[Debian-med-packaging] Bug#890993: fixed in primer3 2.4.0-2

[Gianfranco Costamagna]

Hello, can you please apply the same on autopkgtests? now autopkgtests failures are considered RC buggy

something like this might work:

--- primer3-2.4.0/debian/changelog	2018-05-28 15:44:30.000000000 +0200
+++ primer3-2.4.0/debian/changelog	2020-06-04 11:47:04.000000000 +0200
@@ -1,3 +1,9 @@
+primer3 (2.4.0-2ubuntu1) groovy; urgency=medium
+
+  * Also skip autopkgtests that fail on big endian (see: 890993)
+
+ -- Gianfranco Costamagna <locutusofborg at debian.org>  Thu, 04 Jun 2020 11:47:04 +0200
+
 primer3 (2.4.0-2) unstable; urgency=medium
 
   [ Liubov Chuprikova ]
diff -Nru primer3-2.4.0/debian/tests/run-unit-test primer3-2.4.0/debian/tests/run-unit-test
--- primer3-2.4.0/debian/tests/run-unit-test	2018-05-28 15:44:30.000000000 +0200
+++ primer3-2.4.0/debian/tests/run-unit-test	2020-06-04 11:47:04.000000000 +0200
@@ -8,6 +8,13 @@
   AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
 
+BUILDARCH=$(dpkg-architecture -q DEB_BUILD_ARCH_ENDIAN)
+
+P3CORE_FAILED_TESTS='primer_masker' \
+             'primer_masker_formatted'
+
+FAILED_TESTS=testmasker
+
 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
 cd $AUTOPKGTEST_TMP
@@ -19,6 +26,16 @@
 ln -s /usr/bin/ntthal ./src/ntthal
 ln -s /usr/bin/oligotm ./src/oligotm
 
+if [ $BUILDARCH = big ]; then
+  cp -a test/p3test.pl test/p3test.pl~
+  cp -a test/Makefile test/Makefile~
+  # exclude tests known to fail on big endian
+  # See README.source for further explanation.
+  for tst in $(P3CORE_FAILED_TESTS) ; do sed -i "/$${tst}/d" test/p3test.pl ; done
+  sed -i "0,/$(FAILED_TESTS)/s///" test/Makefile
+  sed -i "/$(FAILED_TESTS)/,/endif/d" test/Makefile
+fi
+
 cd test/;
 
 echo "testcmdline:"
@@ -36,4 +53,12 @@
 echo "testtm:"
 perl oligotm_test.pl ${TESTOPTS}
 
+cd ..
+
+if [ $BUILDARCH = big ]; then
+  # restore original test file
+  mv test/p3test.pl~ test/p3test.pl
+  mv test/Makefile~ test/Makefile
+fi
+
 echo "PASS"


On Tue, 29 May 2018 17:36:48 +0000 Liubov Chuprikova <chuprikovalv at gmail.com> wrote:
> Source: primer3
> Source-Version: 2.4.0-2
>
> We believe that the bug you reported is fixed in the latest version of
> primer3, which is due to be installed in the Debian FTP archive.
>
> A summary of the changes between this version and the previous one is
> attached.
>
> Thank you for reporting the bug, which will now be closed.  If you
> have further comments please address them to 890993 at bugs.debian.org,
> and the maintainer will reopen the bug report if appropriate.
>
> Debian distribution maintenance software
> pp.
> Liubov Chuprikova <chuprikovalv at gmail.com> (supplier of updated primer3 package)
>
> (This message was generated automatically at their request; if you
> believe that there is a problem with it please contact the archive
> administrators by mailing ftpmaster at ftp-master.debian.org)
>
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA512
>
> Format: 1.8
> Date: Mon, 28 May 2018 13:44:30 +0000
> Source: primer3
> Binary: primer3 primer3-examples
> Architecture: source
> Version: 2.4.0-2
> Distribution: unstable
> Urgency: medium
> Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
> Changed-By: Liubov Chuprikova <chuprikovalv at gmail.com>
> Description:
>  primer3    - tool to design flanking oligo nucleotides for DNA amplification
>  primer3-examples - tool to design flanking oligo nucleotides for DNA amplification (
> Closes: 890993
> Changes:
>  primer3 (2.4.0-2) unstable; urgency=medium
>  .
>    [ Liubov Chuprikova ]
>    * Team upload.
>    * Skip tests that fail on big endian
>      Closes: #890993
>    * Added d/README.source with explanation why some tests are skipped
>    * debian/patches/p3test_fix_exit_status.patch: Fix test to show correct exit
>      status
>  .
>    [ Andreas Tille ]
>    * Point Vcs fields to salsa.debian.org
>    * Standards-Version: 4.1.4
> Checksums-Sha1:
>  ed7288049fca41a312d5d528d3e57e0b51be9bdc 2117 primer3_2.4.0-2.dsc
>  9d7f7874ef42796bd45181a610ad4d2d9193ef02 12060 primer3_2.4.0-2.debian.tar.xz
>  60fe57fc774ab8b537785d4c6d07e54647aabd70 5964 primer3_2.4.0-2_amd64.buildinfo
> Checksums-Sha256:
>  541ec07c9092995dd359620326630c45135321868ee2c2350ef61e1d4d67628d 2117 primer3_2.4.0-2.dsc
>  96247e4223393e0056a8886209b1bb37abfa7dc7fb00eca4e3e695daf62dd71e 12060 primer3_2.4.0-2.debian.tar.xz