Bug#921382: kineticstools: autopkgtest needs update for new version of h5py

[Paul Gevers]

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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