[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_beta #57110
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Thu Jul 23 08:58:09 UTC 2015
See <https://jenkins.debian.net/job/reproducible_builder_beta/57110/>
------------------------------------------
[...truncated 1998 lines...]
42ac19812779e6797fc7a634505ada617d182965 1863936 r-bioc-variantannotation_1.14.6-1_amd64.deb
Checksums-Sha256:
24e1379d132aae7d6ac11de025a8fff2c3600988b275cbc113ea8fc812847f49 8591 r-bioc-variantannotation_1.14.6-1_amd64.buildinfo
1c5c7350a8f4e1351c1abb32be73c1674aa11335065caee30746003c4a2df196 1863936 r-bioc-variantannotation_1.14.6-1_amd64.deb
Files:
5d2a9c10b7d4bdd08d2da1216e87052b 8591 gnu-r optional r-bioc-variantannotation_1.14.6-1_amd64.buildinfo
c777c9d0b54f92012c010c9ec17b8992 1863936 gnu-r optional r-bioc-variantannotation_1.14.6-1_amd64.deb
I: pbuilder-time-stamp: 1437641881
removed ‘/var/lib/jenkins/userContent/reproducible/rbuild/testing/amd64/r-bioc-variantannotation_1.14.4-1.rbuild.log.gz’
removed ‘/var/lib/jenkins/userContent/reproducible/logs/testing/amd64/r-bioc-variantannotation_1.14.4-1.build1.log.gz’
removed ‘/var/lib/jenkins/userContent/reproducible/logs/testing/amd64/r-bioc-variantannotation_1.14.4-1.build2.log.gz’
removed ‘/var/lib/jenkins/userContent/reproducible/buildinfo/testing/amd64/r-bioc-variantannotation_1.14.4-1_amd64.buildinfo’
removed ‘/var/lib/jenkins/userContent/reproducible/logdiffs/testing/amd64/r-bioc-variantannotation_1.14.4-1.diff.gz’
Diff of the two buildlogs:
--
--- b1/build.log 2015-07-23 08:53:28.010940002 +0000
+++ b2/build.log 2015-07-23 08:58:05.236018943 +0000
@@ -1,7 +1,7 @@
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
-I: Current time: Wed Jul 22 20:49:02 GMT+12 2015
-I: pbuilder-time-stamp: 1437641342
+I: Current time: jeudi 23 juillet 2015, 22:53:28 (UTC+1400)
+I: pbuilder-time-stamp: 1437641608
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/testing-reproducible-base.tgz]
I: creating local configuration
@@ -13,6 +13,9 @@
I: Mounting /sys
I: policy-rc.d already exists
I: Installing the build-deps
+I: user script /var/cache/pbuilder/build//22111/tmp/hooks/D01_modify_environment starting
+I: Changing hostname to test build reproducibility
+I: user script /var/cache/pbuilder/build//22111/tmp/hooks/D01_modify_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -82,8 +85,8 @@
0 packages upgraded, 130 newly installed, 0 to remove and 0 not upgraded.
Need to get 95.4 MB of archives. After unpacking 202 MB will be used.
Writing extended state information...
-Get: 1 http://reproducible.alioth.debian.org/debian/ ./ cdbs 0.4.130.0~reproducible2 [77.1 kB]
-Get: 2 http://ftp.de.debian.org/debian/ testing/main libkeyutils1 amd64 1.5.9-5+b1 [12.0 kB]
+Get: 1 http://ftp.de.debian.org/debian/ testing/main libkeyutils1 amd64 1.5.9-5+b1 [12.0 kB]
+Get: 2 http://reproducible.alioth.debian.org/debian/ ./ cdbs 0.4.130.0~reproducible2 [77.1 kB]
Get: 3 http://ftp.de.debian.org/debian/ testing/main libnettle6 amd64 3.1.1-3 [188 kB]
Get: 4 http://ftp.de.debian.org/debian/ testing/main libhogweed4 amd64 3.1.1-3 [136 kB]
Get: 5 http://ftp.de.debian.org/debian/ testing/main libp11-kit0 amd64 0.23.1-3 [112 kB]
@@ -96,7 +99,7 @@
Get: 12 http://ftp.de.debian.org/debian/ testing/main libpng12-0 amd64 1.2.50-2+b2 [172 kB]
Get: 13 http://ftp.de.debian.org/debian/ testing/main libfreetype6 amd64 2.5.2-4 [466 kB]
Get: 14 http://ftp.de.debian.org/debian/ testing/main ucf all 3.0030 [69.7 kB]
-Get: 15 http://ftp.de.debian.org/debian/ testing/main fonts-dejavu-core all 2.35-1 [1064 kB]
+Get: 15 http://ftp.de.debian.org/debian/ testing/main fonts-dejavu-core all 2.35-1 [1'064 kB]
Get: 16 http://ftp.de.debian.org/debian/ testing/main fontconfig-config all 2.11.0-6.3 [273 kB]
Get: 17 http://ftp.de.debian.org/debian/ testing/main libfontconfig1 amd64 2.11.0-6.3 [329 kB]
Get: 18 http://ftp.de.debian.org/debian/ testing/main fontconfig amd64 2.11.0-6.3 [402 kB]
@@ -130,7 +133,7 @@
Get: 46 http://ftp.de.debian.org/debian/ testing/main libxss1 amd64 1:1.2.2-1 [17.5 kB]
Get: 47 http://ftp.de.debian.org/debian/ testing/main libxt6 amd64 1:1.1.4-1+b1 [186 kB]
Get: 48 http://ftp.de.debian.org/debian/ testing/main libjbig0 amd64 2.1-3.1 [30.7 kB]
-Get: 49 http://ftp.de.debian.org/debian/ testing/main libssl1.0.0 amd64 1.0.2d-1 [1274 kB]
+Get: 49 http://ftp.de.debian.org/debian/ testing/main libssl1.0.0 amd64 1.0.2d-1 [1'274 kB]
Get: 50 http://ftp.de.debian.org/debian/ testing/main libkrb5support0 amd64 1.12.1+dfsg-20 [58.6 kB]
Get: 51 http://ftp.de.debian.org/debian/ testing/main libk5crypto3 amd64 1.12.1+dfsg-20 [115 kB]
Get: 52 http://ftp.de.debian.org/debian/ testing/main libkrb5-3 amd64 1.12.1+dfsg-20 [303 kB]
@@ -139,9 +142,9 @@
Get: 55 http://ftp.de.debian.org/debian/ testing/main openssl amd64 1.0.2d-1 [695 kB]
Get: 56 http://ftp.de.debian.org/debian/ testing/main ca-certificates all 20150426 [208 kB]
Get: 57 http://ftp.de.debian.org/debian/ testing/main libgfortran-4.9-dev amd64 4.9.3-2 [281 kB]
-Get: 58 http://ftp.de.debian.org/debian/ testing/main gfortran-4.9 amd64 4.9.3-2 [5310 kB]
-Get: 59 http://ftp.de.debian.org/debian/ testing/main gfortran amd64 4:4.9.2-4 [1288 B]
-Get: 60 http://ftp.de.debian.org/debian/ testing/main libblas-common amd64 1.2.20110419-10 [8496 B]
+Get: 58 http://ftp.de.debian.org/debian/ testing/main gfortran-4.9 amd64 4.9.3-2 [5'310 kB]
+Get: 59 http://ftp.de.debian.org/debian/ testing/main gfortran amd64 4:4.9.2-4 [1'288 B]
+Get: 60 http://ftp.de.debian.org/debian/ testing/main libblas-common amd64 1.2.20110419-10 [8'496 B]
Get: 61 http://ftp.de.debian.org/debian/ testing/main libblas3 amd64 1.2.20110419-10 [167 kB]
Get: 62 http://ftp.de.debian.org/debian/ testing/main libblas-dev amd64 1.2.20110419-10 [163 kB]
Get: 63 http://ftp.de.debian.org/debian/ testing/main libbz2-dev amd64 1.0.6-8 [29.0 kB]
@@ -150,8 +153,8 @@
Get: 66 http://ftp.de.debian.org/debian/ testing/main libjpeg62-turbo amd64 1:1.4.0-7 [124 kB]
Get: 67 http://ftp.de.debian.org/debian/ testing/main libjpeg62-turbo-dev amd64 1:1.4.0-7 [473 kB]
Get: 68 http://ftp.de.debian.org/debian/ testing/main libjpeg-dev all 1:1.4.0-7 [50.8 kB]
-Get: 69 http://ftp.de.debian.org/debian/ testing/main liblapack3 amd64 3.5.0-4 [1852 kB]
-Get: 70 http://ftp.de.debian.org/debian/ testing/main liblapack-dev amd64 3.5.0-4 [1884 kB]
+Get: 69 http://ftp.de.debian.org/debian/ testing/main liblapack3 amd64 3.5.0-4 [1'852 kB]
+Get: 70 http://ftp.de.debian.org/debian/ testing/main liblapack-dev amd64 3.5.0-4 [1'884 kB]
Get: 71 http://ftp.de.debian.org/debian/ testing/main liblzma-dev amd64 5.1.1alpha+20120614-2.1 [255 kB]
Get: 72 http://ftp.de.debian.org/debian/ testing/main libtinfo-dev amd64 5.9+20150516-2 [76.8 kB]
Get: 73 http://ftp.de.debian.org/debian/ testing/main libncurses5-dev amd64 5.9+20150516-2 [176 kB]
@@ -162,7 +165,7 @@
Get: 78 http://ftp.de.debian.org/debian/ testing/main zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB]
Get: 79 http://ftp.de.debian.org/debian/ testing/main libpng12-dev amd64 1.2.50-2+b2 [248 kB]
Get: 80 http://ftp.de.debian.org/debian/ testing/main libreadline6-dev amd64 6.3-8+b3 [124 kB]
-Get: 81 http://ftp.de.debian.org/debian/ testing/main libreadline-dev amd64 6.3-8+b3 [1002 B]
+Get: 81 http://ftp.de.debian.org/debian/ testing/main libreadline-dev amd64 6.3-8+b3 [1'002 B]
Get: 82 http://ftp.de.debian.org/debian/ testing/main libtcl8.6 amd64 8.6.4+dfsg-2 [983 kB]
Get: 83 http://ftp.de.debian.org/debian/ testing/main libtiff5 amd64 4.0.3-13 [212 kB]
Get: 84 http://ftp.de.debian.org/debian/ testing/main libtk8.6 amd64 8.6.4+dfsg-2 [758 kB]
@@ -171,21 +174,21 @@
Get: 87 http://ftp.de.debian.org/debian/ testing/main xdg-utils all 1.1.0~rc1+git20111210-7.4 [65.0 kB]
Get: 88 http://ftp.de.debian.org/debian/ testing/main r-base-core amd64 3.2.1-4 [20.4 MB]
Get: 89 http://ftp.de.debian.org/debian/ testing/main littler amd64 0.2.3-2 [39.2 kB]
-Get: 90 http://ftp.de.debian.org/debian/ testing/main r-base-dev all 3.2.1-4 [4288 B]
+Get: 90 http://ftp.de.debian.org/debian/ testing/main r-base-dev all 3.2.1-4 [4'288 B]
Get: 91 http://ftp.de.debian.org/debian/ testing/main r-cran-dbi amd64 0.3.1-1 [157 kB]
Get: 92 http://ftp.de.debian.org/debian/ testing/main r-cran-rsqlite amd64 1.0.0-1 [302 kB]
Get: 93 http://ftp.de.debian.org/debian/ testing/main r-bioc-biocgenerics all 0.14.0-1 [440 kB]
-Get: 94 http://ftp.de.debian.org/debian/ testing/main r-bioc-biobase amd64 2.28.0-1 [1993 kB]
+Get: 94 http://ftp.de.debian.org/debian/ testing/main r-bioc-biobase amd64 2.28.0-1 [1'993 kB]
Get: 95 http://ftp.de.debian.org/debian/ testing/main r-bioc-s4vectors amd64 0.6.2-1 [752 kB]
-Get: 96 http://ftp.de.debian.org/debian/ testing/main r-bioc-iranges amd64 2.2.5-1 [1522 kB]
+Get: 96 http://ftp.de.debian.org/debian/ testing/main r-bioc-iranges amd64 2.2.5-1 [1'522 kB]
Get: 97 http://ftp.de.debian.org/debian/ testing/main r-bioc-genomeinfodb all 1.4.1-1 [431 kB]
-Get: 98 http://ftp.de.debian.org/debian/ testing/main r-bioc-annotationdbi all 1.30.1-1 [4177 kB]
+Get: 98 http://ftp.de.debian.org/debian/ testing/main r-bioc-annotationdbi all 1.30.1-1 [4'177 kB]
Get: 99 http://ftp.de.debian.org/debian/ testing/main r-cran-checkmate amd64 1.6.0-1 [270 kB]
Get: 100 http://ftp.de.debian.org/debian/ testing/main r-cran-bbmisc amd64 1.9-1 [280 kB]
Get: 101 http://ftp.de.debian.org/debian/ testing/main r-cran-brew amd64 1.0-6-1 [61.4 kB]
Get: 102 http://ftp.de.debian.org/debian/ testing/main r-cran-digest amd64 0.6.8-1 [92.5 kB]
Get: 103 http://ftp.de.debian.org/debian/ testing/main r-cran-pkgkitten all 0.1.3-1 [18.3 kB]
-Get: 104 http://ftp.de.debian.org/debian/ testing/main r-cran-rcpp amd64 0.11.6-1 [2122 kB]
+Get: 104 http://ftp.de.debian.org/debian/ testing/main r-cran-rcpp amd64 0.11.6-1 [2'122 kB]
Get: 105 http://ftp.de.debian.org/debian/ testing/main r-cran-plyr amd64 1.8.3-1 [730 kB]
Get: 106 http://ftp.de.debian.org/debian/ testing/main r-cran-stringr all 0.6.2-2 [71.8 kB]
Get: 107 http://ftp.de.debian.org/debian/ testing/main r-cran-base64enc amd64 0.1-2-1 [19.9 kB]
@@ -200,19 +203,19 @@
Get: 116 http://ftp.de.debian.org/debian/ testing/main r-cran-futile.logger all 1.4.1-1 [84.4 kB]
Get: 117 http://ftp.de.debian.org/debian/ testing/main r-cran-snow all 1:0.3.13-1 [66.7 kB]
Get: 118 http://ftp.de.debian.org/debian/ testing/main r-bioc-biocparallel all 1.2.6-1 [600 kB]
-Get: 119 http://ftp.de.debian.org/debian/ testing/main r-cran-xml amd64 3.98-1.3-1 [1650 kB]
+Get: 119 http://ftp.de.debian.org/debian/ testing/main r-cran-xml amd64 3.98-1.3-1 [1'650 kB]
Get: 120 http://ftp.de.debian.org/debian/ testing/main r-cran-bitops amd64 1.0-6-1 [22.3 kB]
Get: 121 http://ftp.de.debian.org/debian/ testing/main r-cran-rcurl amd64 1.95-4.3-2 [526 kB]
Get: 122 http://ftp.de.debian.org/debian/ testing/main r-bioc-biomart all 2.24.0-1 [384 kB]
Get: 123 http://ftp.de.debian.org/debian/ testing/main r-bioc-xvector amd64 0.8.0-1 [324 kB]
Get: 124 http://ftp.de.debian.org/debian/ testing/main r-bioc-biostrings amd64 2.36.1-1 [13.5 MB]
-Get: 125 http://ftp.de.debian.org/debian/ testing/main r-bioc-genomicranges amd64 1.20.5-1 [1429 kB]
-Get: 126 http://ftp.de.debian.org/debian/ testing/main r-bioc-rsamtools amd64 1.20.4-1 [3214 kB]
-Get: 127 http://ftp.de.debian.org/debian/ testing/main r-bioc-genomicalignments amd64 1.4.1-1 [1278 kB]
-Get: 128 http://ftp.de.debian.org/debian/ testing/main r-bioc-rtracklayer amd64 1.28.6-1 [1772 kB]
-Get: 129 http://ftp.de.debian.org/debian/ testing/main r-bioc-bsgenome all 1.36.2-1 [6460 kB]
+Get: 125 http://ftp.de.debian.org/debian/ testing/main r-bioc-genomicranges amd64 1.20.5-1 [1'429 kB]
+Get: 126 http://ftp.de.debian.org/debian/ testing/main r-bioc-rsamtools amd64 1.20.4-1 [3'214 kB]
+Get: 127 http://ftp.de.debian.org/debian/ testing/main r-bioc-genomicalignments amd64 1.4.1-1 [1'278 kB]
+Get: 128 http://ftp.de.debian.org/debian/ testing/main r-bioc-rtracklayer amd64 1.28.6-1 [1'772 kB]
+Get: 129 http://ftp.de.debian.org/debian/ testing/main r-bioc-bsgenome all 1.36.2-1 [6'460 kB]
Get: 130 http://ftp.de.debian.org/debian/ testing/main r-bioc-genomicfeatures all 1.20.1-1 [993 kB]
-Fetched 95.4 MB in 7s (13.5 MB/s)
+Fetched 95.4 MB in 6s (14.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libkeyutils1:amd64.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 20214 files and directories currently installed.)
@@ -777,7 +780,7 @@
I: copying [./r-bioc-variantannotation_1.14.6-1.debian.tar.xz]
I: Extracting source
gpgv: keyblock resource `/tmp/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Fri Jul 17 09:26:33 2015 GMT+12 using RSA key ID D1C646D1
+gpgv: Signature made sam 18 jui 2015 11:26:33 GMT-14 using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-bioc-variantannotation_1.14.6-1.dsc
dpkg-source: info: extracting r-bioc-variantannotation in r-bioc-variantannotation-1.14.6
@@ -786,7 +789,8 @@
dpkg-source: info: applying use_debian_packaged_zlib.patch
dpkg-source: info: applying drop_tests_requiring_large_data_sets.patch
I: Building the package
-I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" dpkg-buildpackage -us -uc -b -rfakeroot
+W: no hooks of type A found -- ignoring
+I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" dpkg-buildpackage -us -uc -b -rfakeroot
dpkg-buildpackage: source package r-bioc-variantannotation
dpkg-buildpackage: source version 1.14.6-1
dpkg-buildpackage: source distribution unstable
@@ -824,7 +828,7 @@
"--built-timestamp=\"Fri, 17 Jul 2015 23:24:42 +0200\"" \
; \
fi
-* installing *source* package 'VariantAnnotation' ...
+* installing *source* package ‘VariantAnnotation’ ...
** libs
make[1]: Entering directory '/tmp/buildd/r-bioc-variantannotation-1.14.6/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o
@@ -846,14 +850,14 @@
** R
** inst
** preparing package for lazy loading
-Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
-Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
+Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
+Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
-Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
+Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (VariantAnnotation)
rm -vf /tmp/buildd/r-bioc-variantannotation-1.14.6/debian/r-bioc-variantannotation/usr/lib/R/site-library/R.css \
/tmp/buildd/r-bioc-variantannotation-1.14.6/debian/r-bioc-variantannotation/usr/lib/R/site-library/VariantAnnotation/COPYING \
@@ -908,12 +912,13 @@
dpkg-genchanges: binary-only upload (no source code included)
dpkg-source --after-build r-bioc-variantannotation-1.14.6
dpkg-buildpackage: binary-only upload (no source included)
+W: no hooks of type B found -- ignoring
I: unmounting /sys filesystem
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: cleaning the build env
-I: removing directory /var/cache/pbuilder/build//23306 and its subdirectories
-I: Current time: Wed Jul 22 20:53:28 GMT+12 2015
-I: pbuilder-time-stamp: 1437641608
+I: removing directory /var/cache/pbuilder/build//22111 and its subdirectories
+I: Current time: jeudi 23 juillet 2015, 22:58:01 (UTC+1400)
+I: pbuilder-time-stamp: 1437641881
Compressing the logs...
/var/lib/jenkins/userContent/reproducible/logdiffs/testing/amd64/r-bioc-variantannotation_1.14.6-1.diff: 74.8% -- replaced with /var/lib/jenkins/userContent/reproducible/logdiffs/testing/amd64/r-bioc-variantannotation_1.14.6-1.diff.gz
b2/build.log: 82.8%
b1/build.log: 83.0%
/var/lib/jenkins/userContent/reproducible/rbuild/testing/amd64/r-bioc-variantannotation_1.14.6-1.rbuild.log: 81.0% -- replaced with /var/lib/jenkins/userContent/reproducible/rbuild/testing/amd64/r-bioc-variantannotation_1.14.6-1.rbuild.log.gz
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/buildinfo/testing/amd64/r-bioc-variantannotation_1.14.4-1_amd64.buildinfo
CRITICAL: https://reproducible.debian.net/testing/amd64/r-bioc-variantannotation didn't produce a buildlog, even though it has been built.
Thu 23 Jul 08:58:08 UTC 2015 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-raUipHUQ, which will now be removed.
Build step 'Execute shell' marked build as failure
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