[Debian-med-packaging] Bug#916322: tvc: FTBFS with ld --as-needed

[Logan Rosen]

Package: tvc
Version: 5.0.3+git20151221.80e144e+dfsg-1
Severity: normal
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
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
-------------- next part --------------
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)