[Debian-med-packaging] Bug#953897: ncbi-vdb breaks sra-sdk autopkgtest: undefined symbol: vdb_mbedtls_md_setup

[Paul Gevers]

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-ci at lists.debian.org
User: debian-ci at 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: -----------------------]

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 488 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20200314/b88206ac/attachment.sig>