[Debian-med-packaging] New version of python-numpy breaks autopkgtests of pbgenomicconsensus in testing

Andreas Tille andreas at an3as.eu
Wed May 9 10:56:17 BST 2018


Hi Afif,

in the log[4] I've found things like

...
PATH=`pwd`:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games cram --verbose ` ls tests/cram/extra/*.t | grep -v arrow`
tests/cram/extra/convert-to-bed.t: failed
--- tests/cram/extra/convert-to-bed.t
+++ tests/cram/extra/convert-to-bed.t.err
@@ -7,6 +7,8 @@
   $ gffToBed --name=variants \
   >          --description="PacBio variant calls" \
   > variants $INPUT
+  /usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
+    from ._conv import register_converters as _register_converters
   track name=variants description="PacBio variant calls" useScore=0
   gi|160367075|gb|CP000730.1| Staphylococcus aureus subsp. aureus USA300_TCH1516, complete genome\t701414\t701415\t701415del\t46.000\t. (esc)
   gi|160367075|gb|CP000730.1| Staphylococcus aureus subsp. aureus USA300_TCH1516, complete genome\t970969\t970970\t970970del\t48.000\t. (esc)
tests/cram/extra/convert-to-vcf.t: failed
--- tests/cram/extra/convert-to-vcf.t
+++ tests/cram/extra/convert-to-vcf.t.err
@@ -5,6 +5,8 @@
   $ export INPUT=$DATA/converters/variants.gff.gz
 
   $ gffToVcf --globalReference=Staphylococcus_aureus_USA300_TCH1516 $INPUT
+  /usr/lib/python2.7/dist-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
+    from ._conv import register_converters as _register_converters
   ##fileformat=VCFv3.3
   ##fileDate=* (glob)
   ##source=* (glob)



so there really seems to be an issue that might be more or less
easily (? not checked, just wild guessing!) by some

   s/np.floating/np.float64/

at relevant places.

Kind regards

      Andreas.

On Tue, May 08, 2018 at 06:51:30PM +0100, Paul Gevers wrote:
> Dear maintainers,
> 
> [This e-mail is automatically sent. V2 (20180508)]
> 
> As recently announced [1] Debian is now running autopkgtests in testing
> to check if the migration of a new source package causes regressions. It
> does this with the binary packages of the new version of the source
> package from unstable.
> 
> With a recent upload of python-numpy the autopkgtest of pbgenomicconsensus
> started to fail in testing [2]. This is currently delaying the migration
> of python-numpy version 1:1.14.3-2 [3].
> 
> This e-mail is meant to trigger prompt direct communication between the
> maintainers of the involved packages as one party has insight in what
> changed and the other party insight in what is being tested. Please
> therefore get in touch with each other with your ideas about what the
> causes of the problem might be, proposed patches, etc. A regression in a
> reverse dependency can be due to one of the following reasons (of course
> not complete):
> * new bug in the candidate package (fix the package)
> * bug in the test case that only gets triggered due to the update (fix
>   the reverse dependency, but see below)
> * out-of-date reference date in the test case that captures a former bug
>   in the candidate package (fix the reverse dependency, but see below)
> * deprecation of functionality that is used in the reverse dependency
>   and/or its test case (discussion needed)
> Triaging tips are being collected on the Debian Wiki [4].
> 
> Unfortunately sometimes a regression is only intermittent. Ideally this
> should be fixed, but it may be OK to just have the autopkgtest retried
> (a link is available in the excuses [3]).
> 
> There are cases where it is required to have multiple packages migrate
> together to have the test cases pass, e.g. when there was a bug in a
> regressing test case of a reverse dependency and that got fixed. In that
> case the test cases need to be triggered with both packages from
> unstable (reply to this e-mail and/or contact the ci-team [5]) or just
> wait until the aging time is over (if the fixed reverse dependency
> migrates before that time, the failed test can be retriggered [3]).
> 
> Of course no system is perfect. In case a framework issue is suspected,
> don't hesitate to raise the issue via BTS or to the ci-team [5] (reply to
> me is also fine for initial cross-check).
> 
> To avoid stepping on peoples toes, this e-mail does not automatically
> generate a bug in the BTS, but it is highly recommended to forward this
> e-mail there (psuedo-header boilerplate below [6,7]) in case it is
> clear which package should solve this regression.
> 
> It can be appropriate to file an RC bug against the depended-on package,
> if the regression amounts to an RC bug in the depending package, and to
> keep it open while the matter is investigated. That will prevent
> migration of an RC regression.
> 
> If the maintainers of the depending package don't have available effort
> to fix a problem, it is appropriate for the maintainers of the
> depended-on package to consider an NMU of the depending package. Any
> such an NMU should take place in accordance with the normal NMU rules.
> 
> Neither of the above steps should be seen as hostile; they are part of
> trying to work together to keep Debian in tip-top shape.
> 
> If you find that you are not able to agree between you about the right
> next steps, bug severities, etc., please try to find a neutral third
> party to help you mediate and/or provide a third opinion. Failing that
> your best bet is probably to post to debian-devel.
> 
> [1] https://lists.debian.org/debian-devel-announce/2018/05/msg00001.html
> [2] https://ci.debian.net/packages/p/pbgenomicconsensus/testing/amd64/
> [3] https://qa.debian.org/excuses.php?package=python-numpy
> [4] https://wiki.debian.org/ContinuousIntegration/TriagingTips
> [5] #debci on oftc or debian-ci at lists.debian.org
> [6] python-numpy has an issue
> ============
> Source: python-numpy
> Version: 1:1.14.3-2
> Severity: normal or higher
> Control: affects -1 src:pbgenomicconsensus
> User: debian-ci at lists.debian.org
> Usertags: breaks
> ============
> [7] pbgenomicconsensus has an issue
> ============
> Source: pbgenomicconsensus
> Version: 2.1.0-1
> Severity: normal or higher
> Control: affects -1 src:python-numpy
> User: debian-ci at lists.debian.org
> Usertags: needs-update
> ============
> 
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging

-- 
http://fam-tille.de



More information about the Debian-med-packaging mailing list