Mock Version: 1.2.17 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/tophat.spec'], shell=Falseuser='mockbuild'env={'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}uid=1001timeout=0logger=printOutput=Falsegid=135chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-2742/root') Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/tophat.spec'] with env {'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'} and shell False sh: /usr/bin/python: No such file or directory sh: /usr/bin/python: No such file or directory sh: /usr/bin/python: No such file or directory sh: /usr/bin/python: No such file or directory warning: Could not canonicalize hostname: copr-builder-880135801.novalocal Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/tophat-2.1.1-2.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/tophat.spec'], shell=Falseuser='mockbuild'private_network=Trueenv={'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin'}uid=1001timeout=0logger=printOutput=Falsegid=135chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-2742/root') Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/tophat.spec'] with env {'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;\x07"', '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.mtdBvr + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf tophat-2.1.1 + /usr/bin/gzip -dc /builddir/build/SOURCES/tophat-2.1.1.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd tophat-2.1.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.8XXm2N + umask 022 + cd /builddir/build/BUILD + cd tophat-2.1.1 + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98' + export CFLAGS + 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 -O3 -std=gnu++98' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro ' + export LDFLAGS + '[' 1 == 1 ']' + '[' x86_64 == ppc64le ']' ++ find . -name config.guess -o -name config.sub + for i in '$(find . -name config.guess -o -name config.sub)' ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + for i in '$(find . -name config.guess -o -name config.sub)' ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess '/usr/lib/rpm/redhat/config.guess' -> './config.guess' ++ pwd + ./configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-boost-thread=-lboost_thread-mt CPPFLAGS=-I/builddir/build/BUILD/tophat-2.1.1 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-redhat-linux-gnu-g++... no checking for x86_64-redhat-linux-gnu-c++... no checking for x86_64-redhat-linux-gnu-gpp... no checking for x86_64-redhat-linux-gnu-aCC... no checking for x86_64-redhat-linux-gnu-CC... no checking for x86_64-redhat-linux-gnu-cxx... no checking for x86_64-redhat-linux-gnu-cc++... no checking for x86_64-redhat-linux-gnu-cl.exe... no checking for x86_64-redhat-linux-gnu-FCC... no checking for x86_64-redhat-linux-gnu-KCC... no checking for x86_64-redhat-linux-gnu-RCC... no checking for x86_64-redhat-linux-gnu-xlC_r... no checking for x86_64-redhat-linux-gnu-xlC... no checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking for x86_64-redhat-linux-gnu-ar... no checking for x86_64-redhat-linux-gnu-lib... no checking for x86_64-redhat-linux-gnu-link... no checking for ar... ar checking the archiver (ar) interface... ar checking for gawk... (cached) gawk checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) none checking for x86_64-redhat-linux-gnu-gcc... no checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... none checking whether make sets $(MAKE)... (cached) yes checking for x86_64-redhat-linux-gnu-ranlib... no checking for ranlib... ranlib checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib64/python2.7/site-packages checking for boostlib >= 1.38.0... yes checking whether the compiler implements namespaces... yes checking whether the Boost::Thread library is available... yes checking for main in -lboost_thread-lboost_thread-mt... no checking for main in -lboost_thread... yes checking whether Boost::Thread needs Boost::System library... no checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... no checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- tophat 2.1.1 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 Linker flags: -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro BOOST libraries: -lboost_thread GCC version: gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4) Host System type: x86_64-redhat-linux-gnu Install prefix: /usr Install eprefix: /usr See config.h for further configuration information. Email bug reports to . + make make all-recursive make[1]: Entering directory `/builddir/build/BUILD/tophat-2.1.1' Making all in src make[2]: Entering directory `/builddir/build/BUILD/tophat-2.1.1/src' Makefile:1672: warning: overriding recipe for target `libbam.a' Makefile:1203: warning: ignoring old recipe for target `libbam.a' cd ./samtools-0.1.18 && make samtools_0.1.18 && cp libbam.a samtools_0.1.18 .. make[3]: Entering directory `/builddir/build/BUILD/tophat-2.1.1/src/samtools-0.1.18' make[4]: Entering directory `/builddir/build/BUILD/tophat-2.1.1/src/samtools-0.1.18' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o bgzf.c: In function 'bgzf_close': bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count, block_length = deflate_block(fp, 0); ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam.c -o bam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam.c -o sam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function 'resolve_cigar2': bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] int k, is_head = 0; ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. razf.c -o razf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. knetfile.c -o knetfile.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function 'bam_reheader': bam_reheader.c:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] bam_header_t *old; ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function 'kpa_glocal': kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable] int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[4]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1/src/samtools-0.1.18' make[4]: Entering directory `/builddir/build/BUILD/tophat-2.1.1/src/samtools-0.1.18/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf.c -o bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. vcf.c -o vcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. prob1.c -o prob1.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. em.c -o em.o em.c: In function 'bcf_em1': em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] int i, n, n2; ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kmin.c -o kmin.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. index.c -o index.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. fet.c -o fet.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. mut.c -o mut.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o make[4]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1/src/samtools-0.1.18/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview.c -o bam_tview.o bam_tview.c:434:2: warning: #warning "No curses library is available; tview is disabled." [-Wcpp] #warning "No curses library is available; tview is disabled." ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_view.c -o sam_view.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_mate.c -o bam_mate.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_stat.c -o bam_stat.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_color.c -o bam_color.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bamtk.c -o bamtk.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kaln.c -o kaln.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. errmod.c -o errmod.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sample.c -o sample.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. cut_target.c -o cut_target.o cut_target.c: In function 'main_cut_target': cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. phase.c -o phase.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2depth.c -o bam2depth.o gcc -g -Wall -O2 -o samtools_0.1.18 bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lm -lz #-lcurses make[3]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1/src/samtools-0.1.18' g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o GBase.o GBase.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o codons.o codons.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o gdna.o gdna.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o GStr.o GStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o GFaSeqGet.o GFaSeqGet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o gff.o gff.cpp rm -f libgc.a ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o ranlib libgc.a g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o reads.o reads.cpp gcc -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -c alphabet.c cc1: warning: command line option '-std=gnu++98' is valid for C++/ObjC++ but not for C [enabled by default] g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o bwt_map.o bwt_map.cpp bwt_map.cpp: In function 'bool spliceCigar(std::vector&, const std::vector&, std::vector, int&, int, int, CigarOpCode, int&)': bwt_map.cpp:705:9: warning: variable 'prev_opcode' set but not used [-Wunused-but-set-variable] int prev_opcode=0; ^ bwt_map.cpp:706:9: warning: variable 'prev_oplen' set but not used [-Wunused-but-set-variable] int prev_oplen=0; ^ bwt_map.cpp: In member function 'virtual bool BAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)': bwt_map.cpp:1112:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable] int text_mate_pos = hit_buf->core.mpos; ^ bwt_map.cpp:1118:7: warning: variable 'num_hits' set but not used [-Wunused-but-set-variable] int num_hits = 1; ^ bwt_map.cpp: In member function 'virtual bool SplicedBAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)': bwt_map.cpp:1481:7: warning: variable 'text_mate_pos' set but not used [-Wunused-but-set-variable] int text_mate_pos = hit_buf->core.mpos; ^ bwt_map.cpp:1486:8: warning: variable 'spliced_alignment' set but not used [-Wunused-but-set-variable] bool spliced_alignment = false; ^ g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o common.o common.cpp common.cpp: In member function 'void GBamRecord::add_aux(const char*)': common.cpp:1140:29: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *(int16_t*)abuf = (int16_t)x; ^ common.cpp:1145:29: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *(int32_t*)abuf = (int32_t)x; ^ common.cpp:1159:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *(uint16_t*)abuf = (uint16_t)x; ^ common.cpp:1164:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *(uint32_t*)abuf = (uint32_t)x; ^ common.cpp:1173:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *(float*)abuf = (float)atof(str + 5); ^ common.cpp:1177:23: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] *(float*)abuf = (float)atof(str + 9); ^ common.cpp: In member function 'std::string GBamRecord::seqData(std::string*)': common.cpp:1259:8: warning: variable 'mate_num' set but not used [-Wunused-but-set-variable] int mate_num=0; ^ g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o junctions.o junctions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o insertions.o insertions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o deletions.o deletions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o fusions.o fusions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o align_status.o align_status.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o fragments.o fragments.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o tokenize.o tokenize.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o inserts.o inserts.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o qual.o qual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o bam_merge_impl.o bam_merge_impl.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o utils.o utils.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o coverage.o coverage.cpp rm -f libtophat.a ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o ranlib libtophat.a g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o prep_reads.o prep_reads.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o prep_reads prep_reads.o ../src/libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o GTFToFasta.o GTFToFasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o FastaTools.o FastaTools.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o gtf_to_fasta GTFToFasta.o FastaTools.o ../src/libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o fix_map_ordering.o fix_map_ordering.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o fix_map_ordering fix_map_ordering.o ../src/libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o bam2fastx.o bam2fastx.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o bam2fastx bam2fastx.o ../src/libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o segment_juncs.o segment_juncs.cpp segment_juncs.cpp: In member function 'void SegmentSearchWorker::operator()()': segment_juncs.cpp:4625:27: warning: variable 'last_read_id' set but not used [-Wunused-but-set-variable] uint64_t read_id = 0, last_read_id = 0; ^ g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o segment_juncs segment_juncs.o ../src/libtophat.a -lboost_thread -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o gtf_juncs.o gtf_juncs.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o gtf_juncs gtf_juncs.o ../src/libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o juncs_db.o juncs_db.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o juncs_db juncs_db.o ../src/libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o long_spanning_reads.o long_spanning_reads.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o long_spanning_reads long_spanning_reads.o ../src/libtophat.a -lboost_thread -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o bam_merge.o bam_merge.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o bam_merge bam_merge.o ../src/libtophat.a ../src/libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o map2gtf.o map2gtf.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o map2gtf map2gtf.o ../src/libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o tophat_reports.o tophat_reports.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o tophat_reports tophat_reports.o ../src/libtophat.a -lboost_thread -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -I/builddir/build/BUILD/tophat-2.1.1 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -c -o sam_juncs.o sam_juncs.cpp g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -O3 -std=gnu++98 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -L./samtools-0.1.18 -L/usr/lib -Wl,-z,relro -o sam_juncs sam_juncs.o ../src/libtophat.a -lbam -lz cp tophat2.sh tophat2 && chmod 755 tophat2 sed -e 's|__VERSION__|2.1.1|' tophat.py > tophat && chmod 755 tophat make[2]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1/src' make[2]: Entering directory `/builddir/build/BUILD/tophat-2.1.1' make[2]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1' make[1]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.MsRWs6 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64 ++ dirname /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64 + cd tophat-2.1.1 + rm -rf /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64 + make install DESTDIR=/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64 Making install in src make[1]: Entering directory `/builddir/build/BUILD/tophat-2.1.1/src' Makefile:1672: warning: overriding recipe for target `libbam.a' Makefile:1203: warning: ignoring old recipe for target `libbam.a' make[2]: Entering directory `/builddir/build/BUILD/tophat-2.1.1/src' Makefile:1672: warning: overriding recipe for target `libbam.a' Makefile:1203: warning: ignoring old recipe for target `libbam.a' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin' /usr/bin/install -c samtools_0.1.18 prep_reads gtf_to_fasta fix_map_ordering bam2fastx segment_juncs gtf_juncs juncs_db long_spanning_reads bam_merge map2gtf tophat_reports sam_juncs '/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin' /usr/bin/install -c tophat2 tophat '/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin' /usr/bin/mkdir -p '/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin' /usr/bin/install -c contig_to_chr_coords bed_to_juncs sra_to_solid tophat-fusion-post '/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin' make install-data-hook make[3]: Entering directory `/builddir/build/BUILD/tophat-2.1.1/src' Makefile:1672: warning: overriding recipe for target `libbam.a' Makefile:1203: warning: ignoring old recipe for target `libbam.a' cp -r intervaltree sortedcontainers /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin make[3]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1/src' make[2]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1/src' make[1]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1/src' make[1]: Entering directory `/builddir/build/BUILD/tophat-2.1.1' make[2]: Entering directory `/builddir/build/BUILD/tophat-2.1.1' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1' make[1]: Leaving directory `/builddir/build/BUILD/tophat-2.1.1' + mkdir -p /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages + mv /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/intervaltree /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/sortedcontainers /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages + chmod -x /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/intervaltree/__init__.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/intervaltree/interval.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/intervaltree/intervaltree.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/intervaltree/node.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/sortedcontainers/__init__.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/sortedcontainers/sorteddict.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/sortedcontainers/sortedlist.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/sortedcontainers/sortedlistwithkey.py /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7/site-packages/sortedcontainers/sortedset.py + /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/tophat-2.1.1 extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/sam_juncs extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/tophat_reports extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/map2gtf extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/bam_merge extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/long_spanning_reads extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/juncs_db extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/gtf_juncs extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/segment_juncs extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/bam2fastx extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/fix_map_ordering extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/gtf_to_fasta extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/prep_reads extracting debug info from /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/bin/samtools_0.1.18 /usr/lib/rpm/sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. 5473 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 Bytecompiling .py files below /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/lib/python2.7 using /usr/bin/python2.7 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Processing files: tophat-2.1.1-2.el7.centos.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.kfSQ0H + umask 022 + cd /builddir/build/BUILD + cd tophat-2.1.1 + DOCDIR=/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/doc/tophat-2.1.1 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/doc/tophat-2.1.1 + cp -pr README /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/doc/tophat-2.1.1 + cp -pr AUTHORS /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/doc/tophat-2.1.1 + cp -pr THANKS /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/doc/tophat-2.1.1 + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.aeCAAj + umask 022 + cd /builddir/build/BUILD + cd tophat-2.1.1 + LICENSEDIR=/builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/licenses/tophat-2.1.1 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/licenses/tophat-2.1.1 + cp -pr LICENSE /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64/usr/share/licenses/tophat-2.1.1 + exit 0 Provides: bundled(samtools) tophat = 2.1.1-2.el7.centos tophat(x86-64) = 2.1.1-2.el7.centos Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/env libboost_system-mt.so.1.53.0()(64bit) libboost_thread-mt.so.1.53.0()(64bit) 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)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(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) libpthread.so.0(GLIBC_2.3.2)(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_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.2)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) python(abi) = 2.7 rtld(GNU_HASH) Processing files: tophat-debuginfo-2.1.1-2.el7.centos.x86_64 Provides: tophat-debuginfo = 2.1.1-2.el7.centos tophat-debuginfo(x86-64) = 2.1.1-2.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/tophat-2.1.1-2.el7.centos.x86_64 warning: Could not canonicalize hostname: copr-builder-880135801.novalocal Wrote: /builddir/build/RPMS/tophat-2.1.1-2.el7.centos.x86_64.rpm Wrote: /builddir/build/RPMS/tophat-debuginfo-2.1.1-2.el7.centos.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.wng8Lu + umask 022 + cd /builddir/build/BUILD + cd tophat-2.1.1 + rm -rf /builddir/build/BUILDROOT/tophat-2.1.1-2.el7.centos.x86_64 + exit 0 Child return code was: 0