878333">

Debian Bug report logs - #878333
tree-puzzle: frequent parallel FTBFS

version graph

Package: src:tree-puzzle; Maintainer for src:tree-puzzle is Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>;

Reported by: Adrian Bunk <bunk@debian.org>

Date: Thu, 12 Oct 2017 22:09:01 UTC

Severity: important

Tags: patch

Found in version tree-puzzle/5.2-9

Fixed in version tree-puzzle/5.2-10

Done: Andreas Tille <tille@debian.org>

Bug is archived. No further changes may be made.

View this report as an mbox folder, status mbox, maintainer mbox


Report forwarded to debian-bugs-dist@lists.debian.org, Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#878333; Package src:tree-puzzle. (Thu, 12 Oct 2017 22:09:03 GMT) (full text, mbox, link).


Acknowledgement sent to Adrian Bunk <bunk@debian.org>:
New Bug report received and forwarded. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>. (Thu, 12 Oct 2017 22:09:03 GMT) (full text, mbox, link).


Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Adrian Bunk <bunk@debian.org>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: tree-puzzle: frequent parallel FTBFS
Date: Fri, 13 Oct 2017 01:04:23 +0300
Source: tree-puzzle
Version: 5.2-9
Severity: important
Tags: patch

dh compat 10 defaults to parallel building, which frequently
causes FTBFS like:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/tree-puzzle.html

...
gcc  -DHAVE_CONFIG_H -I. -I.. -I.  -Wdate-time -D_FORTIFY_SOURCE=2   -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -c ./gamma.c && mv gamma.o sgamma.o
...
/usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I.  -Wdate-time -D_FORTIFY_SOURCE=2   -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -c ./gamma.c && mv gamma.o pgamma.o
...
/usr/bin/mpicc -DPARALLEL -DHAVE_CONFIG_H -I. -I.. -I.  -Wdate-time -D_FORTIFY_SOURCE=2   -g -O2 -fstack-protector-strong -Wformat -Werror=format-security  -c ./ml2.c && mv ml2.o pml2.o
mv: cannot stat 'gamma.o': No such file or directory
Makefile:716: recipe for target 'sgamma.o' failed
make[3]: *** [sgamma.o] Error 1


That's the same intermediate file twice built and then moved.

The following works around the issue by going back to the
dh compat < 10 default of non-parallel building:

--- debian/rules.old	2017-10-12 22:02:15.000000000 +0000
+++ debian/rules	2017-10-12 22:02:31.000000000 +0000
@@ -8,7 +8,7 @@
 ppkg:=tree-ppuzzle
 
 %:
-	dh $@
+	dh $@ --no-parallel
 
 override_dh_compress:
 	dh_compress --exclude=.pdf --exclude .phy --exclude trees --exclude .b



Reply sent to Andreas Tille <tille@debian.org>:
You have taken responsibility. (Fri, 13 Oct 2017 06:06:03 GMT) (full text, mbox, link).


Notification sent to Adrian Bunk <bunk@debian.org>:
Bug acknowledged by developer. (Fri, 13 Oct 2017 06:06:03 GMT) (full text, mbox, link).


Message #10 received at 878333-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>
To: 878333-close@bugs.debian.org
Subject: Bug#878333: fixed in tree-puzzle 5.2-10
Date: Fri, 13 Oct 2017 06:03:40 +0000
Source: tree-puzzle
Source-Version: 5.2-10

We believe that the bug you reported is fixed in the latest version of
tree-puzzle, 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 878333@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated tree-puzzle 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@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Fri, 13 Oct 2017 07:48:35 +0200
Source: tree-puzzle
Binary: tree-puzzle tree-ppuzzle tree-puzzle-doc
Architecture: source
Version: 5.2-10
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 tree-ppuzzle - Parallelized reconstruction of phylogenetic trees by maximum like
 tree-puzzle - Reconstruction of phylogenetic trees by maximum likelihood
 tree-puzzle-doc - Reconstruction of phylogenetic trees by maximum likelihood (doc)
Closes: 878333
Changes:
 tree-puzzle (5.2-10) unstable; urgency=medium
 .
   * Do not try parallel builds
     Closes: #878333
Checksums-Sha1:
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 347f058d9d9c2eec73ea7bf6f859bad3d98c316a 65552 tree-puzzle_5.2-10.debian.tar.xz
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 d96dbc95c70ead9ac622eb47a5b08ee1866bfbb840d5596e39045628551cabea 65552 tree-puzzle_5.2-10.debian.tar.xz
Files:
 789ce4114f1f16ef3a63210334f9ac6b 2157 science optional tree-puzzle_5.2-10.dsc
 d1183e824918baf74ddb43585b5e2c0c 65552 science optional tree-puzzle_5.2-10.debian.tar.xz

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Bug archived. Request was from Debbugs Internal Request <owner@bugs.debian.org> to internal_control@bugs.debian.org. (Wed, 15 Nov 2017 07:28:11 GMT) (full text, mbox, link).


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