Your message dated Sun, 23 Oct 2016 23:32:21 +0000
with message-id <e1bysfz-0002bo...@franck.debian.org>
and subject line Bug#841671: fixed in pbbam 0.5.0-3
has caused the Debian Bug report #841671,
regarding pbbam: Fix for building with -Wl,--as-needed
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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--
841671: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=841671
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: pbbam
Version: 0.5.0-2
Severity: normal
Tags: patch
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu zesty ubuntu-patch
Hi Afif,
In Ubuntu, pbbam was failing to build because when linking libpbbam.so, the
library arguments were listed on the commandline before the objects being
linked. Ubuntu uses -Wl,--as-needed in its linker arguments, which causes
libraries that aren't used to be ignored; and so libraries listed before the
objects that use them are not linked against.
You can read more about this behavior here:
https://wiki.ubuntu.com/ToolChain/CompilerFlags#Flags_passed_to_the_linker
I've applied a small patch in Ubuntu to fix this, with the following
changelog explanation:
* debian/rules: fix cmake arguments so that library arguments are in the
right order for -Wl,--as-needed.
While Debian does not currently use -Wl,--as-needed by default and this is
not a build issue in Debian, applying this patch will make your package more
portable in general. Please consider applying it.
Thanks,
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer http://www.debian.org/
slanga...@ubuntu.com vor...@debian.org
diff -Nru pbbam-0.5.0/debian/rules pbbam-0.5.0/debian/rules
--- pbbam-0.5.0/debian/rules 2016-07-05 02:49:29.000000000 -0700
+++ pbbam-0.5.0/debian/rules 2016-10-21 16:16:40.000000000 -0700
@@ -16,8 +16,8 @@
-DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \
-DCMAKE_SKIP_RPATH=ON \
-DHTSLIB_INCLUDE_DIRS=/usr/include \
- -DHTSLIB_LIBRARIES=/usr/lib \
- -DCMAKE_SHARED_LINKER_FLAGS="-lssl -lhts $(LDFLAGS)"
+ -DHTSLIB_LIBRARIES="-lssl -lcrypto -lhts" \
+ -DCMAKE_SHARED_LINKER_FLAGS="$(LDFLAGS)"
# -DPacBioBAM_wrap_python=ON \
# -DPacBioBAM_wrap_r=ON
--- End Message ---
--- Begin Message ---
Source: pbbam
Source-Version: 0.5.0-3
We believe that the bug you reported is fixed in the latest version of
pbbam, 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 841...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Afif Elghraoui <a...@debian.org> (supplier of updated pbbam 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: Sun, 23 Oct 2016 14:07:27 -0700
Source: pbbam
Binary: pbbamtools libpbbam libpbbam-dev
Architecture: source
Version: 0.5.0-3
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
libpbbam - Pacific Biosciences binary alignment/map (BAM) library
libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers)
pbbamtools - processing Pacific Biosciences binary alignment/map files
Closes: 841671
Changes:
pbbam (0.5.0-3) unstable; urgency=low
.
* Fix cmake arguments to properly position LDFLAGS for -Wl,--as-needed.
Thanks to Steve Langasek (Closes: #841671)
Checksums-Sha1:
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643b1a6d8e8872db21ccfaee85487e1a40e2ef39 6752 pbbam_0.5.0-3.debian.tar.xz
Checksums-Sha256:
499ff32bae95bbc05e132b29862077fa00bf93c9753e3904da2264e549563f8e 2134
pbbam_0.5.0-3.dsc
fcb61c07854e32783b900733cee8f7271246a0eb0ff9107aaee4a85733eae28c 6752
pbbam_0.5.0-3.debian.tar.xz
Files:
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005014db70c061c975c6f41988da2310 6752 libs optional pbbam_0.5.0-3.debian.tar.xz
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