[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_12 #53580
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat Oct 15 04:17:20 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_12/53580/------------------------------------------
[...truncated 6792 lines...]
if(_isa != NULL) delete[] _isa; _isa = NULL;
^~~~
-ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h:832:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~
-ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~~~~
-ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h:833:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~
-ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~~~~~~~
g++ -O0 -g3 \
- -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=.=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=.=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build-1st/bowtie-1.1.2=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build-1st/bowtie-1.1.2=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now \
+ -DCOMPILER_OPTIONS="\"-O0 -g3 -Wl,--hash-style=both -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=.=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=.=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now\"" -Wl,--hash-style=both -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build-2nd/bowtie-1.1.2=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build-2nd/bowtie-1.1.2=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -Wl,-z,relro -Wl,-z,now \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian-reproducible\"" -DBUILD_TIME="\"`dpkg-parsechangelog --show-field Date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1 | sed 's/ *(.*//'`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall \
-I /usr/include/seqan -I . \
-o bowtie-inspect-l-debug bowtie_inspect.cpp \
@@ -1280,80 +1291,80 @@
In file included from blockwise_sa.h:13:0,
from ebwt.h:27,
from bowtie_inspect.cpp:10:
-diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
-diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
+diff_sample.h:157:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
-diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
-diff_sample.h:158:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+diff_sample.h:158:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
-diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+diff_sample.h:158:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
In file included from ebwt.h:27:0,
from bowtie_inspect.cpp:10:
-blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()':
-blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+blockwise_sa.h: In destructor ‘KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()’:
+blockwise_sa.h:206:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
^~
-blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
^~~
-blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
-blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
+blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::buildSamples()’:
+blockwise_sa.h:380:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<TStr>::Type TAlphabet;
^~~~~~~~~
In file included from ebwt.h:27:0,
from bowtie_inspect.cpp:10:
-blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
-blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
+blockwise_sa.h: In member function ‘virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()’:
+blockwise_sa.h:755:37: warning: typedef ‘TAlphabet’ locally defined but not used [-Wunused-local-typedefs]
typedef typename Value<TStr>::Type TAlphabet;
^~~~~~~~~
In file included from bowtie_inspect.cpp:10:0:
-ebwt.h: In destructor 'Ebwt<TStr>::~Ebwt()':
-ebwt.h:823:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h: In destructor ‘Ebwt<TStr>::~Ebwt()’:
+ebwt.h:823:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_fchr != NULL) delete[] _fchr; _fchr = NULL;
^~
-ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:823:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_fchr != NULL) delete[] _fchr; _fchr = NULL;
^~~~~
-ebwt.h:824:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h:824:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_ftab != NULL) delete[] _ftab; _ftab = NULL;
^~
-ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:824:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_ftab != NULL) delete[] _ftab; _ftab = NULL;
^~~~~
-ebwt.h:825:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h:825:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_eftab != NULL) delete[] _eftab; _eftab = NULL;
^~
-ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_eftab != NULL) delete[] _eftab; _eftab = NULL;
^~~~~~
-ebwt.h:831:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h:831:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_isa != NULL) delete[] _isa; _isa = NULL;
^~
-ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:831:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_isa != NULL) delete[] _isa; _isa = NULL;
^~~~
-ebwt.h:832:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h:832:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~
-ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:832:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~~~~
-ebwt.h:833:4: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
+ebwt.h:833:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~
-ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the 'if'
+ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~~~~~~~
-make[2]: Leaving directory '/build-1st/bowtie-1.1.2'
-make[1]: Leaving directory '/build-1st/bowtie-1.1.2'
+make[2] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
+make[1] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
debian/rules override_dh_auto_test
-make[1]: Entering directory '/build-1st/bowtie-1.1.2'
+make[1] : on entre dans le répertoire « /build-2nd/bowtie-1.1.2 »
ln -s debian/tests
sh debian/tests/run-unit-test test_at_build_time
# reads processed: 1
@@ -1398,76 +1409,78 @@
Reported 1 alignments to 1 output stream(s)
example9 OK
rm -f tests examples[0-9].out
-make[1]: Leaving directory '/build-1st/bowtie-1.1.2'
+make[1] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
dh_installdirs
debian/rules override_dh_auto_install-arch
-make[1]: Entering directory '/build-1st/bowtie-1.1.2'
+make[1] : on entre dans le répertoire « /build-2nd/bowtie-1.1.2 »
# remove strange byte-compyled Python code bowtie-buildc (no idea how and why it was created)
find . -name bowtie-buildc -delete
-make[1]: Leaving directory '/build-1st/bowtie-1.1.2'
+make[1] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
dh_auto_install -Nbowtie
- make -j1 install DESTDIR=/build-1st/bowtie-1.1.2/debian/tmp AM_UPDATE_INFO_DIR=no
-make[1]: Entering directory '/build-1st/bowtie-1.1.2'
-mkdir -p /build-1st/bowtie-1.1.2/debian/tmp/usr/local/bin
+ make -j1 install DESTDIR=/build-2nd/bowtie-1.1.2/debian/tmp AM_UPDATE_INFO_DIR=no
+make[1] : on entre dans le répertoire « /build-2nd/bowtie-1.1.2 »
+mkdir -p /build-2nd/bowtie-1.1.2/debian/tmp/usr/local/bin
for file in bowtie-build-s bowtie-build-l bowtie-align-s bowtie-align-l bowtie-inspect-s bowtie-inspect-l bowtie-inspect bowtie-build bowtie ; do \
- cp -f $file /build-1st/bowtie-1.1.2/debian/tmp/usr/local/bin ; \
+ cp -f $file /build-2nd/bowtie-1.1.2/debian/tmp/usr/local/bin ; \
done
-make[1]: Leaving directory '/build-1st/bowtie-1.1.2'
+make[1] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
dh_install
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman-arch
-make[1]: Entering directory '/build-1st/bowtie-1.1.2'
+make[1] : on entre dans le répertoire « /build-2nd/bowtie-1.1.2 »
help2man --name="ultrafast memory-efficient short read aligner" --no-info \
- /build-1st/bowtie-1.1.2/bowtie > /build-1st/bowtie-1.1.2/debian/bowtie/usr/share/man/man1/bowtie.1
+ /build-2nd/bowtie-1.1.2/bowtie > /build-2nd/bowtie-1.1.2/debian/bowtie/usr/share/man/man1/bowtie.1
help2man --name="building a colorspace index for bowtie" --no-info \
- /build-1st/bowtie-1.1.2/bowtie-build > /build-1st/bowtie-1.1.2/debian/bowtie/usr/share/man/man1/bowtie-build.1
+ /build-2nd/bowtie-1.1.2/bowtie-build > /build-2nd/bowtie-1.1.2/debian/bowtie/usr/share/man/man1/bowtie-build.1
help2man --name="extracts information from a bowtie index" --no-info \
- /build-1st/bowtie-1.1.2/bowtie-inspect > /build-1st/bowtie-1.1.2/debian/bowtie/usr/share/man/man1/bowtie-inspect.1
-make[1]: Leaving directory '/build-1st/bowtie-1.1.2'
+ /build-2nd/bowtie-1.1.2/bowtie-inspect > /build-2nd/bowtie-1.1.2/debian/bowtie/usr/share/man/man1/bowtie-inspect.1
+make[1] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
dh_perl
dh_link
dh_strip_nondeterminism
debian/rules override_dh_compress
-make[1]: Entering directory '/build-1st/bowtie-1.1.2'
+make[1] : on entre dans le répertoire « /build-2nd/bowtie-1.1.2 »
dh_compress -X.ebwt
-make[1]: Leaving directory '/build-1st/bowtie-1.1.2'
+make[1] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
debian/rules override_dh_fixperms-indep
-make[1]: Entering directory '/build-1st/bowtie-1.1.2'
+make[1] : on entre dans le répertoire « /build-2nd/bowtie-1.1.2 »
dh_fixperms
chmod 644 debian/bowtie-examples/usr/share/doc/bowtie/examples/indexes/*
-make[1]: Leaving directory '/build-1st/bowtie-1.1.2'
+make[1] : on quitte le répertoire « /build-2nd/bowtie-1.1.2 »
dh_fixperms -Nbowtie-examples
dh_strip
dh_makeshlibs
dh_shlibdeps
dh_installdeb
dh_gencontrol
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: avertissement: Fichier::FcntlLock non disponible; utilisation de « flock » qui n'est pas sécurisé pour NFS
+dpkg-gencontrol: avertissement: Fichier::FcntlLock non disponible; utilisation de « flock » qui n'est pas sécurisé pour NFS
+dpkg-gencontrol: avertissement: Fichier::FcntlLock non disponible; utilisation de « flock » qui n'est pas sécurisé pour NFS
dh_md5sums
dh_builddeb
dpkg-deb: building package 'bowtie-examples' in '../bowtie-examples_1.1.2-6_all.deb'.
dpkg-deb: building package 'bowtie-dbgsym' in '../bowtie-dbgsym_1.1.2-6_amd64.deb'.
dpkg-deb: building package 'bowtie' in '../bowtie_1.1.2-6_amd64.deb'.
dpkg-genbuildinfo --build=any,all --buildinfo-id=amd64
-dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-genbuildinfo: avertissement: Fichier::FcntlLock non disponible; utilisation de « flock » qui n'est pas sécurisé pour NFS
dpkg-genchanges --build=any,all >../bowtie_1.1.2-6_amd64.changes
-dpkg-genchanges: info: binary-only upload (no source code included)
+dpkg-genchanges: info: envoi des binaires seulement (le code source n'est pas inclus)
dpkg-source --after-build bowtie-1.1.2
-dpkg-buildpackage: info: binary-only upload (no source included)
+dpkg-buildpackage: info: envoi d'un binaire seulement (aucune inclusion de code source)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/55924/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/55924/tmp/hooks/B01_cleanup finished
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/23631 and its subdirectories
-I: Current time: Thu Nov 16 22:22:29 GMT+12 2017
-I: pbuilder-time-stamp: 1510914149
+I: removing directory /srv/workspace/pbuilder/55924 and its subdirectories
+I: Current time: samedi 15 octobre 2016, 18:17:17 (UTC+1400)
+I: pbuilder-time-stamp: 1476505037
/srv/reproducible-results/rbuild-debian-tBaMdkhB/tmp.FcJ4hXoJoe: 89.8% -- replaced with /srv/reproducible-results/rbuild-debian-tBaMdkhB/tmp.FcJ4hXoJoe.gz
INFO: Starting at 2016-10-15 04:17:20.195733
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/testing/i386/bowtie_1.1.2-5_i386.buildinfo
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/testing/armhf/bowtie_1.1.2-5_armhf.buildinfo
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/bowtie_1.1.2-5_amd64.buildinfo
CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/bowtie didn't produce a buildlog, even though it has been built.
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/i386/bowtie_1.1.2-5_i386.buildinfo
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/armhf/bowtie_1.1.2-5_armhf.buildinfo
INFO: Finished at 2016-10-15 04:17:20.300681, took: 0:00:00.104960
Sat 15 Oct 04:17:20 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-kpKIJzuY, which will now be removed.
Build step 'Execute shell' marked build as failure
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