Your message dated Sat, 30 Nov 2013 09:22:20 +0000
with message-id <[email protected]>
and subject line Bug#728190: fixed in mafft 7.127-1
has caused the Debian Bug report #728190,
regarding autopkgtest fails due to stderr output
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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--
728190: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=728190
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: mafft
Version: 7.123-1
Tags: patch
User: [email protected]
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)
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 <[email protected]> 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
--- End Message ---
--- Begin Message ---
Source: mafft
Source-Version: 7.127-1
We believe that the bug you reported is fixed in the latest version of
mafft, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <[email protected]> (supplier of updated mafft 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 30 Nov 2013 17:30:14 +0900
Source: mafft
Binary: mafft
Architecture: source amd64
Version: 7.127-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Charles Plessy <[email protected]>
Description:
mafft - Multiple alignment program for amino acid or nucleotide sequences
Closes: 728190
Changes:
mafft (7.127-1) unstable; urgency=low
.
* New upstream release.
* debian/tests/with-example-data: Don't write progress to stderr on success.
Closes: #728190, thanks to Martin Pitt <[email protected]>.
* Conforms with Policy 3.9.5.
* Pass CPPFLAGS within CFLAGS.
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