Mock Version: 1.1.9 ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/tophat.spec'], False, '/var/lib/mock/fedora-14-x86_64/root/', None, 0, True, 0, 500, 477, None, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/tophat.spec'] Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/tophat-1.2.0-1.fc14.src.rpm Child returncode was: 0 LEAVE do --> ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/tophat.spec'], False, '/var/lib/mock/fedora-14-x86_64/root/', None, 0, True, 0, 500, 477, None, logger=) Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/tophat.spec'] Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.fGxyd3 + umask 022 + cd /builddir/build/BUILD + LANG=C + export LANG + unset DISPLAY + cd /builddir/build/BUILD + rm -rf tophat-1.2.0 + /usr/bin/gzip -dc /builddir/build/SOURCES/tophat-1.2.0.tar.gz + /bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd tophat-1.2.0 + /bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (tophat-sam-header.patch):' Patch #0 (tophat-sam-header.patch): + /bin/cat /builddir/build/SOURCES/tophat-sam-header.patch + /usr/bin/patch -s -p1 --fuzz=0 + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.4PZQrQ + umask 022 + cd /builddir/build/BUILD + cd tophat-1.2.0 + LANG=C + export LANG + unset DISPLAY + autoreconf sh: svnversion: command not found sh: svnversion: command not found + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules' + export FFLAGS + ./configure --build=x86_64-unknown-linux-gnu --host=x86_64-unknown-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 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for x86_64-unknown-linux-gnu-gcc... no checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for x86_64-unknown-linux-gnu-g++... no checking for x86_64-unknown-linux-gnu-c++... no checking for x86_64-unknown-linux-gnu-gpp... no checking for x86_64-unknown-linux-gnu-aCC... no checking for x86_64-unknown-linux-gnu-CC... no checking for x86_64-unknown-linux-gnu-cxx... no checking for x86_64-unknown-linux-gnu-cc++... no checking for x86_64-unknown-linux-gnu-cl.exe... no checking for x86_64-unknown-linux-gnu-FCC... no checking for x86_64-unknown-linux-gnu-KCC... no checking for x86_64-unknown-linux-gnu-RCC... no checking for x86_64-unknown-linux-gnu-xlC_r... no checking for x86_64-unknown-linux-gnu-xlC... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for gawk... (cached) gawk checking for x86_64-unknown-linux-gnu-ranlib... no checking for ranlib... ranlib checking for x86_64-unknown-linux-gnu-ar... no checking for ar... ar checking for perl... /usr/bin/perl checking for bash... /bin/bash 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 bamlib... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /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 if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking how to run the C++ preprocessor... g++ -E 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 stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... no 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 if gcc accepts -m64... yes checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- tophat 1.2.0 Configuration Results -- C compiler: gcc -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG C++ compiler: g++ -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG GCC version: gcc (GCC) 4.5.1 20100924 (Red Hat 4.5.1-4) Host System type: x86_64-unknown-linux-gnu Install prefix: /usr Install eprefix: /usr See config.h for further configuration information. Email with questions and bug reports. + make -j12 make all-recursive make[1]: Entering directory `/builddir/build/BUILD/tophat-1.2.0' Making all in src make[2]: Entering directory `/builddir/build/BUILD/tophat-1.2.0/src' g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o reads.o reads.cpp gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c alphabet.c g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o bwt_map.o bwt_map.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o common.o common.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o junctions.o junctions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o insertions.o insertions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o deletions.o deletions.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o align_status.o align_status.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o fragments.o fragments.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o tokenize.o tokenize.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o inserts.o inserts.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o qual.o qual.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GBase.o GBase.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o codons.o codons.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o gdna.o gdna.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GStr.o GStr.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GFaSeqGet.o GFaSeqGet.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o GFastaIndex.o GFastaIndex.cpp GBase.cpp: In function 'void writeFasta(FILE*, const char*, const char*, const char*, int, int)': GBase.cpp:651:52: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o gff.o gff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o gtf_tracking.o gtf_tracking.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DNDEBUG -c -o prep_reads.o prep_reads.cpp make[2]: *** No rule to make target `../src/libtophat.a', needed by `prep_reads'. Stop. make[2]: *** Waiting for unfinished jobs.... reads.cpp: In function 'void BWA_decode(const std::string&, const std::string&, const std::string&, std::string&)': reads.cpp:434:54: warning: array subscript has type 'char' bwt_map.h: In member function 'bool HitStream::next_read_hits(HitsForRead&)': bwt_map.h:680:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result bwt_map.cpp: In member function 'virtual bool SplicedBowtieHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)': bwt_map.cpp:457:39: warning: comparison between signed and unsigned integer expressions bwt_map.cpp:507:39: warning: comparison between signed and unsigned integer expressions bwt_map.cpp:513:40: warning: comparison between signed and unsigned integer expressions make[2]: Leaving directory `/builddir/build/BUILD/tophat-1.2.0/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/builddir/build/BUILD/tophat-1.2.0' make: *** [all] Error 2 error: Bad exit status from /var/tmp/rpm-tmp.4PZQrQ (%build) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.4PZQrQ (%build) Child returncode was: 1 EXCEPTION: Command failed. See logs for output. # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/tophat.spec'] Traceback (most recent call last): File "/usr/lib/python2.7/site-packages/mock/trace_decorator.py", line 70, in trace result = func(*args, **kw) File "/usr/lib/python2.7/site-packages/mock/util.py", line 325, in do raise mock.exception.Error, ("Command failed. See logs for output.\n # %s" % (command,), child.returncode) Error: Command failed. See logs for output. # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/tophat.spec'] LEAVE do --> EXCEPTION RAISED