[Debian-med-packaging] Bug#799164: snp-sites: FTBFS: undefined reference to `subunit_test_start'

[Chris Lamb]

Source: snp-sites
Version: 2.0.1-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds at 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
     `. `'`      lamby at debian.org / chris-lamb.co.uk
       `-
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