Your message dated Tue, 04 Jun 2019 17:30:00 +0000
with message-id <[email protected]>
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
929924: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=929924
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: release.debian.org
Severity: normal
User: [email protected]
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 <[email protected]> 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 ${AUTOPKGTEST_TMP}/output.txt ]
diff -Nru pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test
pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test
--- pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test 2018-07-14
16:09:27.000000000 +0200
+++ pdb2pqr-2.1.1+dfsg/debian/tests/ligands-test 1970-01-01
02:00:00.000000000 +0200
@@ -1,33 +0,0 @@
-#!/bin/sh
-# autopkgtest check: build and run with default test data
-# Author: Tatiana Malygina <[email protected]>
-
-set -e
-
-pkg=pdb2pqr
-example_pkg=pdb2pqr
-
-if [ "$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: [email protected]
> 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 ---
