger.cpp
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[ 84%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.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/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/MyException.cpp
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[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/EludeModel.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/EludeModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/EludeModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 86%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.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/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.cpp
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BUILDSTDERR: In 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::__cxx11::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:    bool isDecoy_;
BUILDSTDERR:         ^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.h:106:7: warning:   'int ProteinScoreHolder::groupId_' [-Wreorder]
BUILDSTDERR:    int groupId_;
BUILDSTDERR:        ^~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
BUILDSTDERR:  ^~~~~~~~~~~~~~~~~~
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[ 85%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.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/FidoInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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::__cxx11::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:    double mseThreshold_;
BUILDSTDERR:           ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.h:106:8: warning:   'bool FidoInterface::doGridSearch_' [-Wreorder]
BUILDSTDERR:    bool doGridSearch_;
BUILDSTDERR:         ^~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/FidoInterface.cpp:76:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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:    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:      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:      unsigned fpChange = proteinNames[k].size() - tpChange;
BUILDSTDERR:               ^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
[ 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'
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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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::__cxx11::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:    double maxPeptidePval_;
BUILDSTDERR:           ^~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h:82:8: warning:   'bool PickedProteinInterface::reportFragmentProteins_' [-Wreorder]
BUILDSTDERR:    bool reportFragmentProteins_, reportDuplicateProteins_;
BUILDSTDERR:         ^~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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:    bool reportFragmentProteins_, reportDuplicateProteins_;
BUILDSTDERR:                                  ^~~~~~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.h:80:26: warning:   'ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_' [-Wreorder]
BUILDSTDERR:    ProteinInferenceMethod protInferenceMethod_;
BUILDSTDERR:                           ^~~~~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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:      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:          int significantPeptides = 0;
BUILDSTDERR:              ^~~~~~~~~~~~~~~~~~~
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[ 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
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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=
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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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
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
+ popd
+ mkdir -p fido
~/build/BUILD/percolator-rel-3-02-01/fido ~/build/BUILD/percolator-rel-3-02-01
+ 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
-- The C compiler identification is GNU 8.2.1
-- The CXX compiler identification is GNU 8.2.1
-- 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
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
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-02-01/fido
+ /usr/bin/make -O -j4
/usr/bin/cmake -H/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=
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'
[ 50%] Building CXX object CMakeFiles/fido.dir/Numerical.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-02-01/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
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'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
[ 50%] 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'
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/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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: ../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: ../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
[ 12%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o
/usr/bin/c++   -I/src  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,-z,relro -pie -Wl,-z,now -I../src   -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: ../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: ../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
[ 50%] 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: 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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: ../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    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:    int label;
BUILDSTDERR:        ^~~~~
BUILDSTDERR: ../src/Scores.h:52:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
BUILDSTDERR:    PSMDescription* pPSM;
BUILDSTDERR:                    ^~~~
BUILDSTDERR: ../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
BUILDSTDERR:    ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
BUILDSTDERR:    ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/fido'
[100%] Linking CXX static library libfido.a
/usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
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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
+ popd
+ mkdir -p converters
~/build/BUILD/percolator-rel-3-02-01/converters ~/build/BUILD/percolator-rel-3-02-01
+ 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
-- The C compiler identification is GNU 8.2.1
-- The CXX compiler identification is GNU 8.2.1
-- 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
-- Looking for pthread_create - found
-- Found Threads: TRUE  
-- Generating classes from xsd-schema using CodeSynthesis
-- Generating /builddir/build/BUILD/percolator-rel-3-02-01/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-02-01/converters/gaml_tandem1.0.hxx
-- SQL Lite 3 found: /usr/include
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
-- ZLIB found: /usr/include, /usr/lib64/libz.so
-- Using FragSpectrumScanDatabaseTokyodb.cpp
-- Configuring done
-- Generating done
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
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-02-01/converters
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../src/xml/percolator_out.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns ../src/xml/mzIdentML1.1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/gaml_tandem1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/tandem2011.12.01.1.xsd
+ /usr/bin/make -O -j4
/usr/bin/cmake -H/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
/usr/bin/make -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend
/usr/bin/make -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend
/usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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=
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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=
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make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[  3%] Built target generate_perc_xsdfiles
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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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=
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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=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[  5%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o
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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[  7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
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.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/RAMP/ramp.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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.cpp:1698:13: warning: variable 'err' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:          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:  #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:          (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:  #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:    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:  #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:            (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:  #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:            (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:  #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:          (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:  #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:            (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:  #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:            (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:  #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:    (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:  #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:      (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:  #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:            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:  #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:        (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:  #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:          (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:  #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:            (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:  #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:          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:  #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:    (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:  #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:      (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:  #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:      (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:  #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:    (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:  #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:       (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:  #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:        (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
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/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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/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
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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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/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/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx
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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:    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:    DOMImplementation& dom_impl_;
BUILDSTDERR:                       ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
BUILDSTDERR:  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::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, bool)':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
BUILDSTDERR:        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:      int i(1);
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/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Logger.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/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/MyException.cpp
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[ 21%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.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/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/LazyMatrix.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:   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:    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:       *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:        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:            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:     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:               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:    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:    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:    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:      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:      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:    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:      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:        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:      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:      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:      for ( uint i = nrows - offset ; i < nrows; i++ ) {
BUILDSTDERR:                                      ~~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 23%] Building CXX object CMakeFiles/converters.dir/Reader.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/converters.dir/Reader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Reader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:          tmpDirs[lineNumber_par]=tcd;
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 43%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.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/MSConvertFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSConvertFile.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 47%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.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/MSObject.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSObject.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:    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:      for(i=0;i<m.vSpectrum->size();i++){
BUILDSTDERR:              ~^~~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 10%] Building CXX object CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.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/converters.dir/mzIdentML1.1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-02-01/converters/mzIdentML1.1.0.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 52%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.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/MSSingleScan.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSSingleScan.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.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/MSReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:     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:    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:    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:    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:    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:   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:   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:   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:        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:        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:     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:           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:           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:        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:        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:        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:        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:        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:        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:         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:         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:         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:         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:          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:           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:           fgets(tstr,256,fileIn);
BUILDSTDERR:           ~~~~~^~~~~~~~~~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSReader.cpp:377:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
BUILDSTDERR:         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:             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:         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:          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:   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:   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:   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:   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:    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:    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:    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:    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:      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:      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:      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:      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:      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:      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:    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:    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:    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:    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:    fread(&iVersion,4,1,f);
BUILDSTDERR:    ~~~~~^~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 56%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.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/MSTAllRT.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSTAllRT.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:    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:   MSFileFormat ff;
BUILDSTDERR:                ^~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 58%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.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/MSTDemo.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 60%] 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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:    }
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:    }
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:     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:      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:    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:  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:  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:  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:  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:  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:  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:  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:  const static char * valid_fields[] = {
BUILDSTDERR:                      ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 49%] Building CXX object CMakeFiles/converters.dir/MzidentmlReader.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/converters.dir/MzidentmlReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MzidentmlReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:    } 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:    } 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:    } catch (std::exception e) {
BUILDSTDERR:                            ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 45%] Building CXX object CMakeFiles/converters.dir/SqtReader.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/converters.dir/SqtReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/SqtReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 61%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.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/Spectrum.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/Spectrum.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:      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:      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:      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:    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:    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:    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:    for(int i=0; i<vPeaks->size(); i++)
BUILDSTDERR:                 ~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 54%] Building CXX object CMakeFiles/converters.dir/SequestReader.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/converters.dir/SequestReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/SequestReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:      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:      unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
BUILDSTDERR:               ^~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 69%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.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/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/FragSpectrumScanDatabase.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/FragSpectrumScanDatabase.cpp: In member function 'std::__cxx11::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:      if (it->first <= peptideSeq.length()) {
BUILDSTDERR:          ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 65%] Building CXX object CMakeFiles/converters.dir/TandemReader.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/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/TandemReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:      f_seq.push_back( charge == c ? 1.0 : 0.0);
BUILDSTDERR:                       ~~~~~~~^~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 63%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.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/converters.dir/MsgfplusReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MsgfplusReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:              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:              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:      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:      double SpecEValue = 0.0;
BUILDSTDERR:             ^~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 67%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.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/crawutils.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/crawutils.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: /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:      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:      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:        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:      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:      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:      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::__cxx11::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:      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:     int g2_len = g2.size();
BUILDSTDERR:         ^~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 74%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.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/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/FragSpectrumScanDatabaseTokyodb.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:    size_t valueSize(buf.size ());
BUILDSTDERR:           ^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 76%] 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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:  const static char * valid_fields[] = {
BUILDSTDERR:                      ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 70%] Building CXX object CMakeFiles/converters.dir/Interface.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/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Interface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
BUILDSTDERR: In 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:   bool xmlOutput;
BUILDSTDERR:        ^~~~~~~~~
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/Interface.h:47:14: warning:   'std::__cxx11::string Interface::outputFN' [-Wreorder]
BUILDSTDERR:   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:  Interface::Interface() : xmlOutput(false), outputFN("") { }
BUILDSTDERR:  ^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 72%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.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.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:    }
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:    }
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:     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:      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:         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:          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:        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:     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:       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:           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:       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:       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:      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:      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:      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:      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:    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:    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:       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()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat.cpp:680:28: warning: variable 'scan_length' set but not used [-Wunused-but-set-variable]
BUILDSTDERR:    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:    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:    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:      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:      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:                                       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:                                         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:      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:    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:      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:    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:    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:    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:    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:    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:    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:    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:      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:      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:      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:      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:    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:    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:    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:      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:    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:      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:    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:    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:    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:    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:    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:  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:  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:  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:  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:  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:  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:  const static char * valid_fields[] = {
BUILDSTDERR:                      ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 78%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.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_header_parser.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_header_parser.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:    }
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:    }
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:     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:      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:          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:    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:    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:    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:    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:    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:    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:      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:  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:  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:  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:  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:  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:  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:  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:                 ^~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
[ 81%] Linking CXX static library libconverters.a
/usr/bin/cmake -P CMakeFiles/converters.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/converters.dir/link.txt --verbose=1
/usr/bin/ar qc libconverters.a  CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o CMakeFiles/converters.dir/Reader.cpp.o CMakeFiles/converters.dir/SqtReader.cpp.o CMakeFiles/converters.dir/MzidentmlReader.cpp.o CMakeFiles/converters.dir/SequestReader.cpp.o CMakeFiles/converters.dir/MsgfplusReader.cpp.o CMakeFiles/converters.dir/TandemReader.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o CMakeFiles/converters.dir/Interface.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o
/usr/bin/ranlib libconverters.a
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'
[ 87%] Built target converters
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'
[ 80%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.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_test.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/converters/MSToolkit/msmat_test.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
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:    }
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:    }
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:     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:      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:    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:  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:  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:  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:  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:  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:  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:  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:  const static char * valid_fields[] = {
BUILDSTDERR:                      ^~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-02-01/converters/MSToolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1
/usr/bin/ar qc libMSToolkit.a  CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
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/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
+ popd
+ mkdir -p elude
~/build/BUILD/percolator-rel-3-02-01/elude ~/build/BUILD/percolator-rel-3-02-01
+ 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
-- The C compiler identification is GNU 8.2.1
-- The CXX compiler identification is GNU 8.2.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building ELUDE:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-02-01/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
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
-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-02-01/elude
+ /usr/bin/make -O -j4
/usr/bin/cmake -H/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=
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'
[ 17%] 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'
[  8%] Building CXX object CMakeFiles/eludelibrary.dir/LibSVRModel.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/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'
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:     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:     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:  }
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:    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:    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:    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:    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:    svr_parameters_.C = best_c;
BUILDSTDERR:    ~~~~~~~~~~~~~~~~~~^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 21%] Building CXX object CMakeFiles/eludelibrary.dir/LibsvmWrapper.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/LibsvmWrapper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LibsvmWrapper.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
BUILDSTDERR: /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:    int ret;
BUILDSTDERR:        ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 13%] Building CXX object CMakeFiles/eludelibrary.dir/DataManager.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/DataManager.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/DataManager.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
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:      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:    int initial_size = psms.size();
BUILDSTDERR:        ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[  4%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionFeatures.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/RetentionFeatures.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionFeatures.cpp
BUILDSTDERR: /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:    int end_position, len = peptide.size();
BUILDSTDERR:                      ^~~
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'
[ 26%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionModel.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/RetentionModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/RetentionModel.cpp:17:1: warning: "/*" within comment [-Wcomment]
BUILDSTDERR:  /*
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:     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:     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:     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:     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:  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:      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:    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:      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:    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:      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:    int number_features, ret;
BUILDSTDERR:                         ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 43%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/Normalizer.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/builddir/build/BUILD/percolator-rel-3-02-01/src/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Normalizer.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'
[ 34%] Building CXX object CMakeFiles/eludelibrary.dir/LTSRegression.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/LTSRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/elude_tool/LTSRegression.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
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:    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:    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:          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:    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:    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:    for (int i = h; i < data.size(); ++i) {
BUILDSTDERR:                    ~~^~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
[ 47%] Building CXX object CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-02-01/src/UniNormalizer.cpp.o
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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/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/svm.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/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/Enzyme.cpp
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[ 30%] Building CXX object CMakeFiles/eludelibrary.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/eludelibrary.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'
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: 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:     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:     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:  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:     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:     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:  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:     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:     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:  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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:        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:      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:    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::__cxx11::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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:    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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:      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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:    if ((pos2 = file_name.find_last_of(".")) != string::npos) {
BUILDSTDERR:        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
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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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/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/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
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()':
BUILDSTDERR: /builddir/build/BUILD/percolator-rel-3-02-01/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
BUILDSTDERR:    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:    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:  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::__cxx11::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:    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:    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:  PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
BUILDSTDERR:  ^~~~~~~~~~~~~~~~~
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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: 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:     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:     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:  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:     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:     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:  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:     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:     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:  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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:        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:      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:    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::__cxx11::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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:    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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:      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 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
BUILDSTDERR:    if ((pos2 = file_name.find_last_of(".")) != string::npos) {
BUILDSTDERR:        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
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/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/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
+ popd
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.cy04Qa
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64
BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64
+ cd percolator-rel-3-02-01
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
/usr/bin/cmake -H/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
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=
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-3.02.01-1.fc29.riscv64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/qvality
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/converters'
/usr/bin/cmake -H/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 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'
[ 27%] Built target generate_perc_xsdfiles
/usr/bin/make -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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'
[ 56%] Built target converters
/usr/bin/make -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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'
[ 61%] Built target RAMP
/usr/bin/make -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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/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'
[ 92%] Built target msgf2pin
/usr/bin/make -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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'
[ 96%] Built target sqt2pin
/usr/bin/make -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/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'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.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-3.02.01-1.fc29.riscv64/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.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'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64 'INSTALL=/usr/bin/install -p' -C elude
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
/usr/bin/cmake -H/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
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
/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-3.02.01-1.fc29.riscv64/usr/bin/elude
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/yeast_20.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/yeast_40.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Jupiter_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Luna_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Luna_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Jupiter_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Jupiter_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Luna_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Jupiter_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Luna_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/tfa.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/yeast_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Luna_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/elude/models/Jupiter_180.model
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-02-01/elude'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.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-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.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-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/lib64/percolator
+ /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 3.02.01-1.fc29 --unique-debug-suffix -3.02.01-1.fc29.riscv64 --unique-debug-src-base percolator-3.02.01-1.fc29.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
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/elude
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/qvality
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/sqt2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/elude
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/qvality
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/sqt2pin
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/tandem2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/tandem2pin
explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/percolator
extracting debug info from /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/bin/percolator
/usr/lib/rpm/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
BUILDSTDERR: 6007 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
BUILDSTDERR: /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /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 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-1.fc29.riscv64/elude/Globals.h is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-1.fc29.riscv64/src/parser.hxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-1.fc29.riscv64/src/parser.cxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-1.fc29.riscv64/src/serializer.hxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-1.fc29.riscv64/src/serializer.cxx is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-1.fc29.riscv64/percolator/src/Globals.h is executable but has empty or no shebang, removing executable bit
BUILDSTDERR: *** WARNING: ./usr/src/debug/percolator-3.02.01-1.fc29.riscv64/converters/Globals.h is executable but has empty or no shebang, removing executable bit
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.9dCt55
Processing files: percolator-3.02.01-1.fc29.riscv64
Provides: percolator = 3.02.01-1.fc29 percolator(riscv-64) = 3.02.01-1.fc29
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) 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_3.4.5)(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-3.02.01-1.fc29.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Rau4cX
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/doc/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/doc/percolator-data
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.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-3.02.01-1.fc29.riscv64/usr/share/doc/percolator-data
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.jJVxFQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-data
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-data
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-data
+ exit 0
Provides: percolator-data = 3.02.01-1.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.02.01-1.fc29.riscv64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.9QjIvV
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/doc/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/doc/percolator-static
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.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-3.02.01-1.fc29.riscv64/usr/share/doc/percolator-static
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.fH6Bj4
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-static
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-static
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64/usr/share/licenses/percolator-static
+ exit 0
Provides: percolator-static = 3.02.01-1.fc29 percolator-static(riscv-64) = 3.02.01-1.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.02.01-1.fc29.riscv64
Provides: percolator-debugsource = 3.02.01-1.fc29 percolator-debugsource(riscv-64) = 3.02.01-1.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.02.01-1.fc29.riscv64
Provides: debuginfo(build-id) = 17317abd160d7841f8f0edcdd62393941ecc89aa debuginfo(build-id) = 18a4e111125791a4d3cb0cfad16e0022dddaaa2e debuginfo(build-id) = 62bd9c21cb744bed9e62f0e061113da72f6b1aea debuginfo(build-id) = 7f562d9d950c9cdc707771bfd7f9b26d801ed7f9 debuginfo(build-id) = b5d318282f15154278a1eba77fac7a99ac07dd8e debuginfo(build-id) = ce40a2ddc278324cfac95571da561d76c98e3ebb percolator-debuginfo = 3.02.01-1.fc29 percolator-debuginfo(riscv-64) = 3.02.01-1.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(riscv-64) = 3.02.01-1.fc29
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64
Wrote: /builddir/build/RPMS/percolator-3.02.01-1.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.02.01-1.fc29.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.02.01-1.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.02.01-1.fc29.riscv64.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.02.01-1.fc29.riscv64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.2U92jv
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-02-01
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.02.01-1.fc29.riscv64
+ exit 0
Child return code was: 0