Mock Version: 1.2.17
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/XTandem.spec'], env={'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}shell=Falseuid=1001chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-3296/root'printOutput=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7ff6c0d69860>user='mockbuild'timeout=0gid=135)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/XTandem.spec'] with env {'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'} and shell False
warning: Could not canonicalize hostname: copr-builder-791631832.novalocal
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/XTandem-150401.1-3.el7.centos.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/XTandem.spec'], env={'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}shell=Falsetimeout=0chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-3296/root'printOutput=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7ff6c0d69860>user='mockbuild'private_network=Trueuid=1001gid=135)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/XTandem.spec'] with env {'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'TERM': 'vt100', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'} and shell False
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.n3Hm2p
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf tandem-linux-15-04-01-1
+ /usr/bin/unzip -qq /builddir/build/SOURCES/tandem-linux-15-04-01-1.zip
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd tandem-linux-15-04-01-1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ dos2unix src/tandem.cpp
dos2unix: converting file src/tandem.cpp to Unix format ...
+ echo 'Patch #0 (XTandem-fix-missing-include-string-h.patch):'
Patch #0 (XTandem-fix-missing-include-string-h.patch):
+ /usr/bin/patch -p1 --fuzz=0
+ /usr/bin/cat /builddir/build/SOURCES/XTandem-fix-missing-include-string-h.patch
patching file src/base64.cpp
patching file src/saxhandler.h
patching file src/mhistogram.h
patching file src/mcleave.h
patching file src/mmotif.h
patching file src/msequenceserver.cpp
patching file src/p3msequenceserver.cpp
+ echo 'Patch #1 (XTandem-input_parameters_error.patch):'
Patch #1 (XTandem-input_parameters_error.patch):
+ /usr/bin/patch -p0 --fuzz=0
+ /usr/bin/cat /builddir/build/SOURCES/XTandem-input_parameters_error.patch
patching file src/tandem.cpp
+ sed -e 's|./bin/tandem.exe|./bin/tandem|g' -i src/Makefile
+ sed -e 's|./bin/p3.exe|./bin/p3|g' -i src/Makefile
+ sed -i 's/\r$//' README
+ sed -i 's/\r$//' LICENSE
++ find ./bin -type f '(' -name '*.exe' ')'
+ for i in '`find ./bin -type f \( -name "*.exe" \)`'
+ rm -f ./bin/tandem.exe
+ for i in '`find ./bin -type f \( -name "*.exe" \)`'
+ rm -f ./bin/rhel_static_link/tandem.exe
+ for i in '`find ./bin -type f \( -name "*.exe" \)`'
+ rm -f ./bin/fasta_pro.exe
+ rm -f src/expat.h src/expat_external.h
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.yVB7tu
+ umask 022
+ cd /builddir/build/BUILD
+ cd tandem-linux-15-04-01-1
+ make -j2 -C src 'CXXFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3' 'LDFLAGS=-Wl,-z,relro  -L/usr/lib64 -lpthread -lm -lexpat'
make: Entering directory `/builddir/build/BUILD/tandem-linux-15-04-01-1/src'
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mrefine.cpp > mrefine.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmzxmlhandler.cpp > saxmzxmlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmzxmlhandler.cpp | sed s/\\.o/.d/ > saxmzxmlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mrefine.cpp | sed s/\\.o/.d/ > mrefine.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 msequtilities.cpp > msequtilities.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxhandler.cpp > saxhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 msequtilities.cpp | sed s/\\.o/.d/ > msequtilities.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxhandler.cpp | sed s/\\.o/.d/ > saxhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mscore.cpp > mscore.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mpam.cpp > mpam.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mscore.cpp | sed s/\\.o/.d/ > mscore.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mpam.cpp | sed s/\\.o/.d/ > mpam.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mbiomlreport.cpp > mbiomlreport.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 masscalc.cpp > masscalc.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mbiomlreport.cpp | sed s/\\.o/.d/ > mbiomlreport.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 masscalc.cpp | sed s/\\.o/.d/ > masscalc.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mtermmods.cpp > mtermmods.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 stdafx.cpp > stdafx.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 stdafx.cpp | sed s/\\.o/.d/ > stdafx.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mtermmods.cpp | sed s/\\.o/.d/ > mtermmods.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 msequencecollection.cpp > msequencecollection.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mpmods.cpp > mpmods.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 msequencecollection.cpp | sed s/\\.o/.d/ > msequencecollection.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mpmods.cpp | sed s/\\.o/.d/ > mpmods.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 MSNumpress.cpp > MSNumpress.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 p3.cpp > p3.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 MSNumpress.cpp | sed s/\\.o/.d/ > MSNumpress.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 p3.cpp | sed s/\\.o/.d/ > p3.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxbiomlhandler.cpp > saxbiomlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmzdatahandler.cpp > saxmzdatahandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxbiomlhandler.cpp | sed s/\\.o/.d/ > saxbiomlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmzdatahandler.cpp | sed s/\\.o/.d/ > saxmzdatahandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mzid_report.cpp > mzid_report.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxtaxhandler.cpp > saxtaxhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mzid_report.cpp | sed s/\\.o/.d/ > mzid_report.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxtaxhandler.cpp | sed s/\\.o/.d/ > saxtaxhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 p3msequenceserver.cpp > p3msequenceserver.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mxxcleavage.cpp > mxxcleavage.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 p3msequenceserver.cpp | sed s/\\.o/.d/ > p3msequenceserver.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mxxcleavage.cpp | sed s/\\.o/.d/ > mxxcleavage.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 msequenceserver.cpp > msequenceserver.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 msequenceserver.cpp | sed s/\\.o/.d/ > msequenceserver.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmzmlhandler.cpp > saxmzmlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmodhandler.cpp > saxmodhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmzmlhandler.cpp | sed s/\\.o/.d/ > saxmzmlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxmodhandler.cpp | sed s/\\.o/.d/ > saxmodhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mspectrumcondition.cpp > mspectrumcondition.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mplugin.cpp > mplugin.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mspectrumcondition.cpp | sed s/\\.o/.d/ > mspectrumcondition.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mplugin.cpp | sed s/\\.o/.d/ > mplugin.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mreport.cpp > mreport.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 xmltaxonomy.cpp > xmltaxonomy.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mreport.cpp | sed s/\\.o/.d/ > mreport.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 xmltaxonomy.cpp | sed s/\\.o/.d/ > xmltaxonomy.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxtandeminputhandler.cpp > saxtandeminputhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxsaphandler.cpp > saxsaphandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxtandeminputhandler.cpp | sed s/\\.o/.d/ > saxtandeminputhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxsaphandler.cpp | sed s/\\.o/.d/ > saxsaphandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mscore_tandem.cpp > mscore_tandem.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mprocess.cpp > mprocess.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mscore_tandem.cpp | sed s/\\.o/.d/ > mscore_tandem.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 mprocess.cpp | sed s/\\.o/.d/ > mprocess.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 xmlparameter.cpp > xmlparameter.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 loadmspectrum.cpp > loadmspectrum.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 xmlparameter.cpp | sed s/\\.o/.d/ > xmlparameter.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 loadmspectrum.cpp | sed s/\\.o/.d/ > loadmspectrum.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 p3mprocess.cpp > p3mprocess.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 tandem.cpp > tandem.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 p3mprocess.cpp | sed s/\\.o/.d/ > p3mprocess.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 tandem.cpp | sed s/\\.o/.d/ > tandem.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxgamlhandler.cpp > saxgamlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 base64.cpp > base64.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 saxgamlhandler.cpp | sed s/\\.o/.d/ > saxgamlhandler.d
g++ -M -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 base64.cpp | sed s/\\.o/.d/ > base64.d
make: Leaving directory `/builddir/build/BUILD/tandem-linux-15-04-01-1/src'
make: Entering directory `/builddir/build/BUILD/tandem-linux-15-04-01-1/src'
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o tandem.o tandem.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o p3mprocess.o p3mprocess.cpp
In file included from msequtilities.h:142:0,
                 from tandem.cpp:148:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
In file included from msequtilities.h:142:0,
                 from p3mprocess.cpp:156:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
In file included from mspectrum.h:142:0,
                 from tandem.cpp:149:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from mspectrum.h:142:0,
                 from p3mprocess.cpp:157:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxmzdatahandler.o saxmzdatahandler.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzdatahandler.h:4,
                 from saxmzdatahandler.cpp:28:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mspectrumcondition.o mspectrumcondition.cpp
In file included from msequtilities.h:142:0,
                 from mspectrumcondition.cpp:153:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.cpp:154:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mspectrumcondition.cpp: In member function 'bool mspectrumcondition::condition(mspectrum&, mscore&)':
mspectrumcondition.cpp:287:9: warning: unused variable 'tSize' [-Wunused-variable]
  size_t tSize = _s.m_vMI.size();
         ^
mspectrumcondition.cpp:288:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
mspectrumcondition.cpp:289:8: warning: unused variable 'fMaxI' [-Wunused-variable]
  float fMaxI = 0;
        ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o masscalc.o masscalc.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mprocess.o mprocess.cpp
In file included from msequtilities.h:142:0,
                 from mprocess.cpp:156:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
In file included from mspectrum.h:142:0,
                 from mprocess.cpp:157:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mprocess.cpp: In member function 'virtual bool mprocess::create_score(const msequence&, size_t, size_t, long int, bool)':
mprocess.cpp:439:7: warning: unused variable 'bC' [-Wunused-variable]
  bool bC = false;
       ^
mprocess.cpp: In member function 'bool mprocess::mark_repeats()':
mprocess.cpp:1102:8: warning: unused variable 'fMH' [-Wunused-variable]
  float fMH = 0.0;
        ^
mprocess.cpp: In member function 'bool mprocess::process()':
mprocess.cpp:1684:9: warning: unused variable 'tLength' [-Wunused-variable]
  size_t tLength = 0;
         ^
mprocess.cpp:1711:7: warning: unused variable 'b' [-Wunused-variable]
  long b = 0;
       ^
mprocess.cpp:1712:7: warning: unused variable 'bForward' [-Wunused-variable]
  bool bForward = true;
       ^
mprocess.cpp:1713:7: warning: variable 'pLine' set but not used [-Wunused-but-set-variable]
  char pLine[32];
       ^
mprocess.cpp:1715:7: warning: unused variable 'cBs' [-Wunused-variable]
  char cBs = 0x08;
       ^
mprocess.cpp:1726:16: warning: unused variable 'lWaste' [-Wunused-variable]
  unsigned long lWaste = 0;
                ^
mprocess.cpp:1727:7: warning: unused variable 'lReadTime' [-Wunused-variable]
  long lReadTime = 0;
       ^
mprocess.cpp:1728:7: warning: unused variable 'lTempTime' [-Wunused-variable]
  long lTempTime = 0;
       ^
mprocess.cpp: In member function 'bool mprocess::report_valid(double)':
mprocess.cpp:2441:9: warning: unused variable 'c' [-Wunused-variable]
  size_t c = 0;
         ^
mprocess.cpp:2445:9: warning: unused variable 'tLast' [-Wunused-variable]
  size_t tLast = 0;
         ^
mprocess.cpp: In member function 'bool mprocess::score_single(const msequence&)':
mprocess.cpp:3360:46: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
       if(m_iCurrentRound == 1 && (m_bPermute && m_bCrcCheck || m_bPermuteHigh)) {
                                              ^
mprocess.cpp:3204:7: warning: variable 'bBreak' set but not used [-Wunused-but-set-variable]
  bool bBreak = false;
       ^
mprocess.cpp:3205:13: warning: unused variable 'lSpectra' [-Wunused-variable]
  const long lSpectra = (long) m_tSpectra;
             ^
mprocess.cpp: In member function 'bool mprocess::score_terminus(const string&)':
mprocess.cpp:3628:40: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pScore->m_seqUtil.m_pdAaMod[_s[tAt]] = dValue;
                                        ^
mprocess.cpp:3629:43: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pScore->m_seqUtilAvg.m_pdAaMod[_s[tAt]] = dValue;
                                           ^
mprocess.cpp: In member function 'bool mprocess::spectra()':
mprocess.cpp:3736:21: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
   if(pValue[0] == 1 && pValue[1] == -95 || (pValue[3] == 'F' && pValue[5] == 'i' && pValue[7] == 'n') ) {
                     ^
mprocess.cpp: In member function 'bool mprocess::subtract()':
mprocess.cpp:4309:9: warning: unused variable 'dDot2' [-Wunused-variable]
  double dDot2 = 0.0;
         ^
mprocess.cpp:4327:9: warning: unused variable 'dTotal' [-Wunused-variable]
  double dTotal = 0.;
         ^
mprocess.cpp: In member function 'bool mprocess::serialize()':
mprocess.cpp:4644:8: warning: unused variable 'fV' [-Wunused-variable]
  float fV = 0.0;
        ^
mprocess.cpp: In member function 'bool mprocess::initialize_crc()':
mprocess.cpp:4781:14: warning: unused variable 'crc' [-Wunused-variable]
     uint64_t crc = INITIALCRC, part = 0;
              ^
mprocess.cpp: In member function 'bool mprocess::restore()':
mprocess.cpp:4681:48: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
  fread((void *)&tLength,sizeof(size_t),1,pFile);
                                                ^
mprocess.cpp:4707:45: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread((void *)&tId,sizeof(size_t),1,pFile);
                                             ^
mprocess.cpp:4708:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fread((void *)&tL,sizeof(size_t),1,pFile);
                                            ^
mprocess.cpp:4711:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
    fread((void *)&fV,sizeof(float),1,pFile);
                                            ^
mprocess.cpp:4713:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
    fread((void *)&fV,sizeof(float),1,pFile);
                                            ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mreport.o mreport.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mreport.cpp:143:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from msequtilities.h:142:0,
                 from mreport.cpp:147:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
mreport.cpp: In member function 'bool mreport::masses(msequtilities&)':
mreport.cpp:654:78: warning: array subscript has type 'char' [-Wchar-subscripts]
   sprintf(pLine,"\t<aa type=\"%c\" mass=\"%.6lf\" />\n",cAa,_p.m_pdAaMass[cAa]);
                                                                              ^
mreport.cpp:645:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mscore_tandem.o mscore_tandem.cpp
In file included from mspectrum.h:142:0,
                 from mscore_tandem.cpp:135:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from msequtilities.h:142:0,
                 from mscore_tandem.cpp:136:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
mscore_tandem.cpp: In member function 'bool mscore_tandem::blur(std::vector<mi>&)':
mscore_tandem.cpp:287:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(uType.m_lM == lValue + a) {
                               ^
mscore_tandem.cpp: In member function 'virtual double mscore_tandem::dot(long unsigned int*)':
mscore_tandem.cpp:357:8: warning: unused variable 'fValue0' [-Wunused-variable]
  float fValue0 = 0.0;
        ^
mscore_tandem.cpp:361:9: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
mscore_tandem.cpp: In member function 'virtual float mscore_tandem::ion_check(long unsigned int, size_t)':
mscore_tandem.cpp:580:16: warning: unused variable 'a' [-Wunused-variable]
  unsigned long a = 0;
                ^
mscore_tandem.cpp:581:16: warning: unused variable 'lCount' [-Wunused-variable]
  unsigned long lCount = 0;
                ^
mscore_tandem.cpp:582:7: warning: unused variable 'lType' [-Wunused-variable]
  long lType = 0;
       ^
mscore_tandem.cpp:583:9: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o loadmspectrum.o loadmspectrum.cpp
In file included from mspectrum.h:142:0,
                 from loadmspectrum.cpp:142:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
loadmspectrum.cpp: In member function 'virtual bool loadmatrix::get(mspectrum&)':
loadmspectrum.cpp:425:7: warning: unused variable 'bFirst' [-Wunused-variable]
  bool bFirst = true;
       ^
loadmspectrum.cpp:426:7: warning: unused variable 'lId' [-Wunused-variable]
  long lId = 0;
       ^
loadmspectrum.cpp:441:7: warning: unused variable 'bNext' [-Wunused-variable]
  bool bNext = true;
       ^
loadmspectrum.cpp: In member function 'virtual bool loadpkl::get(mspectrum&)':
loadmspectrum.cpp:621:7: warning: unused variable 'lId' [-Wunused-variable]
  long lId = 0;
       ^
loadmspectrum.cpp: In member function 'virtual bool loaddta::get(mspectrum&)':
loadmspectrum.cpp:842:7: warning: unused variable 'lId' [-Wunused-variable]
  long lId = 0;
       ^
loadmspectrum.cpp: In member function 'virtual bool loadcmn::get(mspectrum&)':
loadmspectrum.cpp:1036:7: warning: unused variable 'lId' [-Wunused-variable]
  long lId = 0;
       ^
loadmspectrum.cpp:1038:7: warning: unused variable 'bNext' [-Wunused-variable]
  bool bNext = true;
       ^
loadmspectrum.cpp:1049:9: warning: variable 'tS' set but not used [-Wunused-but-set-variable]
  size_t tS = 0;
         ^
loadmspectrum.cpp: In member function 'virtual bool loadcmn::open(std::string&)':
loadmspectrum.cpp:1152:9: warning: unused variable 'tS' [-Wunused-variable]
  size_t tS = fread((void *)pLine,1,256,m_pFile);
         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o msequencecollection.o msequencecollection.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mplugin.o mplugin.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxsaphandler.o saxsaphandler.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from saxsaphandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxtaxhandler.o saxtaxhandler.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from saxtaxhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mscore.o mscore.cpp
saxtaxhandler.cpp: In member function 'virtual void SAXTaxHandler::startElement(const XML_Char*, const XML_Char**)':
saxtaxhandler.cpp:197:6: warning: unused variable 'i' [-Wunused-variable]
  int i=1;
      ^
saxtaxhandler.cpp: In member function 'virtual void SAXTaxHandler::endElement(const XML_Char*)':
saxtaxhandler.cpp:216:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a=0;
         ^
mscore.cpp:589:1: warning: "/*" within comment [-Wcomment]
 /*
 ^
mscore.cpp:681:1: warning: "/*" within comment [-Wcomment]
 /*
 ^
mscore.cpp:798:1: warning: "/*" within comment [-Wcomment]
 /*
 ^
In file included from msequtilities.h:142:0,
                 from mscore.cpp:152:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
In file included from mspectrum.h:142:0,
                 from mscore.cpp:153:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
mscore.cpp: In member function 'bool mscore::add_A(long unsigned int, long int)':
mscore.cpp:318:15: warning: unused variable 'dZ' [-Wunused-variable]
  const double dZ = (double)_c;
               ^
mscore.cpp: In member function 'bool mscore::add_B(long unsigned int, long int)':
mscore.cpp:411:56: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                        ^
mscore.cpp:390:15: warning: unused variable 'dZ' [-Wunused-variable]
  const double dZ = (double)_c;
               ^
mscore.cpp: In member function 'bool mscore::add_C(long unsigned int, long int)':
mscore.cpp:488:56: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfSeq[lCount] = pfScore[tC]*pfScorePlus[m_pSeq[a+1]];
                                                        ^
mscore.cpp:466:9: warning: unused variable 'dZ' [-Wunused-variable]
  double dZ = (double)_c;
         ^
mscore.cpp: In member function 'bool mscore::add_X(long unsigned int, long int)':
mscore.cpp:528:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^
mscore.cpp:535:9: warning: unused variable 'dZ' [-Wunused-variable]
  double dZ = (double)_c;
         ^
mscore.cpp: In member function 'bool mscore::add_Y(long unsigned int, long int)':
mscore.cpp:633:59: warning: array subscript has type 'char' [-Wchar-subscripts]
     m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                           ^
mscore.cpp:639:58: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                          ^
mscore.cpp:596:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^
mscore.cpp:606:9: warning: unused variable 'dZ' [-Wunused-variable]
  double dZ = (double)_c;
         ^
mscore.cpp: In member function 'bool mscore::add_Z(long unsigned int, long int)':
mscore.cpp:719:57: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                         ^
mscore.cpp:722:57: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pfSeq[lCount] = pfScore[tC]*pfScoreMinus[m_pSeq[a-1]];
                                                         ^
mscore.cpp:689:8: warning: unused variable 'fSub' [-Wunused-variable]
  float fSub = 0.0;
        ^
mscore.cpp: In member function 'long unsigned int mscore::add_seq(const char*, bool, bool, long unsigned int, int)':
mscore.cpp:880:45: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_seqUtil.m_pdAaMass[m_pSeq[a]] + m_seqUtil.m_pdAaMod[m_pSeq[a]] + m_seqUtil.m_pdAaFullMod[m_pSeq[a]];
                                             ^
mscore.cpp:880:78: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_seqUtil.m_pdAaMass[m_pSeq[a]] + m_seqUtil.m_pdAaMod[m_pSeq[a]] + m_seqUtil.m_pdAaFullMod[m_pSeq[a]];
                                                                              ^
mscore.cpp:880:115: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_seqUtil.m_pdAaMass[m_pSeq[a]] + m_seqUtil.m_pdAaMod[m_pSeq[a]] + m_seqUtil.m_pdAaFullMod[m_pSeq[a]];
                                                                                                                   ^
mscore.cpp: In member function 'bool mscore::get_aa(std::vector<maa>&, size_t, double&)':
mscore.cpp:1053:59: warning: array subscript has type 'char' [-Wchar-subscripts]
     aaValue.m_dPrompt = (float)m_seqUtil.m_pdAaPrompt[cRes];
                                                           ^
mscore.cpp:1076:69: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dMod = (float)(m_seqUtil.m_pdAaMass[m_pSeq[m_Pam.m_tPos]] - m_seqUtil.m_pdAaMass[m_Pam.m_pSeqTrue[m_Pam.m_tPos]]);
                                                                     ^
mscore.cpp:1076:124: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dMod = (float)(m_seqUtil.m_pdAaMass[m_pSeq[m_Pam.m_tPos]] - m_seqUtil.m_pdAaMass[m_Pam.m_pSeqTrue[m_Pam.m_tPos]]);
                                                                                                                            ^
mscore.cpp:1077:74: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dPrompt = (float)(m_seqUtil.m_pdAaPrompt[m_pSeq[m_Pam.m_tPos]] - m_seqUtil.m_pdAaPrompt[m_Pam.m_pSeqTrue[m_Pam.m_tPos]]);
                                                                          ^
mscore.cpp:1077:131: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dPrompt = (float)(m_seqUtil.m_pdAaPrompt[m_pSeq[m_Pam.m_tPos]] - m_seqUtil.m_pdAaPrompt[m_Pam.m_pSeqTrue[m_Pam.m_tPos]]);
                                                                                                                                   ^
mscore.cpp:1087:69: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dMod = (float)(m_seqUtil.m_pdAaMass[m_pSeq[m_Sap.m_tPos]] - m_seqUtil.m_pdAaMass[m_Sap.m_pSeqTrue[m_Sap.m_tPos]]);
                                                                     ^
mscore.cpp:1087:124: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dMod = (float)(m_seqUtil.m_pdAaMass[m_pSeq[m_Sap.m_tPos]] - m_seqUtil.m_pdAaMass[m_Sap.m_pSeqTrue[m_Sap.m_tPos]]);
                                                                                                                            ^
mscore.cpp:1088:74: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dPrompt = (float)(m_seqUtil.m_pdAaPrompt[m_pSeq[m_Sap.m_tPos]] - m_seqUtil.m_pdAaPrompt[m_Sap.m_pSeqTrue[m_Sap.m_tPos]]);
                                                                          ^
mscore.cpp:1088:131: warning: array subscript has type 'char' [-Wchar-subscripts]
   aaValue.m_dPrompt = (float)(m_seqUtil.m_pdAaPrompt[m_pSeq[m_Sap.m_tPos]] - m_seqUtil.m_pdAaPrompt[m_Sap.m_pSeqTrue[m_Sap.m_tPos]]);
                                                                                                                                   ^
mscore.cpp: In member function 'bool mscore::load_next_pam()':
mscore.cpp:1365:66: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_pSeqUtilFrag->m_pdAaMass[m_Pam.m_pAa[m_Pam.m_tAa]];
                                                                  ^
mscore.cpp:1366:72: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMass[m_Pam.m_pSeqTrue[m_Pam.m_tPos]];
                                                                        ^
mscore.cpp:1367:69: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_pSeqUtilFrag->m_pdAaFullMod[m_Pam.m_pAa[m_Pam.m_tAa]];
                                                                     ^
mscore.cpp:1368:75: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH -= m_pSeqUtilFrag->m_pdAaFullMod[m_Pam.m_pSeqTrue[m_Pam.m_tPos]];
                                                                           ^
mscore.cpp: In member function 'bool mscore::check_pam_mass()':
mscore.cpp:1388:54: warning: array subscript has type 'char' [-Wchar-subscripts]
  const float fTrue = m_pSeqUtilFrag->m_pfAaMass[cTrue] + (float)m_pSeqUtilFrag->m_pdAaFullMod[cTrue];
                                                      ^
mscore.cpp:1388:100: warning: array subscript has type 'char' [-Wchar-subscripts]
  const float fTrue = m_pSeqUtilFrag->m_pfAaMass[cTrue] + (float)m_pSeqUtilFrag->m_pdAaFullMod[cTrue];
                                                                                                    ^
mscore.cpp:1389:52: warning: array subscript has type 'char' [-Wchar-subscripts]
  const float fNew = m_pSeqUtilFrag->m_pfAaMass[cNew] + (float)m_pSeqUtilFrag->m_pdAaFullMod[cNew];
                                                    ^
mscore.cpp:1389:97: warning: array subscript has type 'char' [-Wchar-subscripts]
  const float fNew = m_pSeqUtilFrag->m_pfAaMass[cNew] + (float)m_pSeqUtilFrag->m_pdAaFullMod[cNew];
                                                                                                 ^
mscore.cpp: In member function 'bool mscore::load_next_sap()':
mscore.cpp:1437:58: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_pSeqUtilFrag->m_pdAaMass[m_Sap.m_cCurrent] + m_Sap.m_dMod;
                                                          ^
mscore.cpp:1438:72: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH -= m_pSeqUtilFrag->m_pdAaMass[m_Sap.m_pSeqTrue[m_Sap.m_tPos]];
                                                                        ^
mscore.cpp:1439:61: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_pSeqUtilFrag->m_pdAaFullMod[m_Sap.m_cCurrent];
                                                             ^
mscore.cpp:1440:75: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH -= m_pSeqUtilFrag->m_pdAaFullMod[m_Sap.m_pSeqTrue[m_Sap.m_tPos]];
                                                                           ^
mscore.cpp: In member function 'long unsigned int mscore::set_seq(const char*, bool, bool, long unsigned int, int)':
mscore.cpp:1928:45: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_seqUtil.m_pdAaMass[m_pSeq[a]] + m_seqUtil.m_pdAaMod[m_pSeq[a]] + m_seqUtil.m_pdAaFullMod[m_pSeq[a]];
                                             ^
mscore.cpp:1928:78: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_seqUtil.m_pdAaMass[m_pSeq[a]] + m_seqUtil.m_pdAaMod[m_pSeq[a]] + m_seqUtil.m_pdAaFullMod[m_pSeq[a]];
                                                                              ^
mscore.cpp:1928:115: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_dSeqMH += m_seqUtil.m_pdAaMass[m_pSeq[a]] + m_seqUtil.m_pdAaMod[m_pSeq[a]] + m_seqUtil.m_pdAaFullMod[m_pSeq[a]];
                                                                                                                   ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mtermmods.o mtermmods.cpp
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mtermmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from msequtilities.h:142:0,
                 from mscore.h:146,
                 from mtermmods.cpp:138:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mrefine.o mrefine.cpp
In file included from mspectrum.h:142:0,
                 from mrefine.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from msequtilities.h:142:0,
                 from mscore.h:146,
                 from mrefine.cpp:139:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
mrefine.cpp: In member function 'virtual bool mrefine::refine()':
mrefine.cpp:248:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
mrefine.cpp:249:9: warning: unused variable 'tActiveNow' [-Wunused-variable]
  size_t tActiveNow = 0;
         ^
mscore.cpp: In constructor 'mscore::mscore()':
mscore.cpp:200:19: warning: iteration 16u invokes undefined behavior [-Waggressive-loop-optimizations]
   m_plCount[a] = 0;
                   ^
mscore.cpp:199:2: note: containing loop
  while(a < 20) {
  ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxtandeminputhandler.o saxtandeminputhandler.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxhandler.o saxhandler.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from saxtandeminputhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxhandler.cpp:132:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
saxhandler.cpp: In member function 'void SAXSpectraHandler::pushSpectrum()':
saxhandler.cpp:278:6: warning: unused variable 'i' [-Wunused-variable]
  int i=0;
      ^
saxhandler.cpp: In member function 'void SAXSpectraHandler::numDepress(char*, size_t, bool, bool)':
saxhandler.cpp:380:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(resultvector.size() != m_peaksCount) {
                             ^
saxhandler.cpp: In member function 'void SAXSpectraHandler::decode32(bool, bool)':
saxhandler.cpp:424:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(length != size) {
                 ^
saxhandler.cpp: In member function 'void SAXSpectraHandler::decode64(bool, bool)':
saxhandler.cpp:482:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(length != size) {
                  ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o msequtilities.o msequtilities.cpp
In file included from msequtilities.h:142:0,
                 from msequtilities.cpp:140:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
msequtilities.cpp: In constructor 'msequtilities::msequtilities(masscalc::massType)':
msequtilities.cpp:174:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while(a < lValue) {
            ^
msequtilities.cpp: In member function 'bool msequtilities::modify_all(std::string&)':
msequtilities.cpp:352:25: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_pdAaFullMod[_s[tAt]] = fValue;
                         ^
msequtilities.cpp:356:25: warning: array subscript has type 'char' [-Wchar-subscripts]
    m_pdAaFullMod[_s[tAt]] = fValue;
                         ^
msequtilities.cpp: In member function 'bool msequtilities::modify_maybe(std::string&)':
msequtilities.cpp:414:17: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pdAaMod[cRes] = fValue;
                 ^
msequtilities.cpp:415:20: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pdAaPrompt[cRes] = fPrompt;
                    ^
msequtilities.cpp: In member function 'bool msequtilities::modify_annotation(std::string&)':
msequtilities.cpp:475:17: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pdAaMod[cRes] = fValue;
                 ^
msequtilities.cpp:476:20: warning: array subscript has type 'char' [-Wchar-subscripts]
   m_pdAaPrompt[cRes] = fPrompt;
                    ^
msequtilities.cpp: In member function 'bool msequtilities::motif_set(const msequence&)':
msequtilities.cpp:518:9: warning: unused variable 'b' [-Wunused-variable]
  size_t b = 0;
         ^
msequtilities.cpp: In member function 'bool msequtilities::set_a(char, float)':
msequtilities.cpp:799:15: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfAScore[_c] = _f;
               ^
msequtilities.cpp:800:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfA18Score[_c] = _f;
                 ^
msequtilities.cpp:801:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfA17Score[_c] = _f;
                 ^
msequtilities.cpp: In member function 'bool msequtilities::set_b(char, float)':
msequtilities.cpp:809:15: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfBScore[_c] = _f;
               ^
msequtilities.cpp:810:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfB18Score[_c] = _f;
                 ^
msequtilities.cpp:811:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfB17Score[_c] = _f;
                 ^
msequtilities.cpp: In member function 'bool msequtilities::set_x(char, float)':
msequtilities.cpp:819:15: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfXScore[_c] = _f;
               ^
msequtilities.cpp:820:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfX18Score[_c] = _f;
                 ^
msequtilities.cpp:821:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfX17Score[_c] = _f;
                 ^
msequtilities.cpp: In member function 'bool msequtilities::set_y(char, float)':
msequtilities.cpp:829:15: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfYScore[_c] = _f;
               ^
msequtilities.cpp:830:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfY18Score[_c] = _f;
                 ^
msequtilities.cpp:831:17: warning: array subscript has type 'char' [-Wchar-subscripts]
  m_pfY17Score[_c] = _f;
                 ^
msequtilities.cpp: In member function 'bool msequtilities::set_aa_file(std::string&)':
msequtilities.cpp:884:41: warning: array subscript has type 'char' [-Wchar-subscripts]
      m_pdAaMass[cAa+32] = m_pdAaMass[cAa] = dMass;
                                         ^
msequtilities.cpp:885:41: warning: array subscript has type 'char' [-Wchar-subscripts]
      m_pfAaMass[cAa+32] = m_pfAaMass[cAa] = (float)dMass;
                                         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o base64.o base64.cpp
base64.cpp:16:13: warning: 'void encode_group(unsigned char*, const unsigned char*, int)' defined but not used [-Wunused-function]
 static void encode_group (unsigned char output[],
             ^
base64.cpp:44:13: warning: 'void decode_group(unsigned char*, const unsigned char*, int*)' defined but not used [-Wunused-function]
 static void decode_group (unsigned char output[],
             ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxmodhandler.o saxmodhandler.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o xmlparameter.o xmlparameter.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmodhandler.h:140,
                 from saxmodhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtandeminputhandler.h:140,
                 from xmlparameter.cpp:144:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxmzxmlhandler.o saxmzxmlhandler.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o xmltaxonomy.o xmltaxonomy.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzxmlhandler.h:4,
                 from saxmzxmlhandler.cpp:20:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxtaxhandler.h:140,
                 from xmltaxonomy.cpp:160:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxmzmlhandler.o saxmzmlhandler.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o msequenceserver.o msequenceserver.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxmzmlhandler.h:4,
                 from saxmzmlhandler.cpp:33:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
saxmzmlhandler.cpp: In member function 'virtual void SAXMzmlHandler::startElement(const XML_Char*, const XML_Char**)':
saxmzmlhandler.cpp:79:15: warning: unused variable 'name' [-Wunused-variable]
   const char* name = getAttrValue("name", attr);
               ^
saxmzmlhandler.cpp:80:15: warning: unused variable 'accession' [-Wunused-variable]
   const char* accession = getAttrValue("accession", attr);
               ^
saxmzmlhandler.cpp:81:15: warning: unused variable 'version' [-Wunused-variable]
   const char* version = getAttrValue("version", attr);
               ^
msequenceserver.cpp: In member function 'long unsigned int msequenceServer::next_pro(bool)':
msequenceserver.cpp:438:16: warning: unused variable 'cValue' [-Wunused-variable]
  register char cValue = '\0';
                ^
msequenceserver.cpp:439:8: warning: unused variable 'pValue' [-Wunused-variable]
  char *pValue = NULL;
        ^
msequenceserver.cpp:440:8: warning: unused variable 'pEol' [-Wunused-variable]
  char *pEol = NULL;
        ^
msequenceserver.cpp:445:9: warning: variable 'tS' set but not used [-Wunused-but-set-variable]
  size_t tS = 0;
         ^
msequenceserver.cpp: In member function 'long unsigned int msequenceServer::next_l()':
msequenceserver.cpp:560:16: warning: unused variable 'cValue' [-Wunused-variable]
  register char cValue = '\0';
                ^
msequenceserver.cpp:561:8: warning: unused variable 'pValue' [-Wunused-variable]
  char *pValue = NULL;
        ^
msequenceserver.cpp:564:9: warning: unused variable 'a' [-Wunused-variable]
  size_t a = 0;
         ^
msequenceserver.cpp: In member function 'bool msequenceServer::start()':
msequenceserver.cpp:652:9: warning: variable 'tS' set but not used [-Wunused-but-set-variable]
  size_t tS = 0;
         ^
msequenceserver.cpp:653:8: warning: variable 'pS' set but not used [-Wunused-but-set-variable]
  char *pS = NULL;
        ^
msequenceserver.cpp: In member function 'long unsigned int msequenceServer::next(bool)':
msequenceserver.cpp:302:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(pValue,m_lSize,m_pInput);
                                 ^
msequenceserver.cpp:329:34: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
    fgets(pValue,m_lSize,m_pInput);
                                  ^
msequenceserver.cpp: In member function 'long unsigned int msequenceServer::next_l()':
msequenceserver.cpp:569:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
   fgets(pLine,lSize,m_pInput);
                              ^
msequenceserver.cpp:577:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
    fgets(pLine,lSize,m_pInput);
                               ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mxxcleavage.o mxxcleavage.cpp
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mxxcleavage.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o p3msequenceserver.o p3msequenceserver.cpp
In file included from msequtilities.h:142:0,
                 from mscore.h:146,
                 from mxxcleavage.cpp:138:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
p3msequenceserver.cpp: In member function 'long unsigned int p3msequenceServer::u_maps(DESMAP&, std::vector<msequence>&)':
p3msequenceserver.cpp:194:16: warning: unused variable 'cValue' [-Wunused-variable]
  register char cValue = '\0';
                ^
p3msequenceserver.cpp:195:8: warning: unused variable 'pValue' [-Wunused-variable]
  char *pValue = NULL;
        ^
p3msequenceserver.cpp:196:8: warning: unused variable 'pEol' [-Wunused-variable]
  char *pEol = NULL;
        ^
p3msequenceserver.cpp:201:9: warning: variable 'sT' set but not used [-Wunused-but-set-variable]
  size_t sT = 0;
         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mzid_report.o mzid_report.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxsaphandler.h:140,
                 from mzid_report.cpp:142:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from msequtilities.h:142:0,
                 from mzid_report.cpp:146:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
mzid_report.cpp: In member function 'bool mzid_report::add_analysis(std::vector<mspectrum>&, std::vector<std::basic_string<char> >&, XmlParameter&)':
mzid_report.cpp:369:51: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat=]
     sprintf(pLine,"%i_%i_%i", _vs[a].m_tId,b+1,c+1);
                                                   ^
mzid_report.cpp:369:51: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp:369:51: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp:408:51: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat=]
      sprintf(pLine,"%i_%i_%i",_vs[a].m_tId,b+1,c+1);
                                                   ^
mzid_report.cpp:408:51: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp:408:51: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp: In member function 'bool mzid_report::add_peptide_evidence(std::vector<mspectrum>&)':
mzid_report.cpp:623:50: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat=]
     sprintf(pLine,"%i_%i_%i",_vs[a].m_tId,b+1,c+1);
                                                  ^
mzid_report.cpp:623:50: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp:623:50: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp:608:9: warning: unused variable 'tStart' [-Wunused-variable]
  size_t tStart = 0;
         ^
mzid_report.cpp:609:9: warning: unused variable 'tEnd' [-Wunused-variable]
  size_t tEnd = 0;
         ^
mzid_report.cpp: In member function 'bool mzid_report::add_peptides(std::vector<mspectrum>&)':
mzid_report.cpp:704:50: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat=]
     sprintf(pLine,"%i_%i_%i",_vs[a].m_tId,b+1,c+1); 
                                                  ^
mzid_report.cpp:704:50: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp:704:50: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat=]
mzid_report.cpp:674:9: warning: variable 'tUid' set but not used [-Wunused-but-set-variable]
  size_t tUid = 0;
         ^
mzid_report.cpp:680:9: warning: unused variable 'tS' [-Wunused-variable]
  size_t tS = 0;
         ^
mzid_report.cpp:681:9: warning: unused variable 'tE' [-Wunused-variable]
  size_t tE = 0;
         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxbiomlhandler.o saxbiomlhandler.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxbiomlhandler.h:140,
                 from saxbiomlhandler.cpp:140:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o p3.o p3.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mpmods.o mpmods.cpp
In file included from msequtilities.h:142:0,
                 from p3.cpp:148:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpmods.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from mspectrum.h:142:0,
                 from p3.cpp:149:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from msequtilities.h:142:0,
                 from mscore.h:146,
                 from mpmods.cpp:138:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
p3.cpp: In function 'int main(int, char**)':
p3.cpp:185:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  if(argc < 2 || argc > 1 && strstr(argv[1],"-L") == argv[1] || argc > 1 && strstr(argv[1],"-h") == argv[1]) {
                          ^
p3.cpp:185:73: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  if(argc < 2 || argc > 1 && strstr(argv[1],"-L") == argv[1] || argc > 1 && strstr(argv[1],"-h") == argv[1]) {
                                                                         ^
p3.cpp:287:10: warning: unused variable 'tCount' [-Wunused-variable]
   size_t tCount = pProcess[0]->m_vSpectra.size();
          ^
p3.cpp:336:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(dCount < lThreads) {
                  ^
p3.cpp:427:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while(a < dCount) {
            ^
p3.cpp:434:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while(a < dCount) {
            ^
p3.cpp:458:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   while(dCount < lThreads) {
                  ^
p3.cpp:543:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  while(a < dCount) {
            ^
p3.cpp:585:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if(lE != -1) {
            ^
p3.cpp:414:6: warning: variable 'wait' set but not used [-Wunused-but-set-variable]
  int wait;
      ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o stdafx.o stdafx.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mbiomlreport.o mbiomlreport.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o saxgamlhandler.o saxgamlhandler.cpp
In file included from mspectrum.h:142:0,
                 from saxhandler.h:137,
                 from saxgamlhandler.h:140,
                 from saxgamlhandler.cpp:139:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o MSNumpress.o MSNumpress.cpp
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3   -c -o mpam.o mpam.cpp
In file included from mspectrum.h:142:0,
                 from mspectrumcondition.h:153,
                 from mprocess.h:143,
                 from mpam.cpp:137:
mhistogram.h: In member function 'bool mhistogram::model()':
mhistogram.h:442:7: warning: unused variable 'lZeros' [-Wunused-variable]
   int lZeros = m_lHigh - a - 1;
       ^
In file included from msequtilities.h:142:0,
                 from mscore.h:146,
                 from mpam.cpp:138:
mmotif.h: In member function 'bool mmotifres::set(const char*)':
mmotif.h:187:9: warning: unused variable 'pEnd' [-Wunused-variable]
   char *pEnd = pStart;
         ^
g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -DGCC4_3 -DPLUGGABLE_SCORING -DX_P3 -o ../bin/tandem tandem.o p3mprocess.o saxmzdatahandler.o mspectrumcondition.o masscalc.o mprocess.o mreport.o mscore_tandem.o loadmspectrum.o msequencecollection.o mplugin.o saxsaphandler.o saxtaxhandler.o mscore.o mtermmods.o mrefine.o saxtandeminputhandler.o saxhandler.o msequtilities.o base64.o saxmodhandler.o xmlparameter.o saxmzxmlhandler.o xmltaxonomy.o saxmzmlhandler.o msequenceserver.o mxxcleavage.o p3msequenceserver.o mzid_report.o saxbiomlhandler.o p3.o mpmods.o stdafx.o mbiomlreport.o saxgamlhandler.o MSNumpress.o mpam.o -Wl,-z,relro  -L/usr/lib64 -lpthread -lm -lexpat
make: Leaving directory `/builddir/build/BUILD/tandem-linux-15-04-01-1/src'
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.T6fWd1
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64
++ dirname /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64
+ cd tandem-linux-15-04-01-1
+ mkdir -p /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/bin
+ install -pm 755 bin/tandem /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/bin
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/tandem-linux-15-04-01-1
extracting debug info from /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/bin/tandem
dwz: Too few files for multifile optimization
/usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
2100 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.0L1jvB
~/build/BUILD/tandem-linux-15-04-01-1/bin ~/build/BUILD/tandem-linux-15-04-01-1
+ umask 022
+ cd /builddir/build/BUILD
+ cd tandem-linux-15-04-01-1
+ pushd bin
+ ./tandem input.xml
X! P3 Piledriver (2015.04.01.1)
Loading spectra (mgf). loaded.
Spectra matching criteria = 511
Pluggable scoring enabled.
Starting threads . started.
Computing models:
	testin	sequences modelled = 4 ks
Model refinement:
	partial cleavage ..... done.
	unanticipated cleavage ..... done.
	modified N-terminus 42.0106@[ ..... done.
	finishing refinement ... done.
Creating report:
	initial calculations  ..... done.
	sorting  ..... done.
	finding repeats ..... done.
	evaluating results ..... done.
	calculating expectations ..... done.
	writing results ..... done.
Valid models = 201
Unique models = 197
Estimated false positives = 2 &#177; 1
~/build/BUILD/tandem-linux-15-04-01-1
+ popd
+ exit 0
Processing files: XTandem-150401.1-3.el7.centos.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.xtmLYd
+ umask 022
+ cd /builddir/build/BUILD
+ cd tandem-linux-15-04-01-1
+ DOCDIR=/builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/share/doc/XTandem-150401.1
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/share/doc/XTandem-150401.1
+ cp -pr README /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/share/doc/XTandem-150401.1
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.EjSptQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd tandem-linux-15-04-01-1
+ LICENSEDIR=/builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/share/licenses/XTandem-150401.1
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/share/licenses/XTandem-150401.1
+ cp -pr LICENSE /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64/usr/share/licenses/XTandem-150401.1
+ exit 0
Provides: XTandem = 150401.1-3.el7.centos XTandem(x86-64) = 150401.1-3.el7.centos
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libexpat.so.1()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Processing files: XTandem-debuginfo-150401.1-3.el7.centos.x86_64
Provides: XTandem-debuginfo = 150401.1-3.el7.centos XTandem-debuginfo(x86-64) = 150401.1-3.el7.centos
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64
warning: Could not canonicalize hostname: copr-builder-791631832.novalocal
Wrote: /builddir/build/RPMS/XTandem-150401.1-3.el7.centos.x86_64.rpm
Wrote: /builddir/build/RPMS/XTandem-debuginfo-150401.1-3.el7.centos.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.NJLxwM
+ umask 022
+ cd /builddir/build/BUILD
+ cd tandem-linux-15-04-01-1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/XTandem-150401.1-3.el7.centos.x86_64
+ exit 0
Child return code was: 0