[Debian-med-packaging] Bug#919306: ncbi-vdb breaks sra-sdk autopkgtest and hints at broken API

[Paul Gevers]

Source: ncbi-vdb
Version: 2.9.3+dfsg-1
Control: affects -1 src:sra-sdk
X-Debbugs-CC: debian-ci at lists.debian.org, sra-sdk at packages.debian.org
User: debian-ci at lists.debian.org
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: -----------------------]

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