Your message dated Thu, 13 Dec 2018 07:53:00 +0000
with message-id <[email protected]>
and subject line Bug#916322: fixed in tvc 5.0.3+git20151221.80e144e+dfsg-2
has caused the Debian Bug report #916322,
regarding tvc: FTBFS with ld --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.
(NB: If you are a system administrator and have no idea what this
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--
916322: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=916322
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-1
Severity: normal
Tags: patch
User: [email protected]
Usertags: origin-ubuntu disco ubuntu-patch
Dear Maintainer,
tvc fails to build from source with ld --as-needed [1], which is enabled by
default in Ubuntu. This is because libsmithwaterman.so requires the
libdisorder library, but ld --as-needed requires that anything needed by
something else comes after it in the linking order. Can you please
change the order in your patch accordingly?
In Ubuntu, the attached patch was applied to achieve the following:
* d/p/debian/patches/use_debian_packaged_smithwaterman.patch: Switch linking
order of smithwaterman and disorder to fix FTBFS with ld --as-needed.
Thanks for considering the patch.
Logan Rosen
[1]
https://launchpad.net/ubuntu/+source/tvc/5.0.3+git20151221.80e144e+dfsg-1/+build/15640108
-- System Information:
Debian Release: buster/sid
APT prefers cosmic-updates
APT policy: (500, 'cosmic-updates'), (500, 'cosmic-security'), (500,
'cosmic'), (400, 'cosmic-proposed'), (100, 'cosmic-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.18.0-12-generic (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
diff -Nru
tvc-5.0.3+git20151221.80e144e+dfsg/debian/patches/use_debian_packaged_smithwaterman.patch
tvc-5.0.3+git20151221.80e144e+dfsg/debian/patches/use_debian_packaged_smithwaterman.patch
---
tvc-5.0.3+git20151221.80e144e+dfsg/debian/patches/use_debian_packaged_smithwaterman.patch
2018-09-27 04:09:12.000000000 -0400
+++
tvc-5.0.3+git20151221.80e144e+dfsg/debian/patches/use_debian_packaged_smithwaterman.patch
2018-12-12 22:57:22.000000000 -0500
@@ -20,7 +20,7 @@
add_executable(tvc ${tvcSRCS})
-target_link_libraries(tvc bamtools z pthread blas lapack armadillo jsoncpp)
-+target_link_libraries(tvc bamtools z pthread blas lapack armadillo jsoncpp
disorder smithwaterman)
++target_link_libraries(tvc bamtools z pthread blas lapack armadillo jsoncpp
smithwaterman disorder)
add_executable(tvcassembly
@@ -36,7 +36,7 @@
)
-target_link_libraries(tvcutils bamtools z jsoncpp)
-+target_link_libraries(tvcutils bamtools z jsoncpp disorder smithwaterman)
++target_link_libraries(tvcutils bamtools z jsoncpp smithwaterman disorder)
install(TARGETS tvc
DESTINATION bin)
install(TARGETS tvcassembly
DESTINATION bin)
--- End Message ---
--- Begin Message ---
Source: tvc
Source-Version: 5.0.3+git20151221.80e144e+dfsg-2
We believe that the bug you reported is fixed in the latest version of
tvc, 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.
Andreas Tille <[email protected]> (supplier of updated tvc 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: SHA256
Format: 1.8
Date: Thu, 13 Dec 2018 08:07:07 +0100
Source: tvc
Binary: tvc
Architecture: source
Version: 5.0.3+git20151221.80e144e+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
tvc - genetic variant caller for Ion Torrent sequencing platforms
Closes: 916322
Changes:
tvc (5.0.3+git20151221.80e144e+dfsg-2) unstable; urgency=medium
.
[ Logan Rosen ]
* Enable build with ld --as-needed
Closes: #916322
.
[ Andreas Tille ]
* Remove trailing whitespace in debian/changelog
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