Your message dated Mon, 14 Jan 2019 21:36:23 +0000
with message-id <[email protected]>
and subject line Bug#919306: fixed in ncbi-vdb 2.9.3+dfsg-2
has caused the Debian Bug report #919306,
regarding ncbi-vdb breaks sra-sdk autopkgtest and hints at broken API
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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--
919306: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919306
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ncbi-vdb
Version: 2.9.3+dfsg-1
Control: affects -1 src:sra-sdk
X-Debbugs-CC: [email protected], [email protected]
User: [email protected]
Usertags: breaks
Dear maintainers,
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 2.9.3+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. Reading the
error message it seems like ncbi-vdb dropped a symbol used by sra-sdk
and as such it should have bumped the soname.
Currently this regression is blocking the migration of ncbi-vdb to
testing [1]. Can you please investigate the situation? If needed, please
change the bug's severity.
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/1700788/log.gz
autopkgtest [04:38:00]: 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:
/usr/lib/x86_64-linux-gnu/libncbi-vdb.so.2: undefined symbol:
vdb_mbedtls_ssl_conf_authmode
autopkgtest [04:38:00]: test run-unit-test: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: ncbi-vdb
Source-Version: 2.9.3+dfsg-2
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 14 Jan 2019 21:54:31 +0100
Source: ncbi-vdb
Binary: libncbi-vdb2 libncbi-vdb-dev libkdf5-2 libkdf5-dev libncbi-wvdb2
libncbi-wvdb-dev libvdb-sqlite2 libvdb-sqlite-dev
Architecture: source
Version: 2.9.3+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
libkdf5-2 - hdf5 access to data in the INSDC Sequence Read Archives
libkdf5-dev - hdf5 access to data in the INSDC Sequence Read Archives (devel)
libncbi-vdb-dev - libraries for using data in the INSDC Sequence Read Archives
(dev
libncbi-vdb2 - libraries for using data in the INSDC Sequence Read Archives
libncbi-wvdb-dev - virtual layer update modul of ncbi-vdb library (devel)
libncbi-wvdb2 - virtual layer update modul of ncbi-vdb library
libvdb-sqlite-dev - sqlite modul of ncbi-vdb library (devel)
libvdb-sqlite2 - sqlite modul of ncbi-vdb library
Closes: 919306
Changes:
ncbi-vdb (2.9.3+dfsg-2) unstable; urgency=medium
.
* Replace remainin occurrence of vdb_mbedtls_ssl_conf_authmode by
mbedtls_ssl_conf_authmode
Closes: #919306
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