Your message dated Thu, 21 May 2020 02:36:31 +0000
with message-id <e1jbb4r-000bhr...@fasolo.debian.org>
and subject line Bug#952627: fixed in ncbi-vdb 2.10.6+dfsg-2
has caused the Debian Bug report #952627,
regarding libncbi-vdb2 uses undefined symbols
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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952627: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=952627
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: ncbi-vdb, sra-sdk
Control: found -1 ncbi-vdb/2.10.3+dfsg-1
Control: found -1 sra-sdk/2.9.3+dfsg-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian...@lists.debian.org
User: debian...@lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of ncbi-vdb the autopkgtest of sra-sdk fails in
testing when that autopkgtest is run with the binary packages of
ncbi-vdb from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
ncbi-vdb from testing 2.10.3+dfsg-1
sra-sdk from testing 2.9.3+dfsg-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of ncbi-vdb to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=ncbi-vdb
https://ci.debian.net/data/autopkgtest/testing/amd64/s/sra-sdk/4556611/log.gz
autopkgtest [21:40:51]: test run-unit-test: [-----------------------
>>>>>Decompressing test-data archive...
dbGaP-0/
dbGaP-0/SRR2042184.fasta
meta/
meta/SRR6650398_experiment.xml
meta/SRR6650398_illumina_run.xml
meta/SRR2042184_run.xml
meta/SRR6650398_fastq_run.xml
meta/SRR6650398.bam
meta/SRR7032226_run.xml
meta/reference.fna
meta/SRR7032226_experiment.xml
meta/dbGaP-0.enc_key
meta/SRR2042184_experiment.xml
public/
public/wgs/
public/refseq/
public/refseq/NC_000962.3
public/files/
public/nannot/
public/sra/
public/sra/SRR2042184.sra
public/sra/SRR7032226.sra
public/sra/SRR6650398.sra
>>>>>Running test-sra...
test-sra: symbol lookup error: /lib/x86_64-linux-gnu/libncbi-vdb.so.2:
undefined symbol: vdb_mbedtls_md_setup
autopkgtest [21:40:51]: test run-unit-test: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: ncbi-vdb
Source-Version: 2.10.6+dfsg-2
Done: u...@debian.org (Aaron M. Ucko)
We believe that the bug you reported is fixed in the latest version of
ncbi-vdb, 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 952...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Aaron M. Ucko <u...@debian.org> (supplier of updated ncbi-vdb 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: SHA256
Format: 1.8
Date: Wed, 20 May 2020 22:13:24 -0400
Source: ncbi-vdb
Architecture: source
Version: 2.10.6+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Aaron M. Ucko <u...@debian.org>
Closes: 952623 952627 953897
Changes:
ncbi-vdb (2.10.6+dfsg-2) unstable; urgency=medium
.
* Install libs/vfs/services-priv.h as .../services-priv-internal.h to
distinguish it from interfaces/vfs/services-priv.h. (Neither can
stand in for the other.)
* Formally refresh patches that developed offsets.
* Factor out a new DSLMFLAGS macro for common d-shlibmove flags; include
the libmbedx509-0 quirk there since it will soon be needed everywhere.
* Address remaining underlinkage of system libraries (mbed*, z, bz2).
At this point, the only remaining unresolved references are of libkdf5
against symbols that could come from either libncbi-vdb or libncbi-wvdb.
(Closes: #952623, #952627, #953897.)
* Copy headers rather than moving them to allow for consecutive builds.
* Fix typo in override_dh_missing name; supply debian/not-installed.
* Add myself to Uploaders.
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ncbi-vdb_2.10.6+dfsg-2.debian.tar.xz
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ncbi-vdb_2.10.6+dfsg-2_source.buildinfo
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Files:
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ncbi-vdb_2.10.6+dfsg-2.dsc
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