Bug#1098343: marked as done (libbio-procedural-perl: FTBFS: Failed 1/7 test programs)

Debian Bug Tracking System Wed, 09 Apr 2025 03:51:23 -0700

Your message dated Wed, 09 Apr 2025 10:49:17 +0000
with message-id <e1u2szd-00agbj...@fasolo.debian.org>
and subject line Bug#1098343: fixed in libbio-procedural-perl 1.7.4-5
has caused the Debian Bug report #1098343,
regarding libbio-procedural-perl: FTBFS: Failed 1/7 test programs
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.

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-- 
1098343: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1098343
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Package: src:libbio-procedural-perl
Version: 1.7.4-4
Severity: serious
Tags: ftbfs trixie sid

Hello Andreas. Yes, I know 1.7.4-4 was uploaded two days ago, but it still fails
for me, and not only in the future, but also in the present, and the failure
happens 100% of the time here.

Maybe the proxy trick did not work, or maybe there is something we are missing.
Please try to build it with plain dpkg-buildpackage in a chroot, because that's
the most simple way it fails for me. Remember that I always offer a VM
in case you could not reproduce it.


During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   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

[... snipped ...]

# 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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: WebDBSeqI Request Error:
# 500 Can't connect to 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 29 # skip problem connecting to RefSeq:
# ------------- EXCEPTION: Bio::Root::Exception -------------
# MSG: WebDBSeqI Request Error:
# 500 Can't connect to 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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: WebDBSeqI Request Error:
# 500 Can't connect to 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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: WebDBSeqI Request Error:
# 500 Can't connect to 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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: WebDBSeqI Request Error:
# 500 Can't connect to 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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: WebDBSeqI Request Error:
# 500 Can't connect to 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 127.0.0.1:9 (Connection refused)
# Content-Type: text/plain
# Client-Date: Wed, 19 Feb 2025 09:19:39 GMT
# Client-Warning: Internal response
# 
# Can't connect to 127.0.0.1:9 (Connection refused)
# 
# Connection refused 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 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
ok 30 # skip problem connecting to NCBI BLAST:
ok 31 # skip problem connecting to NCBI BLAST:
All 31 subtests passed 
        (less 188 skipped subtests: -157 okay)

Test Summary Report
-------------------
t/Perl.t               (Wstat: 0 Tests: 207 Failed: 176)
  Failed tests:  24, 24, 24, 24, 24, 24, 24, 24-25, 25, 25
                25, 25, 25, 25, 25-26, 26, 26, 26, 26, 26
                26, 26, 26, 26, 26, 26, 26, 26, 26, 26-27
                27, 27, 27, 27, 27, 27, 27, 27, 27, 27
                27, 27, 27, 27, 27-28, 28, 28, 28, 28, 28
                28, 28, 28, 28, 28, 28, 28, 28, 28, 28
                28, 28, 28, 28, 28, 28, 28, 28, 28, 28
                28, 28, 28, 28, 28, 28-29, 29, 29, 29, 29
                29, 29, 29, 29, 29, 29, 29, 29, 29, 29
                29, 29, 29, 29, 29, 29, 29, 29, 29, 29
                29, 29, 29, 29, 29, 29, 29-30, 30, 30, 30
                30, 30, 30, 30, 30, 30, 30, 30, 30, 30
                30, 30, 30, 30, 30, 30, 30, 30, 30, 30
                30, 30, 30, 30, 30, 30, 30, 30-31, 31, 31
                31, 31, 31, 31, 31, 31, 31, 31, 31, 31
                31, 31, 31, 31, 31, 31, 31, 31, 31, 31
                31, 31, 31, 31, 31, 31, 31, 31, 31
  Parse errors: Tests out of sequence.  Found (20) but expected (22)
                Tests out of sequence.  Found (21) but expected (23)
                Tests out of sequence.  Found (22) but expected (24)
                Tests out of sequence.  Found (22) but expected (25)
                Tests out of sequence.  Found (23) but expected (26)
Displayed the first 5 of 187 TAP syntax errors.
Re-run prove with the -p option to see them all.
Files=7, Tests=209, 13 wallclock secs ( 0.04 usr  0.01 sys +  0.25 cusr  0.08 
csys =  0.38 CPU)
Result: FAIL
Failed 1/7 test programs. 176/209 subtests failed.
make[1]: *** [Makefile:878: test_dynamic] Error 255
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: error: make -j2 test TEST_VERBOSE=1 returned exit code 2
make: *** [debian/rules:7: binary] Error 25
dpkg-buildpackage: error: debian/rules binary 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/202502/

About the archive rebuild: The build was made on virtual machines from AWS,
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 add an affects on src:libbio-procedural-perl, so that this is still
visible in the BTS web page for this package.

Thanks.

--- End Message ---

--- Begin Message ---

Source: libbio-procedural-perl
Source-Version: 1.7.4-5
Done: Étienne Mollier <emoll...@debian.org>

We believe that the bug you reported is fixed in the latest version of
libbio-procedural-perl, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1098...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated 
libbio-procedural-perl package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Wed, 09 Apr 2025 12:10:15 +0200
Source: libbio-procedural-perl
Architecture: source
Version: 1.7.4-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1098343
Changes:
 libbio-procedural-perl (1.7.4-5) unstable; urgency=medium
 .
   * Team upload.
   * no_remote_tests.patch: unconditional skip of network tests.
     (Closes: #1098343)
   * d/rules: remove unneeded proxy settings.
   * d/control: declare compliance to standards version 4.7.2.
Checksums-Sha1:
 27da10bc7fe93d8c0ca5ece6b759777191b9514d 2508 
libbio-procedural-perl_1.7.4-5.dsc
 265d8dc19dab826aaaf2aabea616fbe3db459c3d 2384 
libbio-procedural-perl_1.7.4-5.debian.tar.xz
Checksums-Sha256:
 d1b68fdba18fed08e253fb97a8adbac6a43d66edd7016ae4205df8381fbd5cd8 2508 
libbio-procedural-perl_1.7.4-5.dsc
 5385da4795897bbe9388de6031b76b1ecec77d53c243832a1f31d03ecec0e5f4 2384 
libbio-procedural-perl_1.7.4-5.debian.tar.xz
Files:
 b060434a8623831120907543fe7aa0ab 2508 perl optional 
libbio-procedural-perl_1.7.4-5.dsc
 0a3c3d5f939638638f4f7ac99343c561 2384 perl optional 
libbio-procedural-perl_1.7.4-5.debian.tar.xz

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--- End Message ---

Bug#1098343: marked as done (libbio-procedural-perl: FTBFS: Failed 1/7 test programs)

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