Bug#1078626: libbio-procedural-perl: will FTBFS during trixie support period
Package: src:libbio-procedural-perl
Version: 1.7.4-2
User: debian-qa@lists.debian.org
Usertags: ftbfs-during-trixie-support-period
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable in the year 2028, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules build
dh build
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro"
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Bio::Procedural
Writing MYMETA.yml and MYMETA.json
dh_auto_build
make -j2
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp lib/Bio/Perl.pm blib/lib/Bio/Perl.pm
cp lib/Bio/Procedural.pm blib/lib/Bio/Procedural.pm
Manifying 2 pod documents
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test
make -j2 test TEST_VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
t/00-compile.t ...........
1..2
ok 1 - Bio/Perl.pm loaded ok
ok 2 - Bio/Procedural.pm loaded ok
ok
t/author-eol.t ........... skipped: these tests are for testing by the author
t/author-mojibake.t ...... skipped: these tests are for testing by the author
t/author-no-tabs.t ....... skipped: these tests are for testing by the author
t/author-pod-coverage.t .. skipped: these tests are for testing by the author
t/author-pod-syntax.t .... skipped: these tests are for testing by the author
--------------------- WARNING ---------------------
MSG: req was POST https://blast.ncbi.nlm.nih.gov/Blast.cgi
User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.7.8
Content-Length: 4109
Content-Type: application/x-www-form-urlencoded
COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&DESCRIPTIONS=100&ALIGNMENT_VIEW=Pairwise&FORMAT_TYPE=Text&SERVICE=plain&PROGRAM=blastn&ALIGNMENTS=50&FILTER=L&CMD=Put&DATABASE=nr&QUERY=%3ENM_006732+Homo+sapiens+FosB+proto-oncogene%2C+AP-1+transcription+factor+subunit+(FOSB)%2C+transcript+variant+1%2C+mRNA.%0D%0AATTCATAAGACTCAGAGCTACGGCCACGGCAGGGACACGCGGAACCAAGACTTGGAAACTTGATTGTTGTGGTTCTTCTTGGGGGTTATGAAATTTCATTAATCTTTTTTTTTCCGGGGAGAAAGTTTTTGGAAAGATTCTTCCAGATATTTCTTCATTTTCTTTTGGAGGACCGACTTACTTTTTTTGGTCTTCTTTATTACTCCCCTCCCCCCGTGGGACCCGCCGGACGCGTGGAGGAGACCGTAGCTGAAGCTGATTCTGTACAGCGGGACAGCGCTTTCTGCCCCTGGGGGAGCAACCCCTCCCTCGCCCCTGGGTCCTACGGAGCCTGCACTTTCAAGAGGTACAGCGGCATCCTGTGGGGGCCTGGGCACCGCAGGAAGACTGCACAGAAACTTTGCCATTGTTGGAACGGGACGTTGCTCCTTCCCCGAGCTTCCCCGGACAGCGTACTTTGAGGACTCGCTCAGCTCACCGGGGACTCCCACGGCTCACCCCGGACTTGCACCTTACTTCCCCAACCCGGCCATAGCCTTGGCTTCCCGGCGACCTCAGCGTGGTCACAGGGGCCCCCCTGTGCCCAGGGAAATGTTTCAGGCTTTCCCCGGAGACTACGACTCCGGCTCCCGGTGCAGCTCCTCACCCTCTGCCGAGTCTCAATATCTGTCTTCGGTGGACTCCTTCGGCAGTCCACCCACCGCCGCCGCCTCCCAGGAGTGCGCCGGTCTCGGGGAAATGCCCGGTTCCTTCGTGCCCACGGTCACCGCGATCACAACCAGCCAGGACCTCCAGTGGCTTGTGCAACCCACCCTCATCTCTTCCATGGCCCAGTCCCAGGGGCAGCCACTGGCCTCCCAGCCCCCGGTCGTCGACCCCTACGACATGCCGGGAACCAGCTACTCCACACCAGGCATGAGTGGCTACAGCAGTGGCGGAGCGAGTGGCAGTGGTGGGCCTTCCACCAGCGGAACTACCAGTGGGCCTGGGCCTGCCCGCCCAGCCCGAGCCCGGCCTAGGAGACCCCGAGAGGAGACGCTCACCCCAGAGGAAGAGGAGAAGCGAAGGGTGCGCCGGGAACGAAATAAACTAGCAGCAGCTAAATGCAGGAACCGGCGGAGGGAGCTGACCGACCGACTCCAGGCGGAGACAGATCAGTTGGAGGAAGAAAAAGCAGAGCTGGAGTCGGAGATCGCCGAGCTCCAAAAGGAGAAGGAACGTCTGGAGTTTGTGCTGGTGGCCCACAAACCGGGCTGCAAGATCCCCTACGAAGAGGGGCCCGGGCCGGGCCCGCTGGCGGAGGTGAGAGATTTGCCGGGCTCAGCACCGGCTAAGGAAGATGGCTTCAGCTGGCTGCTGCCGCCCCCGCCACCACCGCCCCTGCCCTTCCAGACCAGCCAAGACGCACCCCCCAACCTGACGGCTTCTCTCTTTACACACAGTGAAGTTCAAGTCCTCGGCGACCCCTTCCCCGTTGTTAACCCTTCGTACACTTCTTCGTTTGTCCTCACCTGCCCGGAGGTCTCCGCGTTCGCCGGCGCCCAACGCACCAGCGGCAGTGACCAGCCTTCCGATCCCCTGAACTCGCCCTCCCTCCTCGCTCTGTGAACTCTTTAGACACACAAAACAAACAAACACATGGGGGAGAGAGACTTGGAAGAGGAGGAGGAGGAGGAGAAGGAGGAGAGAGAGGGGAAGAGACAAAGTGGGTGTGTGGCCTCCCTGGCTCCTCCGTCTGACCCTCTGCGGCCACTGCGCCACTGCCATCGGACAGGAGGATTCCTTGTGTTTTGTCCTGCCTCTTGTTTCTGTGCCCCGGCGAGGCCGGAGAGCTGGTGACTTTGGGGACAGGGGGTGGGAAGGGGATGGACACCCCCAGCTGACTGTTGGCTCTCTGACGTCAACCCAAGCTCTGGGGATGGGTGGGGAGGGGGGCGGGTGACGCCCACCTTCGGGCAGTCCTGTGTGAGGATTAAGGGACGGGGGTGGGAGGTAGGCTGTGGGGTGGGCTGGAGTCCTCTCCAGAGAGGCTCAACAAGGAAAAATGCCACTCCCTACCCAATGTCTCCCACACCCACCCTTTTTTTGGGGTGCCTAGGTTGGTTTCCCCTGCACTCCCGACCTTAGCTTATTGATCCCACATTTCCATGGTGTGAGATCCTCTTTACTCTGGGCAGAAGTGAGCCCCCCCCTTAAAGGGAATTCGATGCCCCCCTAGAATAATCTCATCCCCCCACCCGACTTCTTTTGAAATGTGAACGTCCTTCCTTGACTGTCTAGCCACTCCCTCCCAGAAAAACTGGCTCTGATTGGAATTTCTGGCCTCCTAAGGCTCCCCACCCCGAAATCAGCCCCCAGCCTTGTTTCTGATGACAGTGTTATCCCAAGACCCTGCCCCCTGCCAGCCGACCCTCCTGGCCTTCCTCGTTGGGCCGCTCTGATTTCAGGCAGCAGGGGCTGCTGTGATGCCGTCCTGCTGGAGTGATTTATACTGTGAAATGAGTTGGCCAGATTGTGGGGTGCAGCTGGGTGGGGCAGCACACCTCTGGGGGGATAATGTCCCCACTCCCGAAAGCCTTTCCTCGGTCTCCCTTCCGTCCATCCCCCTTCTTCCTCCCCTCAACAGTGAGTTAGACTCAAGGGGGTGACAGAACCGAGAAGGGGGTGACAGTCCTCCATCCACGTGGCCTCTCTCTCTCTCCTCAGGACCCTCAGCCCTGGCCTTTTTCTTTAAGGTCCCCCGACCAATCCCCAGCCTAGGACGCCAACTTCTCCCACCCCTTGGCCCCTCACATCCTCTCCAGGAAGGGAGTGAGGGGCTGTGACATTTTTCCGGAGAAGATTTCAGAGCTGAGGCTTTGGTACCCCCAAACCCCCAATATTTTTGGACTGGCAGACTCAAGGGGCTGGAATCTCATGATTCCATGCCCGAGTCCGCCCATCCCTGACCATGGTTTTGGCTCTCCCACCCCGCCGTTCCCTGCGCTTCATCTCATGAGGATTTCTTTATGAGGCAAATTTATATTTTTTAATATCGGGGGGTGGACCACGCCGCCCTCCATCCGTGCTGCATGAAAAACATTCCACGTGCCCCTTGTCGCGCGTCTCCCATCCTGATCCCAGACCCATTCCTTAGCTATTTATCCCTTTCCTGGTTTCCGAAAGGCAATTATATCTATTATGTATAAGTAAATATATTATATATGGATGTGTGTGTGTGCGTGCGCGTGAGTGTGTGAGCGCTTCTGCAGCCTCGGCCTAGGTCACGTTGGCCCTCAAAGCGAGCCGTTGAATTGGAAACTGCTTCTAGAAACTCTGGCTCAGCCTGTCTCGGGCTGACCCTTTTCTGATCGTCTCGGCCCCTCTGATTGTTCCCGATGGTCTCTCTCCCTCTGTCTTTTCTCCTCCGCCTGTGTCCATCTGACCGTTTTCACTTGTCTCCTTTCTGACTGTCCCTGCCAATGCTCCAGCTGTCGTCTGACTCTGGGTTCGTTGGGGACATGAGATTTTATTTTTTGTGAGTGAGACTGAGGGATCGTAGATTTTTACAATCTGTATCTTTGACAATTCTGGGTGCGAGTGTGAGAGTGTGAGCAGGGCTTGCTCCTGCCAACCACAATTCAATGAATCCCCGACCCCCCTACCCCATGCTGTACTTGTGGTTCTCTTTTTGTATTTTGCATCTGACCCCGGGGGGCTGGGACAGATTGGCAATGGGCCGTCCCCTCTCCCCTTGGTTCTGCACTGTTGCCAATAAAAAGCTCTTAAAAACGCA&FORMAT_OBJECT=Alignment
<html>
<head><title>An Error Occurred</title></head>
<body>
<h1>An Error Occurred</h1>
<p>500 Can't connect to blast.ncbi.nlm.nih.gov:443 (certificate verify failed)</p>
</body>
</html>
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: req was POST https://blast.ncbi.nlm.nih.gov/Blast.cgi
User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.7.8
Content-Length: 4109
Content-Type: application/x-www-form-urlencoded
COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&DESCRIPTIONS=100&ALIGNMENT_VIEW=Pairwise&FORMAT_TYPE=Text&SERVICE=plain&PROGRAM=blastn&ALIGNMENTS=50&FILTER=L&CMD=Put&DATABASE=nr&QUERY=%3ENM_006732+Homo+sapiens+FosB+proto-oncogene%2C+AP-1+transcription+factor+subunit+(FOSB)%2C+transcript+variant+1%2C+mRNA.%0D%0AATTCATAAGACTCAGAGCTACGGCCACGGCAGGGACACGCGGAACCAAGACTTGGAAACTTGATTGTTGTGGTTCTTCTTGGGGGTTATGAAATTTCATTAATCTTTTTTTTTCCGGGGAGAAAGTTTTTGGAAAGATTCTTCCAGATATTTCTTCATTTTCTTTTGGAGGACCGACTTACTTTTTTTGGTCTTCTTTATTACTCCCCTCCCCCCGTGGGACCCGCCGGACGCGTGGAGGAGACCGTAGCTGAAGCTGATTCTGTACAGCGGGACAGCGCTTTCTGCCCCTGGGGGAGCAACCCCTCCCTCGCCCCTGGGTCCTACGGAGCCTGCACTTTCAAGAGGTACAGCGGCATCCTGTGGGGGCCTGGGCACCGCAGGAAGACTGCACAGAAACTTTGCCATTGTTGGAACGGGACGTTGCTCCTTCCCCGAGCTTCCCCGGACAGCGTACTTTGAGGACTCGCTCAGCTCACCGGGGACTCCCACGGCTCACCCCGGACTTGCACCTTACTTCCCCAACCCGGCCATAGCCTTGGCTTCCCGGCGACCTCAGCGTGGTCACAGGGGCCCCCCTGTGCCCAGGGAAATGTTTCAGGCTTTCCCCGGAGACTACGACTCCGGCTCCCGGTGCAGCTCCTCACCCTCTGCCGAGTCTCAATATCTGTCTTCGGTGGACTCCTTCGGCAGTCCACCCACCGCCGCCGCCTCCCAGGAGTGCGCCGGTCTCGGGGAAATGCCCGGTTCCTTCGTGCCCACGGTCACCGCGATCACAACCAGCCAGGACCTCCAGTGGCTTGTGCAACCCACCCTCATCTCTTCCATGGCCCAGTCCCAGGGGCAGCCACTGGCCTCCCAGCCCCCGGTCGTCGACCCCTACGACATGCCGGGAACCAGCTACTCCACACCAGGCATGAGTGGCTACAGCAGTGGCGGAGCGAGTGGCAGTGGTGGGCCTTCCACCAGCGGAACTACCAGTGGGCCTGGGCCTGCCCGCCCAGCCCGAGCCCGGCCTAGGAGACCCCGAGAGGAGACGCTCACCCCAGAGGAAGAGGAGAAGCGAAGGGTGCGCCGGGAACGAAATAAACTAGCAGCAGCTAAATGCAGGAACCGGCGGAGGGAGCTGACCGACCGACTCCAGGCGGAGACAGATCAGTTGGAGGAAGAAAAAGCAGAGCTGGAGTCGGAGATCGCCGAGCTCCAAAAGGAGAAGGAACGTCTGGAGTTTGTGCTGGTGGCCCACAAACCGGGCTGCAAGATCCCCTACGAAGAGGGGCCCGGGCCGGGCCCGCTGGCGGAGGTGAGAGATTTGCCGGGCTCAGCACCGGCTAAGGAAGATGGCTTCAGCTGGCTGCTGCCGCCCCCGCCACCACCGCCCCTGCCCTTCCAGACCAGCCAAGACGCACCCCCCAACCTGACGGCTTCTCTCTTTACACACAGTGAAGTTCAAGTCCTCGGCGACCCCTTCCCCGTTGTTAACCCTTCGTACACTTCTTCGTTTGTCCTCACCTGCCCGGAGGTCTCCGCGTTCGCCGGCGCCCAACGCACCAGCGGCAGTGACCAGCCTTCCGATCCCCTGAACTCGCCCTCCCTCCTCGCTCTGTGAACTCTTTAGACACACAAAACAAACAAACACATGGGGGAGAGAGACTTGGAAGAGGAGGAGGAGGAGGAGAAGGAGGAGAGAGAGGGGAAGAGACAAAGTGGGTGTGTGGCCTCCCTGGCTCCTCCGTCTGACCCTCTGCGGCCACTGCGCCACTGCCATCGGACAGGAGGATTCCTTGTGTTTTGTCCTGCCTCTTGTTTCTGTGCCCCGGCGAGGCCGGAGAGCTGGTGACTTTGGGGACAGGGGGTGGGAAGGGGATGGACACCCCCAGCTGACTGTTGGCTCTCTGACGTCAACCCAAGCTCTGGGGATGGGTGGGGAGGGGGGCGGGTGACGCCCACCTTCGGGCAGTCCTGTGTGAGGATTAAGGGACGGGGGTGGGAGGTAGGCTGTGGGGTGGGCTGGAGTCCTCTCCAGAGAGGCTCAACAAGGAAAAATGCCACTCCCTACCCAATGTCTCCCACACCCACCCTTTTTTTGGGGTGCCTAGGTTGGTTTCCCCTGCACTCCCGACCTTAGCTTATTGATCCCACATTTCCATGGTGTGAGATCCTCTTTACTCTGGGCAGAAGTGAGCCCCCCCCTTAAAGGGAATTCGATGCCCCCCTAGAATAATCTCATCCCCCCACCCGACTTCTTTTGAAATGTGAACGTCCTTCCTTGACTGTCTAGCCACTCCCTCCCAGAAAAACTGGCTCTGATTGGAATTTCTGGCCTCCTAAGGCTCCCCACCCCGAAATCAGCCCCCAGCCTTGTTTCTGATGACAGTGTTATCCCAAGACCCTGCCCCCTGCCAGCCGACCCTCCTGGCCTTCCTCGTTGGGCCGCTCTGATTTCAGGCAGCAGGGGCTGCTGTGATGCCGTCCTGCTGGAGTGATTTATACTGTGAAATGAGTTGGCCAGATTGTGGGGTGCAGCTGGGTGGGGCAGCACACCTCTGGGGGGATAATGTCCCCACTCCCGAAAGCCTTTCCTCGGTCTCCCTTCCGTCCATCCCCCTTCTTCCTCCCCTCAACAGTGAGTTAGACTCAAGGGGGTGACAGAACCGAGAAGGGGGTGACAGTCCTCCATCCACGTGGCCTCTCTCTCTCTCCTCAGGACCCTCAGCCCTGGCCTTTTTCTTTAAGGTCCCCCGACCAATCCCCAGCCTAGGACGCCAACTTCTCCCACCCCTTGGCCCCTCACATCCTCTCCAGGAAGGGAGTGAGGGGCTGTGACATTTTTCCGGAGAAGATTTCAGAGCTGAGGCTTTGGTACCCCCAAACCCCCAATATTTTTGGACTGGCAGACTCAAGGGGCTGGAATCTCATGATTCCATGCCCGAGTCCGCCCATCCCTGACCATGGTTTTGGCTCTCCCACCCCGCCGTTCCCTGCGCTTCATCTCATGAGGATTTCTTTATGAGGCAAATTTATATTTTTTAATATCGGGGGGTGGACCACGCCGCCCTCCATCCGTGCTGCATGAAAAACATTCCACGTGCCCCTTGTCGCGCGTCTCCCATCCTGATCCCAGACCCATTCCTTAGCTATTTATCCCTTTCCTGGTTTCCGAAAGGCAATTATATCTATTATGTATAAGTAAATATATTATATATGGATGTGTGTGTGTGCGTGCGCGTGAGTGTGTGAGCGCTTCTGCAGCCTCGGCCTAGGTCACGTTGGCCCTCAAAGCGAGCCGTTGAATTGGAAACTGCTTCTAGAAACTCTGGCTCAGCCTGTCTCGGGCTGACCCTTTTCTGATCGTCTCGGCCCCTCTGATTGTTCCCGATGGTCTCTCTCCCTCTGTCTTTTCTCCTCCGCCTGTGTCCATCTGACCGTTTTCACTTGTCTCCTTTCTGACTGTCCCTGCCAATGCTCCAGCTGTCGTCTGACTCTGGGTTCGTTGGGGACATGAGATTTTATTTTTTGTGAGTGAGACTGAGGGATCGTAGATTTTTACAATCTGTATCTTTGACAATTCTGGGTGCGAGTGTGAGAGTGTGAGCAGGGCTTGCTCCTGCCAACCACAATTCAATGAATCCCCGACCCCCCTACCCCATGCTGTACTTGTGGTTCTCTTTTTGTATTTTGCATCTGACCCCGGGGGGCTGGGACAGATTGGCAATGGGCCGTCCCCTCTCCCCTTGGTTCTGCACTGTTGCCAATAAAAAGCTCTTAAAAACGCA&FORMAT_OBJECT=Alignment
<html>
<head><title>An Error Occurred</title></head>
<body>
<h1>An Error Occurred</h1>
<p>500 Can't connect to blast.ncbi.nlm.nih.gov:443 (certificate verify failed)</p>
</body>
</html>
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: req was POST https://blast.ncbi.nlm.nih.gov/Blast.cgi
User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.7.8
Content-Length: 4109
Content-Type: application/x-www-form-urlencoded
DATABASE=nr&ALIGNMENTS=50&CMD=Put&FILTER=L&QUERY=%3ENM_006732+Homo+sapiens+FosB+proto-oncogene%2C+AP-1+transcription+factor+subunit+(FOSB)%2C+transcript+variant+1%2C+mRNA.%0D%0AATTCATAAGACTCAGAGCTACGGCCACGGCAGGGACACGCGGAACCAAGACTTGGAAACTTGATTGTTGTGGTTCTTCTTGGGGGTTATGAAATTTCATTAATCTTTTTTTTTCCGGGGAGAAAGTTTTTGGAAAGATTCTTCCAGATATTTCTTCATTTTCTTTTGGAGGACCGACTTACTTTTTTTGGTCTTCTTTATTACTCCCCTCCCCCCGTGGGACCCGCCGGACGCGTGGAGGAGACCGTAGCTGAAGCTGATTCTGTACAGCGGGACAGCGCTTTCTGCCCCTGGGGGAGCAACCCCTCCCTCGCCCCTGGGTCCTACGGAGCCTGCACTTTCAAGAGGTACAGCGGCATCCTGTGGGGGCCTGGGCACCGCAGGAAGACTGCACAGAAACTTTGCCATTGTTGGAACGGGACGTTGCTCCTTCCCCGAGCTTCCCCGGACAGCGTACTTTGAGGACTCGCTCAGCTCACCGGGGACTCCCACGGCTCACCCCGGACTTGCACCTTACTTCCCCAACCCGGCCATAGCCTTGGCTTCCCGGCGACCTCAGCGTGGTCACAGGGGCCCCCCTGTGCCCAGGGAAATGTTTCAGGCTTTCCCCGGAGACTACGACTCCGGCTCCCGGTGCAGCTCCTCACCCTCTGCCGAGTCTCAATATCTGTCTTCGGTGGACTCCTTCGGCAGTCCACCCACCGCCGCCGCCTCCCAGGAGTGCGCCGGTCTCGGGGAAATGCCCGGTTCCTTCGTGCCCACGGTCACCGCGATCACAACCAGCCAGGACCTCCAGTGGCTTGTGCAACCCACCCTCATCTCTTCCATGGCCCAGTCCCAGGGGCAGCCACTGGCCTCCCAGCCCCCGGTCGTCGACCCCTACGACATGCCGGGAACCAGCTACTCCACACCAGGCATGAGTGGCTACAGCAGTGGCGGAGCGAGTGGCAGTGGTGGGCCTTCCACCAGCGGAACTACCAGTGGGCCTGGGCCTGCCCGCCCAGCCCGAGCCCGGCCTAGGAGACCCCGAGAGGAGACGCTCACCCCAGAGGAAGAGGAGAAGCGAAGGGTGCGCCGGGAACGAAATAAACTAGCAGCAGCTAAATGCAGGAACCGGCGGAGGGAGCTGACCGACCGACTCCAGGCGGAGACAGATCAGTTGGAGGAAGAAAAAGCAGAGCTGGAGTCGGAGATCGCCGAGCTCCAAAAGGAGAAGGAACGTCTGGAGTTTGTGCTGGTGGCCCACAAACCGGGCTGCAAGATCCCCTACGAAGAGGGGCCCGGGCCGGGCCCGCTGGCGGAGGTGAGAGATTTGCCGGGCTCAGCACCGGCTAAGGAAGATGGCTTCAGCTGGCTGCTGCCGCCCCCGCCACCACCGCCCCTGCCCTTCCAGACCAGCCAAGACGCACCCCCCAACCTGACGGCTTCTCTCTTTACACACAGTGAAGTTCAAGTCCTCGGCGACCCCTTCCCCGTTGTTAACCCTTCGTACACTTCTTCGTTTGTCCTCACCTGCCCGGAGGTCTCCGCGTTCGCCGGCGCCCAACGCACCAGCGGCAGTGACCAGCCTTCCGATCCCCTGAACTCGCCCTCCCTCCTCGCTCTGTGAACTCTTTAGACACACAAAACAAACAAACACATGGGGGAGAGAGACTTGGAAGAGGAGGAGGAGGAGGAGAAGGAGGAGAGAGAGGGGAAGAGACAAAGTGGGTGTGTGGCCTCCCTGGCTCCTCCGTCTGACCCTCTGCGGCCACTGCGCCACTGCCATCGGACAGGAGGATTCCTTGTGTTTTGTCCTGCCTCTTGTTTCTGTGCCCCGGCGAGGCCGGAGAGCTGGTGACTTTGGGGACAGGGGGTGGGAAGGGGATGGACACCCCCAGCTGACTGTTGGCTCTCTGACGTCAACCCAAGCTCTGGGGATGGGTGGGGAGGGGGGCGGGTGACGCCCACCTTCGGGCAGTCCTGTGTGAGGATTAAGGGACGGGGGTGGGAGGTAGGCTGTGGGGTGGGCTGGAGTCCTCTCCAGAGAGGCTCAACAAGGAAAAATGCCACTCCCTACCCAATGTCTCCCACACCCACCCTTTTTTTGGGGTGCCTAGGTTGGTTTCCCCTGCACTCCCGACCTTAGCTTATTGATCCCACATTTCCATGGTGTGAGATCCTCTTTACTCTGGGCAGAAGTGAGCCCCCCCCTTAAAGGGAATTCGATGCCCCCCTAGAATAATCTCATCCCCCCACCCGACTTCTTTTGAAATGTGAACGTCCTTCCTTGACTGTCTAGCCACTCCCTCCCAGAAAAACTGGCTCTGATTGGAATTTCTGGCCTCCTAAGGCTCCCCACCCCGAAATCAGCCCCCAGCCTTGTTTCTGATGACAGTGTTATCCCAAGACCCTGCCCCCTGCCAGCCGACCCTCCTGGCCTTCCTCGTTGGGCCGCTCTGATTTCAGGCAGCAGGGGCTGCTGTGATGCCGTCCTGCTGGAGTGATTTATACTGTGAAATGAGTTGGCCAGATTGTGGGGTGCAGCTGGGTGGGGCAGCACACCTCTGGGGGGATAATGTCCCCACTCCCGAAAGCCTTTCCTCGGTCTCCCTTCCGTCCATCCCCCTTCTTCCTCCCCTCAACAGTGAGTTAGACTCAAGGGGGTGACAGAACCGAGAAGGGGGTGACAGTCCTCCATCCACGTGGCCTCTCTCTCTCTCCTCAGGACCCTCAGCCCTGGCCTTTTTCTTTAAGGTCCCCCGACCAATCCCCAGCCTAGGACGCCAACTTCTCCCACCCCTTGGCCCCTCACATCCTCTCCAGGAAGGGAGTGAGGGGCTGTGACATTTTTCCGGAGAAGATTTCAGAGCTGAGGCTTTGGTACCCCCAAACCCCCAATATTTTTGGACTGGCAGACTCAAGGGGCTGGAATCTCATGATTCCATGCCCGAGTCCGCCCATCCCTGACCATGGTTTTGGCTCTCCCACCCCGCCGTTCCCTGCGCTTCATCTCATGAGGATTTCTTTATGAGGCAAATTTATATTTTTTAATATCGGGGGGTGGACCACGCCGCCCTCCATCCGTGCTGCATGAAAAACATTCCACGTGCCCCTTGTCGCGCGTCTCCCATCCTGATCCCAGACCCATTCCTTAGCTATTTATCCCTTTCCTGGTTTCCGAAAGGCAATTATATCTATTATGTATAAGTAAATATATTATATATGGATGTGTGTGTGTGCGTGCGCGTGAGTGTGTGAGCGCTTCTGCAGCCTCGGCCTAGGTCACGTTGGCCCTCAAAGCGAGCCGTTGAATTGGAAACTGCTTCTAGAAACTCTGGCTCAGCCTGTCTCGGGCTGACCCTTTTCTGATCGTCTCGGCCCCTCTGATTGTTCCCGATGGTCTCTCTCCCTCTGTCTTTTCTCCTCCGCCTGTGTCCATCTGACCGTTTTCACTTGTCTCCTTTCTGACTGTCCCTGCCAATGCTCCAGCTGTCGTCTGACTCTGGGTTCGTTGGGGACATGAGATTTTATTTTTTGTGAGTGAGACTGAGGGATCGTAGATTTTTACAATCTGTATCTTTGACAATTCTGGGTGCGAGTGTGAGAGTGTGAGCAGGGCTTGCTCCTGCCAACCACAATTCAATGAATCCCCGACCCCCCTACCCCATGCTGTACTTGTGGTTCTCTTTTTGTATTTTGCATCTGACCCCGGGGGGCTGGGACAGATTGGCAATGGGCCGTCCCCTCTCCCCTTGGTTCTGCACTGTTGCCAATAAAAAGCTCTTAAAAACGCA&FORMAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&DESCRIPTIONS=100&EXPECT=1e-10&FORMAT_TYPE=Text&ALIGNMENT_VIEW=Pairwise&SERVICE=plain&PROGRAM=blastn
<html>
<head><title>An Error Occurred</title></head>
<body>
<h1>An Error Occurred</h1>
<p>500 Can't connect to blast.ncbi.nlm.nih.gov:443 (certificate verify failed)</p>
</body>
</html>
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: req was POST https://blast.ncbi.nlm.nih.gov/Blast.cgi
User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.7.8
Content-Length: 4109
Content-Type: application/x-www-form-urlencoded
ALIGNMENT_VIEW=Pairwise&CMD=Put&FILTER=L&QUERY=%3ENM_006732+Homo+sapiens+FosB+proto-oncogene%2C+AP-1+transcription+factor+subunit+(FOSB)%2C+transcript+variant+1%2C+mRNA.%0D%0AATTCATAAGACTCAGAGCTACGGCCACGGCAGGGACACGCGGAACCAAGACTTGGAAACTTGATTGTTGTGGTTCTTCTTGGGGGTTATGAAATTTCATTAATCTTTTTTTTTCCGGGGAGAAAGTTTTTGGAAAGATTCTTCCAGATATTTCTTCATTTTCTTTTGGAGGACCGACTTACTTTTTTTGGTCTTCTTTATTACTCCCCTCCCCCCGTGGGACCCGCCGGACGCGTGGAGGAGACCGTAGCTGAAGCTGATTCTGTACAGCGGGACAGCGCTTTCTGCCCCTGGGGGAGCAACCCCTCCCTCGCCCCTGGGTCCTACGGAGCCTGCACTTTCAAGAGGTACAGCGGCATCCTGTGGGGGCCTGGGCACCGCAGGAAGACTGCACAGAAACTTTGCCATTGTTGGAACGGGACGTTGCTCCTTCCCCGAGCTTCCCCGGACAGCGTACTTTGAGGACTCGCTCAGCTCACCGGGGACTCCCACGGCTCACCCCGGACTTGCACCTTACTTCCCCAACCCGGCCATAGCCTTGGCTTCCCGGCGACCTCAGCGTGGTCACAGGGGCCCCCCTGTGCCCAGGGAAATGTTTCAGGCTTTCCCCGGAGACTACGACTCCGGCTCCCGGTGCAGCTCCTCACCCTCTGCCGAGTCTCAATATCTGTCTTCGGTGGACTCCTTCGGCAGTCCACCCACCGCCGCCGCCTCCCAGGAGTGCGCCGGTCTCGGGGAAATGCCCGGTTCCTTCGTGCCCACGGTCACCGCGATCACAACCAGCCAGGACCTCCAGTGGCTTGTGCAACCCACCCTCATCTCTTCCATGGCCCAGTCCCAGGGGCAGCCACTGGCCTCCCAGCCCCCGGTCGTCGACCCCTACGACATGCCGGGAACCAGCTACTCCACACCAGGCATGAGTGGCTACAGCAGTGGCGGAGCGAGTGGCAGTGGTGGGCCTTCCACCAGCGGAACTACCAGTGGGCCTGGGCCTGCCCGCCCAGCCCGAGCCCGGCCTAGGAGACCCCGAGAGGAGACGCTCACCCCAGAGGAAGAGGAGAAGCGAAGGGTGCGCCGGGAACGAAATAAACTAGCAGCAGCTAAATGCAGGAACCGGCGGAGGGAGCTGACCGACCGACTCCAGGCGGAGACAGATCAGTTGGAGGAAGAAAAAGCAGAGCTGGAGTCGGAGATCGCCGAGCTCCAAAAGGAGAAGGAACGTCTGGAGTTTGTGCTGGTGGCCCACAAACCGGGCTGCAAGATCCCCTACGAAGAGGGGCCCGGGCCGGGCCCGCTGGCGGAGGTGAGAGATTTGCCGGGCTCAGCACCGGCTAAGGAAGATGGCTTCAGCTGGCTGCTGCCGCCCCCGCCACCACCGCCCCTGCCCTTCCAGACCAGCCAAGACGCACCCCCCAACCTGACGGCTTCTCTCTTTACACACAGTGAAGTTCAAGTCCTCGGCGACCCCTTCCCCGTTGTTAACCCTTCGTACACTTCTTCGTTTGTCCTCACCTGCCCGGAGGTCTCCGCGTTCGCCGGCGCCCAACGCACCAGCGGCAGTGACCAGCCTTCCGATCCCCTGAACTCGCCCTCCCTCCTCGCTCTGTGAACTCTTTAGACACACAAAACAAACAAACACATGGGGGAGAGAGACTTGGAAGAGGAGGAGGAGGAGGAGAAGGAGGAGAGAGAGGGGAAGAGACAAAGTGGGTGTGTGGCCTCCCTGGCTCCTCCGTCTGACCCTCTGCGGCCACTGCGCCACTGCCATCGGACAGGAGGATTCCTTGTGTTTTGTCCTGCCTCTTGTTTCTGTGCCCCGGCGAGGCCGGAGAGCTGGTGACTTTGGGGACAGGGGGTGGGAAGGGGATGGACACCCCCAGCTGACTGTTGGCTCTCTGACGTCAACCCAAGCTCTGGGGATGGGTGGGGAGGGGGGCGGGTGACGCCCACCTTCGGGCAGTCCTGTGTGAGGATTAAGGGACGGGGGTGGGAGGTAGGCTGTGGGGTGGGCTGGAGTCCTCTCCAGAGAGGCTCAACAAGGAAAAATGCCACTCCCTACCCAATGTCTCCCACACCCACCCTTTTTTTGGGGTGCCTAGGTTGGTTTCCCCTGCACTCCCGACCTTAGCTTATTGATCCCACATTTCCATGGTGTGAGATCCTCTTTACTCTGGGCAGAAGTGAGCCCCCCCCTTAAAGGGAATTCGATGCCCCCCTAGAATAATCTCATCCCCCCACCCGACTTCTTTTGAAATGTGAACGTCCTTCCTTGACTGTCTAGCCACTCCCTCCCAGAAAAACTGGCTCTGATTGGAATTTCTGGCCTCCTAAGGCTCCCCACCCCGAAATCAGCCCCCAGCCTTGTTTCTGATGACAGTGTTATCCCAAGACCCTGCCCCCTGCCAGCCGACCCTCCTGGCCTTCCTCGTTGGGCCGCTCTGATTTCAGGCAGCAGGGGCTGCTGTGATGCCGTCCTGCTGGAGTGATTTATACTGTGAAATGAGTTGGCCAGATTGTGGGGTGCAGCTGGGTGGGGCAGCACACCTCTGGGGGGATAATGTCCCCACTCCCGAAAGCCTTTCCTCGGTCTCCCTTCCGTCCATCCCCCTTCTTCCTCCCCTCAACAGTGAGTTAGACTCAAGGGGGTGACAGAACCGAGAAGGGGGTGACAGTCCTCCATCCACGTGGCCTCTCTCTCTCTCCTCAGGACCCTCAGCCCTGGCCTTTTTCTTTAAGGTCCCCCGACCAATCCCCAGCCTAGGACGCCAACTTCTCCCACCCCTTGGCCCCTCACATCCTCTCCAGGAAGGGAGTGAGGGGCTGTGACATTTTTCCGGAGAAGATTTCAGAGCTGAGGCTTTGGTACCCCCAAACCCCCAATATTTTTGGACTGGCAGACTCAAGGGGCTGGAATCTCATGATTCCATGCCCGAGTCCGCCCATCCCTGACCATGGTTTTGGCTCTCCCACCCCGCCGTTCCCTGCGCTTCATCTCATGAGGATTTCTTTATGAGGCAAATTTATATTTTTTAATATCGGGGGGTGGACCACGCCGCCCTCCATCCGTGCTGCATGAAAAACATTCCACGTGCCCCTTGTCGCGCGTCTCCCATCCTGATCCCAGACCCATTCCTTAGCTATTTATCCCTTTCCTGGTTTCCGAAAGGCAATTATATCTATTATGTATAAGTAAATATATTATATATGGATGTGTGTGTGTGCGTGCGCGTGAGTGTGTGAGCGCTTCTGCAGCCTCGGCCTAGGTCACGTTGGCCCTCAAAGCGAGCCGTTGAATTGGAAACTGCTTCTAGAAACTCTGGCTCAGCCTGTCTCGGGCTGACCCTTTTCTGATCGTCTCGGCCCCTCTGATTGTTCCCGATGGTCTCTCTCCCTCTGTCTTTTCTCCTCCGCCTGTGTCCATCTGACCGTTTTCACTTGTCTCCTTTCTGACTGTCCCTGCCAATGCTCCAGCTGTCGTCTGACTCTGGGTTCGTTGGGGACATGAGATTTTATTTTTTGTGAGTGAGACTGAGGGATCGTAGATTTTTACAATCTGTATCTTTGACAATTCTGGGTGCGAGTGTGAGAGTGTGAGCAGGGCTTGCTCCTGCCAACCACAATTCAATGAATCCCCGACCCCCCTACCCCATGCTGTACTTGTGGTTCTCTTTTTGTATTTTGCATCTGACCCCGGGGGGCTGGGACAGATTGGCAATGGGCCGTCCCCTCTCCCCTTGGTTCTGCACTGTTGCCAATAAAAAGCTCTTAAAAACGCA&FORMAT_OBJECT=Alignment&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&DESCRIPTIONS=100&FORMAT_TYPE=Text&SERVICE=plain&PROGRAM=blastn&ALIGNMENTS=50&DATABASE=nr
<html>
<head><title>An Error Occurred</title></head>
<body>
<h1>An Error Occurred</h1>
<p>500 Can't connect to blast.ncbi.nlm.nih.gov:443 (certificate verify failed)</p>
</body>
</html>
---------------------------------------------------
# Failed test at t/Perl.t line 141.
# Failed test 'undef isa 'Bio::Search::Result::ResultI''
# at t/Perl.t line 142.
# undef isn't defined
# Failed test at t/Perl.t line 141.
# Failed test at t/Perl.t line 141.
# Failed test 'undef isa 'Bio::Search::Result::ResultI''
# at t/Perl.t line 142.
# Failed test 'undef isa 'Bio::Search::Result::ResultI''
# at t/Perl.t line 142.
# undef isn't defined
# undef isn't defined
# Looks like you failed 2 tests of 31.
# Failed test at t/Perl.t line 141.
# Failed test 'undef isa 'Bio::Search::Result::ResultI''
# at t/Perl.t line 142.
# undef isn't defined
t/Perl.t .................
1..31
ok 1 - use Bio::Perl;
ok 2
ok 3 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 4
ok 5 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 6
ok 7 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 8 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 9
ok 10
ok 11 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 12
ok 13 - An object of class 'Bio::Seq' isa 'Bio::SeqI'
ok 14
ok 15 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeqI'
ok 16
ok 17
ok 18
ok 19
ok 20
ok 21 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 22
ok 23 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 24 # skip problem connecting to GenBank:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: WebDBSeqI Request Error:
# 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
# Content-Type: text/plain
# Client-Date: Sat, 10 Jun 2028 12:00:21 GMT
# Client-Warning: Internal response
#
# Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
#
# SSL connect attempt failed error:0A000086:SSL routines::certificate verify failed at /usr/share/perl5/LWP/Protocol/http.pm line 49.
#
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:783
# STACK: Bio::DB::NCBIHelper::get_seq_stream /usr/share/perl5/Bio/DB/NCBIHelper.pm:326
# STACK: Bio::DB::NCBIHelper::get_Stream_by_acc /usr/share/perl5/Bio/DB/NCBIHelper.pm:639
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:97
# -----------------------------------------------------------
#
ok 25 # skip problem connecting to GenBank:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: WebDBSeqI Request Error:
# 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
# Content-Type: text/plain
# Client-Date: Sat, 10 Jun 2028 12:00:21 GMT
# Client-Warning: Internal response
#
# Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
#
# SSL connect attempt failed error:0A000086:SSL routines::certificate verify failed at /usr/share/perl5/LWP/Protocol/http.pm line 49.
#
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:783
# STACK: Bio::DB::NCBIHelper::get_seq_stream /usr/share/perl5/Bio/DB/NCBIHelper.pm:326
# STACK: Bio::DB::NCBIHelper::get_Stream_by_acc /usr/share/perl5/Bio/DB/NCBIHelper.pm:639
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:97
# -----------------------------------------------------------
#
ok 24 # skip problem connecting to GenBank:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: acc AI129902 does not exist
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:97
# -----------------------------------------------------------
#
ok 25 # skip problem connecting to GenBank:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: acc AI129902 does not exist
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:97
# -----------------------------------------------------------
#
ok 26
ok 27 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 26
ok 27 - An object of class 'Bio::Seq::RichSeq' isa 'Bio::SeqI'
ok 28 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: acc AAC06201 does not exist
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
ok 29 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: acc AAC06201 does not exist
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
ok 28 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: WebDBSeqI Request Error:
# 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
# Content-Type: text/plain
# Client-Date: Sat, 10 Jun 2028 12:00:25 GMT
# Client-Warning: Internal response
#
# Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
#
# SSL connect attempt failed error:0A000086:SSL routines::certificate verify failed at /usr/share/perl5/LWP/Protocol/http.pm line 49.
#
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:783
# STACK: Bio::DB::NCBIHelper::get_seq_stream /usr/share/perl5/Bio/DB/NCBIHelper.pm:326
# STACK: Bio::DB::NCBIHelper::get_Stream_by_acc /usr/share/perl5/Bio/DB/NCBIHelper.pm:639
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
ok 29 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: WebDBSeqI Request Error:
# 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
# Content-Type: text/plain
# Client-Date: Sat, 10 Jun 2028 12:00:25 GMT
# Client-Warning: Internal response
#
# Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
#
# SSL connect attempt failed error:0A000086:SSL routines::certificate verify failed at /usr/share/perl5/LWP/Protocol/http.pm line 49.
#
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:783
# STACK: Bio::DB::NCBIHelper::get_seq_stream /usr/share/perl5/Bio/DB/NCBIHelper.pm:326
# STACK: Bio::DB::NCBIHelper::get_Stream_by_acc /usr/share/perl5/Bio/DB/NCBIHelper.pm:639
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
ok 28 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: acc AAC06201 does not exist
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
ok 29 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: acc AAC06201 does not exist
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:203
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
ok 28 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: WebDBSeqI Request Error:
# 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
# Content-Type: text/plain
# Client-Date: Sat, 10 Jun 2028 12:00:25 GMT
# Client-Warning: Internal response
#
# Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
#
# SSL connect attempt failed error:0A000086:SSL routines::certificate verify failed at /usr/share/perl5/LWP/Protocol/http.pm line 49.
#
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:783
# STACK: Bio::DB::NCBIHelper::get_seq_stream /usr/share/perl5/Bio/DB/NCBIHelper.pm:326
# STACK: Bio::DB::NCBIHelper::get_Stream_by_acc /usr/share/perl5/Bio/DB/NCBIHelper.pm:639
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
ok 29 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: WebDBSeqI Request Error:
# 500 Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
# Content-Type: text/plain
# Client-Date: Sat, 10 Jun 2028 12:00:25 GMT
# Client-Warning: Internal response
#
# Can't connect to eutils.ncbi.nlm.nih.gov:443 (certificate verify failed)
#
# SSL connect attempt failed error:0A000086:SSL routines::certificate verify failed at /usr/share/perl5/LWP/Protocol/http.pm line 49.
#
# STACK: Error::throw
# STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449
# STACK: Bio::DB::WebDBSeqI::_stream_request /usr/share/perl5/Bio/DB/WebDBSeqI.pm:783
# STACK: Bio::DB::NCBIHelper::get_seq_stream /usr/share/perl5/Bio/DB/NCBIHelper.pm:326
# STACK: Bio::DB::NCBIHelper::get_Stream_by_acc /usr/share/perl5/Bio/DB/NCBIHelper.pm:639
# STACK: Bio::DB::WebDBSeqI::get_Seq_by_acc /usr/share/perl5/Bio/DB/WebDBSeqI.pm:194
# STACK: Bio::Perl::get_sequence /<<PKGBUILDDIR>>/blib/lib/Bio/Perl.pm:285
# STACK: t/Perl.t:123
# -----------------------------------------------------------
#
not ok 30
not ok 31 - undef isa 'Bio::Search::Result::ResultI'
not ok 30
not ok 30
not ok 31 - undef isa 'Bio::Search::Result::ResultI'
not ok 31 - undef isa 'Bio::Search::Result::ResultI'
not ok 30
not ok 31 - undef isa 'Bio::Search::Result::ResultI'
Dubious, test returned 2 (wstat 512, 0x200)
All 31 subtests passed
(less 12 skipped subtests: 19 okay)
Test Summary Report
-------------------
t/Perl.t (Wstat: 512 (exited 2) Tests: 47 Failed: 16)
Failed tests: 28, 28, 28, 28-29, 29, 29, 29-30, 30, 30
30-31, 31, 31, 31
Non-zero exit status: 2
Parse errors: Tests out of sequence. Found (24) but expected (26)
Tests out of sequence. Found (25) but expected (27)
Tests out of sequence. Found (26) but expected (28)
Tests out of sequence. Found (27) but expected (29)
Tests out of sequence. Found (26) but expected (30)
Displayed the first 5 of 23 TAP syntax errors.
Re-run prove with the -p option to see them all.
Files=7, Tests=49, 13 wallclock secs ( 0.03 usr 0.00 sys + 0.34 cusr 0.12 csys = 0.49 CPU)
Result: FAIL
Failed 1/7 test programs. 16/49 subtests failed.
make[1]: *** [Makefile:878: test_dynamic] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: error: make -j2 test TEST_VERBOSE=1 returned exit code 2
make: *** [debian/rules:4: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/ftbfs-future/
About the archive rebuild: This is an effort to keep trixie free from FTBFS bugs
during its lifetime as a supported distribution, as explained here:
https://lists.debian.org/debian-devel/2024/05/msg00414.html
(While they are not yet, please note that the bugs will be RC for trixie)
The build was made using sbuild and a reduced chroot with only
build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
Reply to: