Source: snp-sites
Version: 2.0.1-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds@lists.alioth.debian.org
Dear Maintainer,
snp-sites fails to build from source in unstable/amd64:
[..]
/bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -g -O2
-fstack-protector-strong -Wformat -Werror=format-security
-Wl,-z,relro -o run-all-tests run_all_tests-check-snp-sites.o
run_all_tests-check-vcf.o run_all_tests-helper-methods.o
run_all_tests-run-all-tests.o -lm -lcheck libsnp-sites.la -lz
-lpthread -lrt
libtool: link: gcc -I../tests -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z -Wl,relro -o .libs/run-all-tests
run_all_tests-check-snp-sites.o run_all_tests-check-vcf.o
run_all_tests-helper-methods.o run_all_tests-run-all-tests.o -lm
-lcheck ./.libs/libsnp-sites.so -lz -lpthread -lrt
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x584): undefined reference to `subunit_test_start'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x63f): undefined reference to `subunit_test_fail'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x654): undefined reference to `subunit_test_pass'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x66f): undefined reference to `subunit_test_error'
collect2: error: ld returned 1 exit status
Makefile:688: recipe for target 'run-all-tests' failed
make[3]: *** [run-all-tests] Error 1
make[3]: Leaving directory '/tmp/buildd/snp-sites-2.0.1/src'
Makefile:1064: recipe for target 'check-am' failed
make[2]: *** [check-am] Error 2
make[2]: Leaving directory '/tmp/buildd/snp-sites-2.0.1/src'
Makefile:399: recipe for target 'check-recursive' failed
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory '/tmp/buildd/snp-sites-2.0.1'
dh_auto_test: make -j1 check returned exit code 2
debian/rules:12: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
[..]
The full build log is attached or can be viewed here:
https://reproducible.debian.net/logs/unstable/amd64/snp-sites_2.0.1-1.build1.log.gz
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` la...@debian.org / chris-lamb.co.uk
`-
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Mon Sep 14 14:06:41 GMT+12 2015
I: pbuilder-time-stamp: 1442282801
I: Building the build Environment
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-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-ma...@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by
pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper (>= 9.0.0), autotools-dev, zlib1g-dev, check, dh-autoreconf,
d-shlibs, libxml2-utils, docbook, docbook-xsl, xsltproc, asciidoc
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dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring
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pbuilder-satisf
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The following NEW packages will be installed:
asciidoc{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a}
check{a} d-shlibs{a} dh-autoreconf{a} docbook{a} docbook-xsl{a}
libexpat1{a} libpython-stdlib{a} libpython2.7-minimal{a}
libpython2.7-stdlib{a} libsigsegv2{a} libssl1.0.0{a} libsubunit-dev{a}
libsubunit0{a} libtool{a} libxml2-utils{a} libxslt1.1{a} m4{a}
mime-support{a} python{a} python-minimal{a} python2.7{a}
python2.7-minimal{a} sgml-base{a} sgml-data{a} xml-core{a} xsltproc{a}
zlib1g-dev{a}
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I: Copying source file
I: copying [snp-sites_2.0.1-1.dsc]
I: copying [./snp-sites_2.0.1.orig.tar.gz]
I: copying [./snp-sites_2.0.1-1.debian.tar.xz]
I: Extracting source
gpgv: keyblock resource `/tmp/buildd/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Jul 27 06:02:08 2015 GMT+12 using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./snp-sites_2.0.1-1.dsc
dpkg-source: info: extracting snp-sites in snp-sites-2.0.1
dpkg-source: info: unpacking snp-sites_2.0.1.orig.tar.gz
dpkg-source: info: unpacking snp-sites_2.0.1-1.debian.tar.xz
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
dpkg-buildpackage: source package snp-sites
dpkg-buildpackage: source version 2.0.1-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Andreas Tille <ti...@debian.org>
dpkg-source --before-build snp-sites-2.0.1
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean --with autoreconf
dh_testdir
dh_auto_clean
dh_autoreconf_clean
dh_clean
debian/rules build
dh build --with autoreconf
dh_testdir
dh_autoreconf
libtoolize: putting auxiliary files in `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
libtoolize: copying file `m4/libtool.m4'
libtoolize: copying file `m4/ltoptions.m4'
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libtoolize: copying file `m4/lt~obsolete.m4'
configure.ac:7: installing './compile'
configure.ac:7: installing './config.guess'
configure.ac:7: installing './config.sub'
configure.ac:2: installing './install-sh'
configure.ac:2: installing './missing'
src/Makefile.am:26: warning: source file '../tests/check-snp-sites.c' is in a
subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding
output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same
subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
src/Makefile.am:26: warning: source file '../tests/check-vcf.c' is in a
subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
src/Makefile.am:26: warning: source file '../tests/helper-methods.c' is in a
subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
src/Makefile.am:26: warning: source file '../tests/run-all-tests.c' is in a
subdirectory,
src/Makefile.am:26: but option 'subdir-objects' is disabled
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
dh_auto_configure
./configure --build=x86_64-linux-gnu --prefix=/usr
--includedir=\${prefix}/include --mandir=\${prefix}/share/man
--infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var
--disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu
--libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode
--disable-dependency-tracking
configure: WARNING: unrecognized options: --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 whether make supports nested variables... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu
format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format...
func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -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 dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
dh_auto_build
make -j1
make[1]: Entering directory '/tmp/buildd/snp-sites-2.0.1'
make all-recursive
make[2]: Entering directory '/tmp/buildd/snp-sites-2.0.1'
Making all in src
make[3]: Entering directory '/tmp/buildd/snp-sites-2.0.1/src'
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -c -o alignment-file.lo alignment-file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
alignment-file.c -fPIC -DPIC -o .libs/alignment-file.o
alignment-file.c: In function 'get_bases_for_each_snp':
alignment-file.c:91:20: warning: format '%d' expects argument of type 'int',
but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat=]
fprintf(stderr, "Alignment %s contains sequences of unequal length.
Expected length is %d but got %d in sequence %s\n\n",filename,
length_of_genome_found, seq->seq.l,seq->name.s);
^
alignment-file.c:91:20: warning: format '%d' expects argument of type 'int',
but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat=]
alignment-file.c: In function 'read_line':
alignment-file.c:229:8: warning: implicit declaration of function
'size_of_string' [-Wimplicit-function-declaration]
if(size_of_string(sequence) > 0)
^
alignment-file.c:233:5: warning: implicit declaration of function
'concat_strings_created_with_malloc' [-Wimplicit-function-declaration]
concat_strings_created_with_malloc(sequence,current_line_buffer);
^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
alignment-file.c -o alignment-file.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -c -o vcf.lo vcf.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c
-fPIC -DPIC -o .libs/vcf.o
vcf.c: In function 'output_vcf_header':
vcf.c:58:29: warning: format '%i' expects argument of type 'int', but argument
3 has type 'size_t {aka long unsigned int}' [-Wformat=]
fprintf( vcf_file_pointer, "##contig=<ID=1,length=%i>\n", length_of_genome );
^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o
vcf.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -c -o phylib-of-snp-sites.lo phylib-of-snp-sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
phylib-of-snp-sites.c -fPIC -DPIC -o .libs/phylib-of-snp-sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
phylib-of-snp-sites.c -o phylib-of-snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -c -o snp-sites.lo snp-sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c snp-sites.c
-fPIC -DPIC -o .libs/snp-sites.o
snp-sites.c: In function 'generate_snp_sites':
snp-sites.c:139:4: warning: implicit declaration of function
'create_fasta_of_snp_sites' [-Wimplicit-function-declaration]
create_fasta_of_snp_sites(multi_fasta_output_filename, number_of_snps,
bases_for_snps, sequence_names, number_of_samples);
^
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c snp-sites.c
-o snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -c -o fasta-of-snp-sites.lo fasta-of-snp-sites.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
fasta-of-snp-sites.c -fPIC -DPIC -o .libs/fasta-of-snp-sites.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
fasta-of-snp-sites.c -o fasta-of-snp-sites.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -c -o parse-phylip.lo parse-phylip.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
parse-phylip.c -fPIC -DPIC -o .libs/parse-phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
parse-phylip.c -o parse-phylip.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -c -o string-cat.lo string-cat.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
string-cat.c -fPIC -DPIC -o .libs/string-cat.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c
string-cat.c -o string-cat.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0
-Wl,-z,relro -o libsnp-sites.la -rpath /usr/lib/x86_64-linux-gnu
alignment-file.lo vcf.lo phylib-of-snp-sites.lo snp-sites.lo
fasta-of-snp-sites.lo parse-phylip.lo string-cat.lo
libtool: link: gcc -shared -fPIC -DPIC .libs/alignment-file.o .libs/vcf.o
.libs/phylib-of-snp-sites.o .libs/snp-sites.o .libs/fasta-of-snp-sites.o
.libs/parse-phylip.o .libs/string-cat.o -O2 -Wl,-z -Wl,relro -Wl,-soname
-Wl,libsnp-sites.so.1 -o .libs/libsnp-sites.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libsnp-sites.so.1" && ln -s
"libsnp-sites.so.1.0.0" "libsnp-sites.so.1")
libtool: link: (cd ".libs" && rm -f "libsnp-sites.so" && ln -s
"libsnp-sites.so.1.0.0" "libsnp-sites.so")
libtool: link: ar cru .libs/libsnp-sites.a alignment-file.o vcf.o
phylib-of-snp-sites.o snp-sites.o fasta-of-snp-sites.o parse-phylip.o
string-cat.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libsnp-sites.a
libtool: link: ( cd ".libs" && rm -f "libsnp-sites.la" && ln -s
"../libsnp-sites.la" "libsnp-sites.la" )
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o
snp-sites main.o -lm libsnp-sites.la -lz -lpthread -lrt
libtool: link: gcc -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z -Wl,relro -o .libs/snp-sites main.o -lm
./.libs/libsnp-sites.so -lz -lpthread -lrt
make[3]: Leaving directory '/tmp/buildd/snp-sites-2.0.1/src'
make[3]: Entering directory '/tmp/buildd/snp-sites-2.0.1'
make[3]: Leaving directory '/tmp/buildd/snp-sites-2.0.1'
make[2]: Leaving directory '/tmp/buildd/snp-sites-2.0.1'
make[1]: Leaving directory '/tmp/buildd/snp-sites-2.0.1'
dh_auto_test
make -j1 check
make[1]: Entering directory '/tmp/buildd/snp-sites-2.0.1'
Making check in src
make[2]: Entering directory '/tmp/buildd/snp-sites-2.0.1/src'
make run-all-tests
make[3]: Entering directory '/tmp/buildd/snp-sites-2.0.1/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o
run_all_tests-check-snp-sites.o `test -f '../tests/check-snp-sites.c' || echo
'./'`../tests/check-snp-sites.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o
run_all_tests-check-vcf.o `test -f '../tests/check-vcf.c' || echo
'./'`../tests/check-vcf.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o
run_all_tests-helper-methods.o `test -f '../tests/helper-methods.c' || echo
'./'`../tests/helper-methods.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o
run_all_tests-run-all-tests.o `test -f '../tests/run-all-tests.c' || echo
'./'`../tests/run-all-tests.c
/bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -o
run-all-tests run_all_tests-check-snp-sites.o run_all_tests-check-vcf.o
run_all_tests-helper-methods.o run_all_tests-run-all-tests.o -lm -lcheck
libsnp-sites.la -lz -lpthread -lrt
libtool: link: gcc -I../tests -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z -Wl,relro -o .libs/run-all-tests
run_all_tests-check-snp-sites.o run_all_tests-check-vcf.o
run_all_tests-helper-methods.o run_all_tests-run-all-tests.o -lm -lcheck
./.libs/libsnp-sites.so -lz -lpthread -lrt
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x584): undefined reference to `subunit_test_start'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x63f): undefined reference to `subunit_test_fail'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x654): undefined reference to `subunit_test_pass'
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcheck.a(check_log.o):
In function `subunit_lfun':
(.text+0x66f): undefined reference to `subunit_test_error'
collect2: error: ld returned 1 exit status
Makefile:688: recipe for target 'run-all-tests' failed
make[3]: *** [run-all-tests] Error 1
make[3]: Leaving directory '/tmp/buildd/snp-sites-2.0.1/src'
Makefile:1064: recipe for target 'check-am' failed
make[2]: *** [check-am] Error 2
make[2]: Leaving directory '/tmp/buildd/snp-sites-2.0.1/src'
Makefile:399: recipe for target 'check-recursive' failed
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory '/tmp/buildd/snp-sites-2.0.1'
dh_auto_test: make -j1 check returned exit code 2
debian/rules:12: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
E: Failed autobuilding of package
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//17753 and its subdirectories
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