Your message dated Fri, 02 Mar 2018 13:49:29 +0000
with message-id <e1erl3x-000gqq...@fasolo.debian.org>
and subject line Bug#891750: fixed in comet-ms 2017014-2
has caused the Debian Bug report #891750,
regarding comet-ms: please add libraries to LIBS and not to CXXFLAGS
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 ow...@bugs.debian.org
immediately.)


-- 
891750: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=891750
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: comet-ms
Version: 2017012-1
Severity: normal
tags: patch


Dear maintainer,

Your Makefile has a little typo, that prevents the package from linking 
correctly when wl-asneeded flag is used (because libraries are stripped, since 
the 
.o file are at the bottom of the link line)

please accept this patch, to solve the issue

--- comet-ms-2017012/debian/Makefile    2017-12-03 21:15:46.000000000 +0100
+++ comet-ms-2017012/debian/Makefile    2018-02-28 15:02:03.000000000 +0100
@@ -1,8 +1,9 @@
 CXX = g++
 GCC = gcc

-CXXFLAGS = -g -O3 -Wall -Wextra -Wno-char-subscripts -D_LARGEFILE_SOURCE 
-D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -lpthread 
-lmstoolkitlite
+CXXFLAGS = -g -O3 -Wall -Wextra -Wno-char-subscripts -D_LARGEFILE_SOURCE 
-D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit
 EXECNAME = comet-ms
+LIBS = -lmstoolkitlite -lpthread

 COMETSEARCH = Comet.o Threading.o CometInterfaces.o CometSearch.o 
CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o 
CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o 
CometSearchManager.o


you can also grab the patch from here:
http://launchpadlibrarian.net/358943993/comet-ms_2017012-1_2017012-1ubuntu1.diff.gz

thanks

Gianfranco

Attachment: signature.asc
Description: OpenPGP digital signature


--- End Message ---
--- Begin Message ---
Source: comet-ms
Source-Version: 2017014-2

We believe that the bug you reported is fixed in the latest version of
comet-ms, 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 891...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Filippo Rusconi <lopi...@debian.org> (supplier of updated comet-ms 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 ftpmas...@ftp-master.debian.org)


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

Format: 1.8
Date: Fri, 02 Mar 2018 11:34:35 +0100
Source: comet-ms
Binary: comet-ms
Architecture: source amd64
Version: 2017014-2
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 comet-ms   - Tandem mass spectrometry (MS/MS) search engine
Closes: 891750
Changes:
 comet-ms (2017014-2) unstable; urgency=medium
 .
   * Fix problem with library linking in the Makefile. Thanks to Gianfranco
     Costamagna <locutusofb...@debian.org> for re-reporting that bug
     (Closes: #891750). In fact, he saw that the rules duplicated code and the
     Makefile such that the Makefile did not direct compilation, since that
     compilation was local.
Checksums-Sha1:
 1ca792a0555787f512678a089a0148e67c9f8b42 2053 comet-ms_2017014-2.dsc
 ebc05ba3872266008f4cac1e5f6efe627cc74211 5932 comet-ms_2017014-2.debian.tar.xz
 6a2ddcf80d4fce3e6264232595589e192793e8f0 1046504 
comet-ms-dbgsym_2017014-2_amd64.deb
 91a38933433a55c902aba24967c56eaa71bd1088 6164 
comet-ms_2017014-2_amd64.buildinfo
 886055d2ce6667fe10975c540731afa8b0b2b39b 851548 comet-ms_2017014-2_amd64.deb
Checksums-Sha256:
 203f9a56db6188c52a0216f68a5443f622d3bdb0f77b704cc1068b0cf7ace955 2053 
comet-ms_2017014-2.dsc
 32eeab4f078ec1c553fa1b0974e5d3ee43013f4399b5736c55ad83f49421c708 5932 
comet-ms_2017014-2.debian.tar.xz
 e2777870c86c44cdca65eab404abc1f0482ab3e72fdb88c4f8c01c6d8ff9e9f6 1046504 
comet-ms-dbgsym_2017014-2_amd64.deb
 8c246319d98beb3be96d052becc83bb66f7edfa9e9a000a5ee3ac027d78432b6 6164 
comet-ms_2017014-2_amd64.buildinfo
 bb575ea348a15b50383b8a87333dc12bed5b01b74169883a9abe42d153585ac6 851548 
comet-ms_2017014-2_amd64.deb
Files:
 abaac9e7bb4aa88837accafd502d5b0c 2053 science optional comet-ms_2017014-2.dsc
 086b457d119e6bbed2af2b9d26214605 5932 science optional 
comet-ms_2017014-2.debian.tar.xz
 0e7b3b76636ed2267dca18c74d81c442 1046504 debug optional 
comet-ms-dbgsym_2017014-2_amd64.deb
 5099beb29065acf731596b0c086c89a6 6164 science optional 
comet-ms_2017014-2_amd64.buildinfo
 1389255c5be9fcb09d5dd2f545ad4229 851548 science optional 
comet-ms_2017014-2_amd64.deb

-----BEGIN PGP SIGNATURE-----
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=Qbc3
-----END PGP SIGNATURE-----

--- End Message ---

Reply via email to