[Debian-med-packaging] Bug#728190: autopkgtest fails due to stderr output

[Martin Pitt]

Package: mafft
Version: 7.123-1
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu ubuntu-patch trusty

Hello,

Thanks for adding an autopkgtest to mafft! However, it currently fails
as it routinely writes stderr output which autopkgtest considers as
failure (unless you use the "allow-stderr" restriction):

| /tmp/mafft-7.123 $ adt-run --no-built-binaries ./ --- adt-virt-schroot sid
| [...]
| adt-run: & tree0t-with-example-data:  - - - - - - - - - - results - - - - - - - - - -
| tree0t-with-example-data FAIL status: 0, stderr: 
| adt-run: & tree0t-with-example-data:  - - - - - - - - - - stderr - - - - - - - - - -
| 
| nseq =  36
| distance =  local
| [...]

The attached patch is one proposal to route the progress output to a
temporary file and only write it to stderr if the test fails (to give
some details why it fails).

Thanks for considering,

Martin

-- 
Martin Pitt                        | http://www.piware.de
Ubuntu Developer (www.ubuntu.com)  | Debian Developer  (www.debian.org)
-------------- next part --------------
diff -Nru mafft-7.123/debian/changelog mafft-7.123/debian/changelog
--- mafft-7.123/debian/changelog	2013-10-16 01:22:22.000000000 +0200
+++ mafft-7.123/debian/changelog	2013-10-29 11:29:49.000000000 +0100
@@ -1,3 +1,9 @@
+mafft (7.123-1ubuntu1) trusty; urgency=low
+
+  * debian/tests/with-example-data: Don't write progress to stderr on success.
+
+ -- Martin Pitt <martin.pitt at ubuntu.com>  Tue, 29 Oct 2013 11:29:22 +0100
+
 mafft (7.123-1) unstable; urgency=low
 
   * New upstream version.
diff -Nru mafft-7.123/debian/tests/with-example-data mafft-7.123/debian/tests/with-example-data
--- mafft-7.123/debian/tests/with-example-data	2013-10-14 03:29:28.000000000 +0200
+++ mafft-7.123/debian/tests/with-example-data	2013-10-29 11:29:15.000000000 +0100
@@ -3,9 +3,11 @@
 MAFFT="mafft --thread 0"
 TESTDATADIR=/usr/share/doc/mafft/test/
 
-$MAFFT                               $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftns2 -
-$MAFFT --maxiterate 100              $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftnsi -
-$MAFFT --globalpair                  $TESTDATADIR/sample | diff $TESTDATADIR/sample.gins1 -
-$MAFFT --globalpair --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.ginsi -
-$MAFFT --localpair                   $TESTDATADIR/sample | diff $TESTDATADIR/sample.lins1 -
-$MAFFT --localpair --maxiterate 100  $TESTDATADIR/sample | diff $TESTDATADIR/sample.linsi -
+PF=$ADTTMP/progress
+
+$MAFFT --progress $PF                               $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftns2 - || cat $PF >&2
+$MAFFT --progress $PF --maxiterate 100              $TESTDATADIR/sample | diff $TESTDATADIR/sample.fftnsi - || cat $PF >&2
+$MAFFT --progress $PF --globalpair                  $TESTDATADIR/sample | diff $TESTDATADIR/sample.gins1 - || cat $PF >&2
+$MAFFT --progress $PF --globalpair --maxiterate 100 $TESTDATADIR/sample | diff $TESTDATADIR/sample.ginsi - || cat $PF >&2
+$MAFFT --progress $PF --localpair                   $TESTDATADIR/sample | diff $TESTDATADIR/sample.lins1 - || cat $PF >&2
+$MAFFT --progress $PF --localpair --maxiterate 100  $TESTDATADIR/sample | diff $TESTDATADIR/sample.linsi - || cat $PF >&2