[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_armhf_1 #10948
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat May 28 10:36:58 UTC 2016
See <https://jenkins.debian.net/job/reproducible_builder_armhf_1/10948/>
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[...truncated 356 lines...]
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Copying source file
I: copying [idba_1.1.2-1.dsc]
I: copying [./idba_1.1.2.orig.tar.gz]
I: copying [./idba_1.1.2-1.debian.tar.xz]
I: Extracting source
gpgv: keyblock resource `/root/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Jun 30 02:37:54 2014 GMT+12 using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./idba_1.1.2-1.dsc
dpkg-source: info: extracting idba in idba-1.1.2
dpkg-source: info: unpacking idba_1.1.2.orig.tar.gz
dpkg-source: info: unpacking idba_1.1.2-1.debian.tar.xz
I: Building the package
I: Running cd /build/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent" dpkg-buildpackage -us -uc -b --buildinfo-identifier=armhf -rfakeroot
dpkg-buildpackage: info: source package idba
dpkg-buildpackage: info: source version 1.1.2-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build idba-1.1.2
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
dh_clean
debian/rules build
dh build
dh_testdir
dh_update_autotools_config
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/idba-1.1.2'
dh_auto_configure -- LDFLAGS="-Wl,-z,relro -Wl,--as-needed" LIBS=" -latomic"
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking "LDFLAGS=-Wl,-z,relro -Wl,--as-needed" "LIBS= -latomic"
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode
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 for g++... g++
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for gcc... gcc
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 dependency style of gcc... none
checking for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
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 stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for working memcmp... yes
checking for vprintf... yes
checking for _doprnt... no
checking for sqrt... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating lib/Makefile
config.status: creating test/Makefile
config.status: creating script/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode
make[1]: Leaving directory '/build/idba-1.1.2'
dh_auto_build
make -j1
make[1]: Entering directory '/build/idba-1.1.2'
make all-recursive
make[2]: Entering directory '/build/idba-1.1.2'
Making all in lib
make[3]: Entering directory '/build/idba-1.1.2/lib'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp
../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)':
../src/misc/log.cpp:121:44: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
write(log_thread.out_fd, line, len);
^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp
../src/graph/contig_graph.cpp: In member function 'void ContigGraph::TopSort(std::deque<ContigGraphVertexAdaptor>&, std::deque<ContigGraphVertexAdaptor>&)':
../src/graph/contig_graph.cpp:1385:30: warning: variable 'end' set but not used [-Wunused-but-set-variable]
ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component);
^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp
../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)':
../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
bool flag = false;
^
../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable]
int aligned[2] = {0};
^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp
rm -f libassembly.a
ar cru libassembly.a math.o hash_aligner.o options_description.o log.o utils.o blat_record.o short_sequence.o sequence_reader.o sequence_writer.o sequence_io.o sequence.o compact_sequence.o contig_graph_branch_group.o hash_graph.o scaffold_graph.o contig_graph.o hash_graph_branch_group.o contig_info.o local_assembler.o assembly_utility.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libassembly.a
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest-all.o `test -f '../gtest_src/gtest/gtest-all.cc' || echo './'`../gtest_src/gtest/gtest-all.cc
rm -f libgtest.a
ar cru libgtest.a gtest_main.o gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
make[3]: Leaving directory '/build/idba-1.1.2/lib'
Making all in bin
make[3]: Entering directory '/build/idba-1.1.2/bin'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o shuffle_reads shuffle_reads.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o scaffold scaffold.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp
../src/tools/validate_component.cpp: In function 'int main(int, char**)':
../src/tools/validate_component.cpp:141:13: warning: unused variable 'ref_id' [-Wunused-variable]
int ref_id = dict[record.ref_name];
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o validate_component validate_component.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o fa2fq fa2fq.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp
../src/tools/validate_rna.cpp: In function 'int main(int, char**)':
../src/tools/validate_rna.cpp:396:55: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &coverage[i]);
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp
../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)':
../src/tools/validate_contigs_mummer.cpp:218:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:219:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:220:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:221:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
../src/tools/validate_contigs_mummer.cpp:222:33: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o filter_contigs filter_contigs.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp
../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const string&)':
../src/tools/parallel_rna_blat.cpp:47:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const string&)':
../src/tools/parallel_rna_blat.cpp:53:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/tools/parallel_rna_blat.cpp: In function 'void Append(const string&, const string&)':
../src/tools/parallel_rna_blat.cpp:59:24: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const string&)':
../src/tools/parallel_rna_blat.cpp:96:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp
../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive
#include "graph/contig_graph.h";
^
../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive
#include "sequence/sequence.h";
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp
../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)':
../src/release/validate_contigs_blat.cpp:388:55: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &coverage[i]);
^
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o idba_ud idba_ud.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp
/srv/reproducible-results/rbuild-debian-vLMCAPFI/tmp.MktLCGocu4: 38.0% -- replaced with /srv/reproducible-results/rbuild-debian-vLMCAPFI/tmp.MktLCGocu4.gz
FATAL: null
java.lang.NullPointerException
at hudson.plugins.build_timeout.BuildTimeoutWrapper$EnvironmentImpl.tearDown(BuildTimeoutWrapper.java:199)
at hudson.model.Build$BuildExecution.doRun(Build.java:173)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1738)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:410)
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