Bug#1078626: marked as done (libbio-procedural-perl: Tries to access the network during build)

To: Andreas Tille <andreas@an3as.eu>
Subject: Bug#1078626: marked as done (libbio-procedural-perl: Tries to access the network during build)
From: "Debian Bug Tracking System" <owner@bugs.debian.org>
Date: Sun, 16 Feb 2025 11:27:03 +0000
Message-id: <[🔎] handler.1078626.D1078626.17397049221353293.ackdone@bugs.debian.org>
Reply-to: 1078626@bugs.debian.org
References: <Z7HKV-W9zIGefnmX@an3as.eu> <1ebae8fb-bcd0-4259-ae4d-8a667a2d1b0e@debian.org>

Your message dated Sun, 16 Feb 2025 12:21:59 +0100
with message-id <Z7HKV-W9zIGefnmX@an3as.eu>
and subject line Re: Bug#1078626: marked as pending in libbio-procedural-perl
has caused the Debian Bug report #1078626,
regarding libbio-procedural-perl: Tries to access the network during build
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
1078626: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1078626
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

--- Begin Message ---

To: Debian BTS <submit@bugs.debian.org>
Subject: libbio-procedural-perl: will FTBFS during trixie support period
From: Santiago Vila <sanvila@debian.org>
Date: Tue, 13 Aug 2024 20:07:11 +0200
Message-id: <1ebae8fb-bcd0-4259-ae4d-8a667a2d1b0e@debian.org>

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.

--- End Message ---

--- Begin Message ---

To: Santiago Vila <sanvila@debian.org>, 1078626-done@bugs.debian.org
Subject: Re: Bug#1078626: marked as pending in libbio-procedural-perl
From: Andreas Tille <andreas@an3as.eu>
Date: Sun, 16 Feb 2025 12:21:59 +0100
Message-id: <Z7HKV-W9zIGefnmX@an3as.eu>
In-reply-to: <[🔎] 8ca4ee56-0fb8-430e-a10c-18509a5afcde@debian.org>
References: <1ebae8fb-bcd0-4259-ae4d-8a667a2d1b0e@debian.org> <67b1b377e82a9_2d545b105444574@godard.mail> <[🔎] ff864684-c9b7-4384-9806-e8c8b9df9efe@debian.org> <1ebae8fb-bcd0-4259-ae4d-8a667a2d1b0e@debian.org> <[🔎] 8ca4ee56-0fb8-430e-a10c-18509a5afcde@debian.org>

Hi Santiago,

Am Sun, Feb 16, 2025 at 11:21:59AM +0100 schrieb Santiago Vila:
> reopen 1078626
> retitle 1078626 libbio-procedural-perl: Tries to access the network during build
> thanks
> 
> Hi. Actually, this bug (while still being RC) belongs to a different category
> and I'm sorry for the confusion.
> 
> When a package tries to access a website using https, the package also
> fails to build in the future (because the https site appears to have
> an expired certificate).

The package is *not* accessing the internet when building.  If there
is *no* result (since the internet is not accessed the first part of

   if ($@ || !defined $seq_object) {

(see patch[1]) is effective and the test is scipped.  Your initial test
seems to have run somehow when being online triggering a bug while
checking some certificate of some server that is not valid in future
any more.  Its pretty save to expect that the certificate will be
refreshed anyway so the bug report seems not be relevant in any case.
 
> So there is some kind of overlap between those two categories, and
> in cases like this one it's better to put it in the category
> "trying internet access".

No, its not.  The case when the test attempts to do so is properly
catched.  I'm building in pbuiler chroot and if you have any doubt you
can see the build log in Salsa CI[2].  In turn you might check your
build environent where you found the series of "FTBFS in future" bugs
whether it rather should have been run offline since in this case this
package would not have been catched.

Thank you for your QA work anyway
   Andreas.

[1] https://salsa.debian.org/med-team/libbio-procedural-perl/-/blob/master/debian/patches/no_remote_tests.patch?ref_type=heads#L17 
[2] https://salsa.debian.org/med-team/libbio-procedural-perl/-/jobs/7099605

-- 
https://fam-tille.de

--- End Message ---

Reply to:

Prev by Date: Processed: Re: Bug#1078626: marked as pending in libbio-procedural-perl
Next by Date: Bug#1078626: marked as pending in libbio-procedural-perl
Previous by thread: Bug#1078626: marked as done (libbio-procedural-perl: will FTBFS during trixie support period)
Next by thread: Re: Packages with a history of security issues and whose packaged version is not up to date
Index(es):
- Date
- Thread