[Crac-bugs] Build failed in Jenkins: crac-distrib #10

ci-crac at inria.fr ci-crac at inria.fr
Mer 8 Mai 02:01:08 CEST 2013


See <https://ci.inria.fr/crac/job/crac-distrib/10/changes>

Changes:

[salson] CRAC: Bug #15577 → Changed getLength() definition in SupportBreak.cpp and modified some calls to getLength() so that they now call support->getLength()

[salson] CRAC: Bug #15577 → The code computing the location for the SAM file has been modified to take advantage of the methods in SupportBreak that can take the strand as a parameter. Thus the code is simpler.
getChrPosStartBreak and getChrPosEndBreak have been modified so that the returned value is updated if the result has been modified

[salson] CRAC: Bug #15577 → modifications have been made in perform_deep_snp_search to adjust the position on the reverse strand.

[nphilippe] add doc for gz

[nphilippe] update ChangeLog

[nphilippe] -#BUG 15577 was not completely fixed because pos_start should be >= getLength and setOutside score should be check. Now it is resolved
-wildcards restored in Makefile.am for a good running of make distcheck

[nphilippe] obsolete removed AC_PROG_RANLIB
make a disable-shared by default 
GNU and Makefile wilcards adapted

------------------------------------------
[...truncated 76 lines...]
U         configure.ac
U         doc/crac-doc.org
U         man/crac.1.in
D         src/libGkArrays/configure
D         src/libGkArrays/Makefile.in
D         src/libGkArrays/aclocal.m4
U         src/libGkArrays/ChangeLog
D         src/libGkArrays/src/Makefile.in
D         src/libGkArrays/src/sux/Makefile.in
D         src/libGkArrays/src/kseq/Makefile.in
D         src/libGkArrays/tests/Makefile.in
U         src/libGkArrays/tests/Makefile.am
U         src/libGkArrays/configure.ac
D         src/libGkArrays/doc/Makefile.in
U         src/libGkArrays/doc/libGkArrays.info
Fetching 'hudson.scm.subversion.SubversionUpdateEventHandler$SVNExternalDetails at 68c9f4a3' at 2,430 into '<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libGkArrays'>
At revision 2430
At revision 2430
no revision recorded for svn+ssh://scm.gforge.inria.fr/svn/crac/releases/gkarrays/2.0.4 in the previous build
[crac-distrib] $ /bin/sh -xe /tmp/hudson1683812149922401728.sh
+ libtoolize --copy --force
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'.
libtoolize: copying file `config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `config/m4'.
libtoolize: copying file `config/m4/libtool.m4'
libtoolize: copying file `config/m4/ltoptions.m4'
libtoolize: copying file `config/m4/ltsugar.m4'
libtoolize: copying file `config/m4/ltversion.m4'
libtoolize: copying file `config/m4/lt~obsolete.m4'
+ aclocal
+ autoconf
+ autoheader
+ automake --add-missing
test_f/Makefile.am:116: shell find . -name "*.should_get": non-POSIX variable name
test_f/Makefile.am:116: (probably a GNU make extension)
test_f/Makefile.am:117: shell find . -name "*.fasta" -o -name "*.fa": non-POSIX variable name
test_f/Makefile.am:117: (probably a GNU make extension)
[crac-distrib] $ /bin/sh -xe /tmp/hudson2315858679930566177.sh
+ ./configure
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... no
checking for mawk... mawk
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 gawk... (cached) mawk
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... gcc3
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++... gcc3
checking how to run the C preprocessor... gcc -E
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking for texi2dvi... texi2dvi
checking for pdftex... no
checking for kpsewhich... no
configure: WARNING: The 'texi2dvi' or 'pdftex' program could not be found. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.
configure: WARNING: The 'texi2dvi' or 'pdftex' is missing a correct latex installation. This isn't critical, but it means that you won't be able to create the documentation and thus to make releases.
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for ar... ar
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for ANSI C header files... no
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 dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for ld used by gcc... (cached) /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... (cached) yes
checking for dpkg... /usr/bin/dpkg
checking for rpmbuild... no
checking for sqrt in -lm... yes
checking for pthread_join in -lpthread... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether sys/types.h defines makedev... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking libintl.h usability... yes
checking libintl.h presence... yes
checking for libintl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking for memory.h... (cached) yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... no
checking for inline... inline
checking for int64_t... yes
checking for off_t... yes
checking for size_t... yes
checking for struct stat.st_blksize... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for ptrdiff_t... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... yes
checking for gettimeofday... yes
checking for memchr... yes
checking for memmove... yes
checking for memset... yes
checking for mkfifo... yes
checking for pow... yes
checking for select... yes
checking for sqrt... yes
checking for strrchr... yes
checking for strstr... yes
checking for strtol... yes
configure: creating ./config.status
config.status: creating control
config.status: creating crac.spec
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating scripts/Makefile
config.status: creating src/libReadsInfo/Makefile
config.status: creating src/libSSA/Makefile
config.status: creating src/libgzstream/Makefile
config.status: creating doc/Makefile
config.status: creating doc/package.texi
config.status: creating man/Makefile
config.status: creating man/crac.1
config.status: creating scripts/crac-client
config.status: creating test_f/Makefile
config.status: creating test_f/bug/Makefile
config.status: creating test_f/causes/Makefile
config.status: creating test_f/cigar/Makefile
config.status: creating config/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in src/libGkArrays (<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libGkArrays)>
configure: WARNING: no configuration information is in src/libGkArrays
+ make dist
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash <https://ci.inria.fr/crac/job/crac-distrib/ws/config/missing> --run autoheader)
rm -f config/stamp-h1
touch config/config.h.in
{ test ! -d "crac-1.3.0" || { find "crac-1.3.0" -type d ! -perm -200 -exec chmod u+w {} ';' && rm -fr "crac-1.3.0"; }; }
test -d "crac-1.3.0" || mkdir "crac-1.3.0"
 (cd src && make  top_distdir=../crac-1.3.0 distdir=../crac-1.3.0/src \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[1]: Entering directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src'>
 (cd libReadsInfo && make  top_distdir=../../crac-1.3.0 distdir=../../crac-1.3.0/src/libReadsInfo \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libReadsInfo'>
make[2]: Leaving directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libReadsInfo'>
 (cd libSSA && make  top_distdir=../../crac-1.3.0 distdir=../../crac-1.3.0/src/libSSA \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libSSA'>
make[2]: Leaving directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libSSA'>
 (cd libgzstream && make  top_distdir=../../crac-1.3.0 distdir=../../crac-1.3.0/src/libgzstream \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libgzstream'>
make[2]: Leaving directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libgzstream'>
 (cd libGkArrays && make  top_distdir=../../crac-1.3.0 distdir=../../crac-1.3.0/src/libGkArrays \
     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
make[2]: Entering directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libGkArrays'>
make[2]: *** No rule to make target `distdir'.  Stop.
make[2]: Leaving directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src/libGkArrays'>
make[1]: *** [distdir] Error 1
make[1]: Leaving directory `<https://ci.inria.fr/crac/job/crac-distrib/ws/src'>
make: *** [distdir] Error 1
Build step 'Execute shell' marked build as failure
Archiving artifacts



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