[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_3 #54873
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat Oct 15 01:59:14 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_3/54873/------------------------------------------
[...truncated 9512 lines...]
+make[4] : on quitte le répertoire « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/tools/cg-load »
+make[3] : on quitte le répertoire « /build/sra-sdk-2.7.0/tools/cg-load »
+make[3] : on entre dans le répertoire « /build/sra-sdk-2.7.0/tools/pileup-stats »
+make[4] : on entre dans le répertoire « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/tools/pileup-stats »
+make[4]: rien à faire pour « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/all-cmn ».
+make[4] : on quitte le répertoire « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/tools/pileup-stats »
+make[3] : on quitte le répertoire « /build/sra-sdk-2.7.0/tools/pileup-stats »
+make[2] : on quitte le répertoire « /build/sra-sdk-2.7.0/tools »
+make[2] : on entre dans le répertoire « /build/sra-sdk-2.7.0/test »
+make[3] : on entre dans le répertoire « /build/sra-sdk-2.7.0/test/fastq-loader »
+make[3]: rien à faire pour « std ».
+make[3] : on quitte le répertoire « /build/sra-sdk-2.7.0/test/fastq-loader »
+make[3] : on entre dans le répertoire « /build/sra-sdk-2.7.0/test/fastq-loader »
+make[4] : on entre dans le répertoire « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader »
g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/build/sra-sdk-2.7.0/interfaces/override -I/build/sra-sdk-2.7.0/test/fastq-loader/linux -I/build/sra-sdk-2.7.0/test/fastq-loader/unix -I/build/sra-sdk-2.7.0/test/fastq-loader -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -MD -o wb-test-fastq.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /build/sra-sdk-2.7.0/test/fastq-loader/wb-test-fastq.cpp -D__mod_name__=test/fastq-loader -D__file_name__=wb-test-fastq -D__file_ext__=cpp
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
@@ -2062,8 +2073,8 @@
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
-make[4]: Leaving directory '/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader'
-make[4]: Entering directory '/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader'
+make[4] : on quitte le répertoire « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader »
+make[4] : on entre dans le répertoire « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader »
g++ -c -DNDEBUG -m64 -DLINUX -DUNIX -D_GNU_SOURCE -D_REENTRANT -D_FILE_OFFSET_BITS=64 -DPKGNAME=linux64 -D_ARCH_BITS=__SIZEOF_POINTER__*__CHAR_BIT__ -DLIBPREFIX=lib -DSHLIBEXT=so -I/build/sra-sdk-2.7.0/interfaces/override -I/build/sra-sdk-2.7.0/test/fastq-loader/linux -I/build/sra-sdk-2.7.0/test/fastq-loader/unix -I/build/sra-sdk-2.7.0/test/fastq-loader -I/usr/include/ncbi-vdb/ -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/usr/include/ncbi-vdb/ext -I/usr/include -I. -MD -o test-fastq-loader.o -O3 -Wno-variadic-macros -fno-strict-aliasing -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=1 -Wall /build/sra-sdk-2.7.0/test/fastq-loader/test-fastq-loader.cpp -D__mod_name__=test/fastq-loader -D__file_name__=test-fastq-loader -D__file_ext__=cpp
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
@@ -2077,10 +2088,10 @@
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
-make[4]: Leaving directory '/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader'
-HOST=profitbricks-build1-amd64
+make[4] : on quitte le répertoire « /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/obj/test/fastq-loader »
+HOST=i-capture-the-hostname
OS=linux
-USER=pbuilder1
+USER=pbuilder2
Fails for user root/superuser: /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/vdb-config -s vdb/schema/paths=/usr/include/ncbi-vdb
running 1.1
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
@@ -2098,40 +2109,40 @@
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /build/sra-sdk-2.7.0/test/fastq-loader/input/2.2.fastq --quality PHRED_33 -o /build/sra-sdk-2.7.0/test/fastq-loader/actual/2.2/obj 1>/build/sra-sdk-2.7.0/test/fastq-loader/actual/2.2/load.stdout 2>/build/sra-sdk-2.7.0/test/fastq-loader/actual/2.2/load.stderr
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
-2016-10-15T01:53:19 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.2.fastq"
-2016-10-15T01:53:19 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.2.fastq:2:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
-2016-10-15T01:53:19 latf-load.2.7 err: libs/kproc/unix/systhread.c:182:KThreadCancel: data invalid while closing table - Too many bad records: records: 2, bad records: 1, bad records percentage: 0.50, allowed percentage: 0.05
-2016-10-15T01:53:19 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
-2016-10-15T01:53:19 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - accession="obj" errors="1" status="failure"
-2016-10-15T01:53:19 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - load failed
+2017-11-17T08:21:18 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.2.fastq"
+2017-11-17T08:21:18 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.2.fastq:2:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kproc/unix/systhread.c:182:KThreadCancel: data invalid while closing table - Too many bad records: records: 2, bad records: 1, bad records percentage: 0.50, allowed percentage: 0.05
+2017-11-17T08:21:18 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - accession="obj" errors="1" status="failure"
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - load failed
running 2.3
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0
command executed:
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq --quality PHRED_33 -o /build/sra-sdk-2.7.0/test/fastq-loader/actual/2.3/obj 1>/build/sra-sdk-2.7.0/test/fastq-loader/actual/2.3/load.stdout 2>/build/sra-sdk-2.7.0/test/fastq-loader/actual/2.3/load.stderr
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
-2016-10-15T01:53:19 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq"
-2016-10-15T01:53:19 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq:2:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
-2016-10-15T01:53:19 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq"
-2016-10-15T01:53:19 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq:4:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
-2016-10-15T01:53:19 latf-load.2.7 err: libs/kproc/unix/systhread.c:182:KThreadCancel: data invalid while closing table - Too many bad records: records: 4, bad records: 2, bad records percentage: 0.50, allowed percentage: 0.05
-2016-10-15T01:53:19 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
-2016-10-15T01:53:20 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - accession="obj" errors="2" status="failure"
-2016-10-15T01:53:20 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - load failed
+2017-11-17T08:21:18 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq"
+2017-11-17T08:21:18 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq:2:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
+2017-11-17T08:21:18 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq"
+2017-11-17T08:21:18 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.3.fastq:4:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kproc/unix/systhread.c:182:KThreadCancel: data invalid while closing table - Too many bad records: records: 4, bad records: 2, bad records percentage: 0.50, allowed percentage: 0.05
+2017-11-17T08:21:18 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - accession="obj" errors="2" status="failure"
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - load failed
running 2.4
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0
command executed:
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq --quality PHRED_33 -o /build/sra-sdk-2.7.0/test/fastq-loader/actual/2.4/obj 1>/build/sra-sdk-2.7.0/test/fastq-loader/actual/2.4/load.stdout 2>/build/sra-sdk-2.7.0/test/fastq-loader/actual/2.4/load.stderr
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
-2016-10-15T01:53:20 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq"
-2016-10-15T01:53:20 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq:6:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
-2016-10-15T01:53:20 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq"
-2016-10-15T01:53:20 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq:8:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
-2016-10-15T01:53:20 latf-load.2.7 err: libs/kproc/unix/systhread.c:182:KThreadCancel: data invalid while closing table - Too many bad records: records: 4, bad records: 2, bad records percentage: 0.50, allowed percentage: 0.05
-2016-10-15T01:53:20 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
-2016-10-15T01:53:20 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - accession="obj" errors="2" status="failure"
-2016-10-15T01:53:20 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - load failed
+2017-11-17T08:21:18 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq"
+2017-11-17T08:21:18 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq:6:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
+2017-11-17T08:21:18 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq"
+2017-11-17T08:21:18 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/2.4.fastq:8:1:syntax error, unexpected fqASCQUAL, expecting fqBASESEQ or fqCOLORSEQ
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kproc/unix/systhread.c:182:KThreadCancel: data invalid while closing table - Too many bad records: records: 4, bad records: 2, bad records percentage: 0.50, allowed percentage: 0.05
+2017-11-17T08:21:18 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - accession="obj" errors="2" status="failure"
+2017-11-17T08:21:18 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: data invalid while closing table - load failed
running 2.5
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 2.6
@@ -2150,25 +2161,25 @@
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /build/sra-sdk-2.7.0/test/fastq-loader/input/3.2a.fastq /build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq --quality PHRED_33 -o /build/sra-sdk-2.7.0/test/fastq-loader/actual/3.2/obj 1>/build/sra-sdk-2.7.0/test/fastq-loader/actual/3.2/load.stdout 2>/build/sra-sdk-2.7.0/test/fastq-loader/actual/3.2/load.stderr
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
-2016-10-15T01:53:21 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq"
-2016-10-15T01:53:21 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq:1:1:syntax error, unexpected '+'
-2016-10-15T01:53:21 latf-load.2.7 err: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq"
-2016-10-15T01:53:21 latf-load.2.7 err: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq:2:1:syntax error, unexpected $undefined
-2016-10-15T01:53:21 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
-2016-10-15T01:53:21 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: format unsupported while parsing file - accession="obj" errors="2" status="failure"
-2016-10-15T01:53:21 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: format unsupported while parsing file - load failed
+2017-11-17T08:21:20 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq"
+2017-11-17T08:21:20 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq:1:1:syntax error, unexpected '+'
+2017-11-17T08:21:20 latf-load.2.7 err: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq"
+2017-11-17T08:21:20 latf-load.2.7 err: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.2b.fastq:2:1:syntax error, unexpected $undefined
+2017-11-17T08:21:20 latf-load.2.7 warn: libs/kdb/wkdb.c:1195:KDBVDrop: path not found while removing directory within database module - table SEQUENCE failed to drop temporary column 'TMP_KEY_ID'
+2017-11-17T08:21:20 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: format unsupported while parsing file - accession="obj" errors="2" status="failure"
+2017-11-17T08:21:20 latf-load.2.7 err: libs/kdb/wkdb.c:1195:KDBVDrop: format unsupported while parsing file - load failed
running 3.3
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load returned 3, expected 0
command executed:
/build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/bin/latf-load /build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq /build/sra-sdk-2.7.0/test/fastq-loader/input/3.3b.fastq --quality PHRED_33 -o /build/sra-sdk-2.7.0/test/fastq-loader/actual/3.3/obj 1>/build/sra-sdk-2.7.0/test/fastq-loader/actual/3.3/load.stdout 2>/build/sra-sdk-2.7.0/test/fastq-loader/actual/3.3/load.stderr
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
-2016-10-15T01:53:21 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq"
-2016-10-15T01:53:21 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq:1:1:syntax error, unexpected '+'
-2016-10-15T01:53:21 latf-load.2.7 err: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq"
-2016-10-15T01:53:21 latf-load.2.7 err: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq:2:1:syntax error, unexpected $undefined
-2016-10-15T01:53:21 latf-load.2.7 err: libs/kproc/queue.c:356:KQueuePop: format unsupported while parsing file - accession="obj" errors="2" status="failure"
-2016-10-15T01:53:21 latf-load.2.7 err: libs/kproc/queue.c:356:KQueuePop: format unsupported while parsing file - load failed
+2017-11-17T08:21:20 latf-load.2.7 warn: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq"
+2017-11-17T08:21:20 latf-load.2.7 warn: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq:1:1:syntax error, unexpected '+'
+2017-11-17T08:21:20 latf-load.2.7 err: file="/build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq"
+2017-11-17T08:21:20 latf-load.2.7 err: /build/sra-sdk-2.7.0/test/fastq-loader/input/3.3a.fastq:2:1:syntax error, unexpected $undefined
+2017-11-17T08:21:20 latf-load.2.7 err: libs/kproc/queue.c:356:KQueuePop: format unsupported while parsing file - accession="obj" errors="2" status="failure"
+2017-11-17T08:21:20 latf-load.2.7 err: libs/kproc/queue.c:356:KQueuePop: format unsupported while parsing file - load failed
running 4.1
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
@@ -2223,17 +2234,17 @@
Running 1 test case...
*** No errors detected
-make[3]: Leaving directory '/build/sra-sdk-2.7.0/test/fastq-loader'
-make[2]: Leaving directory '/build/sra-sdk-2.7.0/test'
-make[1]: Leaving directory '/build/sra-sdk-2.7.0'
+make[3] : on quitte le répertoire « /build/sra-sdk-2.7.0/test/fastq-loader »
+make[2] : on quitte le répertoire « /build/sra-sdk-2.7.0/test »
+make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
dh_testroot
debian/rules override_dh_prep
-make[1]: Entering directory '/build/sra-sdk-2.7.0'
+make[1] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
dh_prep -X debian/tmp
-make[1]: Leaving directory '/build/sra-sdk-2.7.0'
+make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
dh_auto_install
make -j1 install DESTDIR=/build/sra-sdk-2.7.0/debian/sra-toolkit AM_UPDATE_INFO_DIR=no
-make[1]: Entering directory '/build/sra-sdk-2.7.0'
+make[1] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
Checking make status of tools...
NOTE - copycat cannot be built: It requires our internal library 'libkff' which requires 'libmagic' and its development headers.
NOTE - fastq-load cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
@@ -2246,7 +2257,7 @@
NOTE - ccextract cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - pacbio-load cannot be built: It requires our internal library 'libkdf5' which requires 'libhdf5' and its development headers.
NOTE - remote-fuser cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
-make[2]: Entering directory '/build/sra-sdk-2.7.0'
+make[2] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
Installing executables to /build/sra-sdk-2.7.0/debian/tmp/usr/bin/...
Installing abi-dump...done
Installing abi-load...not found
@@ -2286,26 +2297,26 @@
Installing vdb-unlock...done
Installing vdb-validate...done
Installing magic file...done
-Installing configuration files to /etc/ncbi/...mkdir: cannot create directory '/etc/ncbi': Permission denied
+Installing configuration files to /etc/ncbi/...mkdir: impossible de créer le répertoire « /etc/ncbi »: Permission non accordée
done
Updating /etc/profile.d/sra-tools.[c]sh
-/bin/sh: 1: cannot create /etc/profile.d/sra-tools.sh: Permission denied
-/bin/sh: 1: cannot create /etc/profile.d/sra-tools.csh: Permission denied
-make[2]: Leaving directory '/build/sra-sdk-2.7.0'
-make[1]: Leaving directory '/build/sra-sdk-2.7.0'
+/bin/sh: ligne 4: /etc/profile.d/sra-tools.sh: Permission non accordée
+/bin/sh: ligne 4: /etc/profile.d/sra-tools.csh: Permission non accordée
+make[2] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
+make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
debian/rules override_dh_install
-make[1]: Entering directory '/build/sra-sdk-2.7.0'
+make[1] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
# upstream installs versioned *.a libs - we only want a single version
for bin in debian/tmp/usr/bin/*[a-z] ; do \
mv debian/tmp/usr/bin/`readlink $bin` $bin ; \
mv debian/tmp/usr/bin/`readlink $bin` $bin ; \
done
-mv: cannot overwrite non-directory 'debian/tmp/usr/bin/magic' with directory 'debian/tmp/usr/bin/'
-mv: cannot overwrite non-directory 'debian/tmp/usr/bin/magic' with directory 'debian/tmp/usr/bin/'
+mv: impossible d'écraser le non répertoire 'debian/tmp/usr/bin/magic' par le répertoire 'debian/tmp/usr/bin/'
+mv: impossible d'écraser le non répertoire 'debian/tmp/usr/bin/magic' par le répertoire 'debian/tmp/usr/bin/'
dh_install
# remove susipcious file which is not executable and conflicts with package magic
rm -f debian/*/usr/bin/magic
-make[1]: Leaving directory '/build/sra-sdk-2.7.0'
+make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
dh_installdocs
dh_installchangelogs
dh_perl
@@ -2316,9 +2327,9 @@
dh_strip
dh_makeshlibs
dh_shlibdeps
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/vdb-unlock debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/latf-load were not linked against libdl.so.2 (they use none of the library's symbols)
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/vdb-unlock debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/latf-load were not linked against libsz.so.2 (they use none of the library's symbols)
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/vdb-unlock debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/latf-load were not linked against libbz2.so.1.0 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/latf-load debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-unlock were not linked against libdl.so.2 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/latf-load debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-unlock were not linked against libsz.so.2 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/latf-load debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-unlock were not linked against libbz2.so.1.0 (they use none of the library's symbols)
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
@@ -2334,12 +2345,14 @@
dpkg-source --after-build sra-sdk-2.7.0
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/54605/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/54605/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/38328 and its subdirectories
-I: Current time: Fri Oct 14 13:54:07 GMT+12 2016
-I: pbuilder-time-stamp: 1476496447
+I: removing directory /srv/workspace/pbuilder/54605 and its subdirectories
+I: Current time: vendredi 17 novembre 2017, 22:22:11 (UTC+1400)
+I: pbuilder-time-stamp: 1510906931
/srv/reproducible-results/rbuild-debian-Zzbz8RhZ/tmp.nQI5ymfqa0: 93.3% -- replaced with /srv/reproducible-results/rbuild-debian-Zzbz8RhZ/tmp.nQI5ymfqa0.gz
INFO: Starting at 2016-10-15 01:59:13.637297
INFO: Finished at 2016-10-15 01:59:13.747289, took: 0:00:00.110005
Sat 15 Oct 01:59:13 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-n5xgIVGr, which will now be removed.
Build step 'Execute shell' marked build as failure
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