Bug#891750: marked as done (comet-ms: please add libraries to LIBS and not to CXXFLAGS)

2018-03-02 Thread Debian Bug Tracking System 
Your message dated Fri, 02 Mar 2018 13:49:29 +
with message-id 
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/Makefile2017-12-03 21:15:46.0 +0100
+++ comet-ms-2017012/debian/Makefile2018-02-28 15:02:03.0 +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



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  (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 
Changed-By: Filippo Rusconi 
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  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.
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Files:
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Bug#891750: marked as done (comet-ms: please add libraries to LIBS and not to CXXFLAGS)

2018-03-01 Thread Debian Bug Tracking System 
Your message dated Thu, 01 Mar 2018 12:19:29 +
with message-id 
and subject line Bug#891750: fixed in comet-ms 2017014-1
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/Makefile2017-12-03 21:15:46.0 +0100
+++ comet-ms-2017012/debian/Makefile2018-02-28 15:02:03.0 +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



signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: comet-ms
Source-Version: 2017014-1

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  (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: Thu, 01 Mar 2018 11:37:59 +0100
Source: comet-ms
Binary: comet-ms
Architecture: source amd64
Version: 2017014-1
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 comet-ms   - Tandem mass spectrometry (MS/MS) search engine
Closes: 891750
Changes:
 comet-ms (2017014-1) unstable; urgency=medium
 .
   * New upstream version.
 .
   * Updated the patch that modifies the two Makefile_s such that
 libmstoolkitlite is used from the Debian package. Tested the comet-ms
 binary ok.
 .
   * Fix problem with library linking in the Makefile. Thanks to Gianfranco
 Costamagna  for reporting that bug
 (Closes: #891750).
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Files: