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.
