Bug#929924: unblock: pdb2pqr/2.1.1+dfsg-5
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
Hi Release Team
On 2017-06-15, pdb2pqr's autopkgtests started to fail (#903759).
Unfortunately, debci logs for these early failures no longer exist.
The upload of pdb2pqr/2.1.1+dfsg-4 on 2018-07-14 partially fixed the
test failures, and with the recent upload of pdb2pqr/2.1.1+dfsg-5, tests
are now passing again [1].
I have attached a debdiff. Please consider unblocking.
Regards
Graham
[1] https://ci.debian.net/packages/p/pdb2pqr/unstable/amd64/
diff -Nru pdb2pqr-2.1.1+dfsg/debian/changelog pdb2pqr-2.1.1+dfsg/debian/changelog
--- pdb2pqr-2.1.1+dfsg/debian/changelog 2018-07-14 16:09:27.000000000 +0200
+++ pdb2pqr-2.1.1+dfsg/debian/changelog 2019-05-27 07:52:46.000000000 +0200
@@ -1,3 +1,18 @@
+pdb2pqr (2.1.1+dfsg-5) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Andreas Tille ]
+ * Build-Depends: dh-python
+
+ [ Andrius Merkys ]
+ * Fixing autopkgtest 'installation-test' by substituting non-existent PDB
+ file with an existing one. Removing autopkgtest 'ligands-test' as it
+ depended on files that are not shipped by the upstream anymore.
+ (Closes: #903759)
+
+ -- Andrius Merkys <merkys@debian.org> Mon, 27 May 2019 01:52:46 -0400
+
pdb2pqr (2.1.1+dfsg-4) unstable; urgency=medium
* Adapt test to new location of examples
diff -Nru pdb2pqr-2.1.1+dfsg/debian/control pdb2pqr-2.1.1+dfsg/debian/control
--- pdb2pqr-2.1.1+dfsg/debian/control 2018-07-14 16:09:27.000000000 +0200
+++ pdb2pqr-2.1.1+dfsg/debian/control 2019-05-27 07:48:25.000000000 +0200
@@ -6,6 +6,7 @@
Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
+ dh-python,
gfortran,
swig,
xmlto,
diff -Nru pdb2pqr-2.1.1+dfsg/debian/tests/control pdb2pqr-2.1.1+dfsg/debian/tests/control
--- pdb2pqr-2.1.1+dfsg/debian/tests/control 2018-07-14 16:09:27.000000000 +0200
+++ pdb2pqr-2.1.1+dfsg/debian/tests/control 2019-05-27 07:48:25.000000000 +0200
@@ -2,10 +2,6 @@
Depends: pdb2pqr
Restrictions: allow-stderr
-Tests: ligands-test
-Depends: @
-Restrictions: allow-stderr
-
Tests: pdb2pka-test
Depends: @, python-networkx
Restrictions: allow-stderr
diff -Nru pdb2pqr-2.1.1+dfsg/debian/tests/installation-test pdb2pqr-2.1.1+dfsg/debian/tests/installation-test
--- pdb2pqr-2.1.1+dfsg/debian/tests/installation-test 2018-07-14 16:09:27.000000000 +0200
+++ pdb2pqr-2.1.1+dfsg/debian/tests/installation-test 2019-05-27 07:48:25.000000000 +0200
@@ -4,15 +4,6 @@
set -e
-pkg=pdb2pqr
-
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cd $ADTTMP
-
echo "Run pdb2pqr..."
-pdb2pqr --ff=amber "1FAS" output.txt
-[ -s output.txt ]
+pdb2pqr --ff=amber examples/1a1p/1a1p.pdb ${AUTOPKGTEST_TMP}/output.txt
+[ -s ${AUTOPKGTEST_TMP}/output.txt ]
diff -Nru pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test
--- pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test 2018-07-14 16:09:27.000000000 +0200
+++ pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test 1970-01-01 02:00:00.000000000 +0200
@@ -1,33 +0,0 @@
-#!/bin/sh
-# autopkgtest check: build and run with default test data
-# Author: Tatiana Malygina <merlettaia@gmail.com>
-
-set -e
-
-pkg=pdb2pqr
-example_pkg=pdb2pqr
-
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cd $ADTTMP
-
-cp -a /usr/share/doc/${example_pkg}/examples/* .
-find . -type f -name "*.gz" -exec gunzip \{\} \;
-for lnk in `find . -type l -name "*.gz"` ; do
- ln -s `basename $(readlink $lnk) .gz` `echo $lnk | sed 's/\.gz$//'`
- rm $lnk
-done
-
-echo "Run pdb2pqr..."
-
-# following sample call was adopted from fabfile.py,
-# method "linux_bin_cross_platform_test":
-for pdb in 1ABF 1HPV 1HPX 1QBS 1XL5; do
- echo "******** ${pdb} starting"
- pdb2pqr --ff=parse --verbose --ligand="ligands/LIG_${pdb}.mol2" ${pdb} "${pdb}.pqr"
- [ -s "${pdb}.pqr" ]
- echo "******** ${pdb} done"
-done
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