[Debian-med-packaging] Bug#921382: kineticstools: autopkgtest needs update for new version of h5py

[Andreas Tille]

Control: tags -1 help

Hi Paul,

thanks a lot for this bug report.  I'd love to fix this but I have no
idea what to do.  Any hint from h5py at packages.debian.org ?

Kind regards

       Andreas.

On Mon, Feb 04, 2019 at 09:08:55PM +0100, Paul Gevers wrote:
> Source: kineticstools
> Version: 0.6.1+git20180425.27a1878-1
> X-Debbugs-CC: debian-ci at lists.debian.org, h5py at packages.debian.org
> Severity: important
> User: debian-ci at lists.debian.org
> Usertags: needs-update
> Control: affects -1 src:h5py
> 
> Dear maintainers,
> 
> With a recent upload of h5py the autopkgtest of kineticstools fails in
> testing when that autopkgtest is run with the binary packages of h5py
> from unstable. It passes when run with only packages from testing. In
> tabular form:
>                        pass            fail
> h5py                   from testing    2.9.0-1
> kineticstools          from testing    0.6.1+git20180425.27a1878-1
> all others             from testing    from testing
> 
> I copied some of the output at the bottom of this report. It seems to me
> that you need to update the reference of your test (or fix the code to
> not use the deprecated functionality).
> 
> Currently this regression is blocking the migration of h5py to testing
> [1]. Of course, h5py shouldn't just break your autopkgtest (or even
> worse, your package), but it seems to me that the change in h5py was
> intended and your package needs to update to the new 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=h5py
> 
> https://ci.debian.net/data/autopkgtest/testing/amd64/k/kineticstools/1853202/log.gz
> 
> autopkgtest [05:50:26]: test command1: 	cp -r Makefile test $ADTTMP/	&&
> cd $ADTTMP	&& ln -s /usr/share/kineticstools kineticsTools	&& make -k
> unit-tests cram-tests
> autopkgtest [05:50:26]: test command1: [-----------------------
> make: Nothing to be done for 'unit-tests'.
> cram --verbose --xunit-file=cramtests.xml `ls test/cram/*.t | grep -v
> detection_bam`
> test/cram/case-ctrl.t: failed
> --- test/cram/case-ctrl.t
> +++ test/cram/case-ctrl.t.err
> @@ -11,6 +11,8 @@
>  Run basic ipdSummary:
> 
>    $ ipdSummary --log-level=WARNING --numWorkers 1 --csv tmp.csv --gff
> tmp.gff --summary_h5 tmp.h5 --control $INPUT --reference $REFERENCE $INPUT
> +  /usr/lib/python2.7/dist-packages/h5py/_hl/dataset.py:313:
> H5pyDeprecationWarning: dataset.value has been deprecated. Use
> dataset[()] instead.
> +    "Use dataset[()] instead.", H5pyDeprecationWarning)
> 
>  Look at output csv file:
> 
> test/cram/detection.t: failed
> --- test/cram/detection.t
> +++ test/cram/detection.t.err
> @@ -11,6 +11,8 @@
>  Run basic ipdSummary:
> 
>    $ ipdSummary --log-level=WARNING --pvalue 0.001 --numWorkers 1 --csv
> tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --identify "" --reference
> $REFERENCE $INPUT
> +  /usr/lib/python2.7/dist-packages/h5py/_hl/dataset.py:313:
> H5pyDeprecationWarning: dataset.value has been deprecated. Use
> dataset[()] instead.
> +    "Use dataset[()] instead.", H5pyDeprecationWarning)
> 
>  Look at output csv file:
> 
> test/cram/identify.t: failed
> --- test/cram/identify.t
> +++ test/cram/identify.t.err
> @@ -11,6 +11,8 @@
>  Run basic ipdSummary:
> 
>    $ ipdSummary --log-level=WARNING --numWorkers 1 --pvalue 0.001
> --identify m6A,m4C --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5
> --reference $REFERENCE $INPUT
> +  /usr/lib/python2.7/dist-packages/h5py/_hl/dataset.py:313:
> H5pyDeprecationWarning: dataset.value has been deprecated. Use
> dataset[()] instead.
> +    "Use dataset[()] instead.", H5pyDeprecationWarning)
> 
>  Look at output csv file:
> 
> test/cram/methyl-fraction-case-ctrl.t: failed
> --- test/cram/methyl-fraction-case-ctrl.t
> +++ test/cram/methyl-fraction-case-ctrl.t.err
> @@ -11,6 +11,8 @@
>  Run basic ipdSummary:
> 
>    $ ipdSummary --log-level=WARNING --numWorkers 1 --methylFraction
> --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --control $INPUT
> --reference $REFERENCE $INPUT
> +  /usr/lib/python2.7/dist-packages/h5py/_hl/dataset.py:313:
> H5pyDeprecationWarning: dataset.value has been deprecated. Use
> dataset[()] instead.
> +    "Use dataset[()] instead.", H5pyDeprecationWarning)
> 
>  Look at output csv file:
> 
> test/cram/version.t: passed
> # Ran 5 tests, 0 skipped, 4 failed.
> make: *** [Makefile:32: cram-tests] Error 1
> 




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