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Bug#929924: marked as done (unblock: pdb2pqr/2.1.1+dfsg-5)

Your message dated Tue, 04 Jun 2019 17:30:00 +0000
with message-id <617f759e-2352-eab6-ae4e-66426e508043@thykier.net>
and subject line Re: Bug#929924: unblock: pdb2pqr/2.1.1+dfsg-5
has caused the Debian Bug report #929924,
regarding unblock: pdb2pqr/2.1.1+dfsg-5
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

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-- 
929924: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=929924
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
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

--- End Message ---
--- Begin Message --- 
Graham Inggs:
> 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/

Unblocked, thanks.
~Niels

--- End Message ---
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