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Red Hat Bugzilla – Attachment 1253616 Details for
Bug 1424106
primer3: FTBFS in rawhide
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build.log
<fdopen> (text/plain), 8.73 KB, created by
Fedora Release Engineering
on 2017-02-17 15:55:55 UTC
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build.log
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Fedora Release Engineering
Created:
2017-02-17 15:55:55 UTC
Size:
8.73 KB
patch
obsolete
>Mock Version: 1.3.3 >Mock Version: 1.3.3 >ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/primer3.spec'], timeout=172800uid=1000user='mockbuild'gid=425logger=<mockbuild.trace_decorator.getLog object at 0x3fff908d2390>printOutput=Falseenv={'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash'}chrootPath='/var/lib/mock/f26-build-7658624-694502/root'shell=False) >Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target ppc64le --nodeps /builddir/build/SPECS/primer3.spec'] with env {'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash'} and shell False >Building target platforms: ppc64le >Building for target ppc64le >Wrote: /builddir/build/SRPMS/primer3-2.3.6-7.fc26.src.rpm >Child return code was: 0 >ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/primer3.spec'], private_network=Truetimeout=172800uid=1000user='mockbuild'gid=425logger=<mockbuild.trace_decorator.getLog object at 0x3fff908d2390>printOutput=Falseenv={'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash'}chrootPath='/var/lib/mock/f26-build-7658624-694502/root'shell=False) >Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/primer3.spec'] with env {'TERM': 'vt100', 'LANG': 'en_US.UTF-8', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'SHELL': '/bin/bash'} and shell False >Building target platforms: ppc64le >Building for target ppc64le >Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.OvszsA >+ umask 022 >+ cd /builddir/build/BUILD >+ cd /builddir/build/BUILD >+ rm -rf primer3-2.3.6 >+ /usr/bin/gzip -dc /builddir/build/SOURCES/primer3-src-2.3.6.tar.gz >+ /usr/bin/tar -xof - >+ STATUS=0 >+ '[' 0 -ne 0 ']' >+ cd primer3-2.3.6 >+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . >+ chmod -x src/Makefile src/Makefile.OSX src/dpal.c src/dpal.h src/format_output.c src/format_output.h src/gpl-2.0.txt src/humrep_and_simple.txt src/libprimer3.c src/libprimer3.h src/long_seq_tm_test_main.c src/ntdpal_main.c src/oligotm.c src/oligotm.h src/oligotm_main.c src/p3_seq_lib.c src/p3_seq_lib.h src/paranoid_tests.sh src/primer3_boulder_main.c src/primer3_config src/print_boulder.c src/print_boulder.h src/read_boulder.c src/read_boulder.h src/release_notes.txt src/thal.c src/thal.h src/thal_main.c >+ chmod +x src/primer3_config >+ sed -i -e 's|CFLAGS = $(CC_OPTS) $(O_OPTS)|CFLAGS = $(CC_OPTS) $(O_OPTS) $(INIT_CFLAGS)|' src/Makefile >+ sed -i 's/\r//' primer3web_v0_4_0_default_settings.txt >+ sed -i -e 's|/opt/primer3_config|/etc/primer3_config|' src/release_notes.txt src/thal_main.c src/primer3_boulder_main.c primer3_manual.htm >+ exit 0 >Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.w0I0ap >+ umask 022 >+ cd /builddir/build/BUILD >+ cd primer3-2.3.6 >+ cd src >+ export 'INIT_CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8' >+ INIT_CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8' >+ make -j4 >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 primer3_boulder_main.c >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 -o format_output.o format_output.c >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 -o read_boulder.o read_boulder.c >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 -o print_boulder.o print_boulder.c >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 -Wno-deprecated -o libprimer3.o libprimer3.c >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 -o p3_seq_lib.o p3_seq_lib.c >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 -o dpal_primer.o dpal.c >g++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -O2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mcpu=power8 -mtune=power8 -ffloat-store -o thal_primer.o thal.c >dpal.c: In function 'void print_align(const unsigned char*, const unsigned char*, int (*)[1600][3], int, int, const dpal_args*)': >dpal.c:1036:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation] > for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n"); > ^~~ >dpal.c:1036:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' > for(i=j;i<j+70;i++) fprintf(stderr, "%c",sy[i]); fprintf(stderr,"\n"); > ^~~~~~~ >thal.c: In function 'void thal(const unsigned char*, const unsigned char*, const thal_args*, thal_results*)': >thal.c:426:16: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] > if ('\0' == oligo_f) { > ^~~~~~~ >thal.c:431:16: error: ISO C++ forbids comparison between pointer and integer [-fpermissive] > if ('\0' == oligo_r) { > ^~~~~~~ >thal.c: In function 'void tableStartATS(double, double (*)[5])': >thal.c:1198:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation] > for (i = 0; i < 5; ++i) > ^~~ >thal.c:1201:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' > atpS[0][3] = atpS[3][0] = atp_value; > ^~~~ >thal.c: In function 'void tableStartATH(double, double (*)[5])': >thal.c:1210:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation] > for (i = 0; i < 5; ++i) > ^~~ >thal.c:1214:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' > atpH[0][3] = atpH[3][0] = atp_value; > ^~~~ >make: *** [Makefile:192: thal_primer.o] Error 1 >make: *** Waiting for unfinished jobs.... >error: Bad exit status from /var/tmp/rpm-tmp.w0I0ap (%build) > Bad exit status from /var/tmp/rpm-tmp.w0I0ap (%build) >RPM build errors: >Child return code was: 1 >EXCEPTION: [Error()] >Traceback (most recent call last): > File "/usr/lib/python3.5/site-packages/mockbuild/trace_decorator.py", line 89, in trace > result = func(*args, **kw) > File "/usr/lib/python3.5/site-packages/mockbuild/util.py", line 578, in do > raise exception.Error("Command failed. See logs for output.\n # %s" % (command,), child.returncode) >mockbuild.exception.Error: Command failed. See logs for output. > # bash --login -c /usr/bin/rpmbuild -bb --target ppc64le --nodeps /builddir/build/SPECS/primer3.spec
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bug 1424106
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