Your message dated Tue, 10 Apr 2018 08:00:55 +0000 with message-id <e1f5od1-0002it...@fasolo.debian.org> and subject line Bug#895344: fixed in psortb 3.0.5+dfsg-2 has caused the Debian Bug report #895344, regarding psortb: build compatibility 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. (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.) -- 895344: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=895344 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: psortb Version: 3.0.5+dfsg-1 Severity: minor Tags: patch User: ubuntu-de...@lists.ubuntu.com Usertags: origin-ubuntu bionic ubuntu-patch Dear maintainers, The psortb package has been failing to build in Ubuntu because it supplies options to the linker in the wrong order: [...] x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/psortb-3.0.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functi ons -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong S VMLoc.o -o ../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so \ -lm -lsvm -lstdc++ -L/usr/local/lib -lsvmloc \ [...] PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "- e" "undef *Test::Harness::Switches; test_harness(1, '../blib/lib', '../blib/arch ')" t/*.t # Failed test 'use Bio::Tools::PSort::SVMLoc;' # at t/svmloc.t line 11. # Tried to use 'Bio::Tools::PSort::SVMLoc'. # Error: Can't load '/<<BUILDDIR>>/psortb-3.0.5+dfsg/bio-tools-psort-svmloc /../blib/arch/auto/Bio/Tools/PSort/SVMLoc/SVMLoc.so' for module Bio::Tools::PSor t::SVMLoc: /usr/lib/x86_64-linux-gnu/libsvmloc.so.0: undefined symbol: svm_predi ct at /usr/lib/x86_64-linux-gnu/perl/5.26/DynaLoader.pm line 187. # ^@ at t/svmloc.t line 11. # Compilation failed in require at t/svmloc.t line 11. # BEGIN failed--compilation aborted at t/svmloc.t line 11. [...] (https://launchpad.net/ubuntu/+source/psortb/3.0.5+dfsg-1) Per <https://wiki.ubuntu.com/ToolChain/CompilerFlags#A-Wl.2C--as-needed>, libraries must be passed on the commandline after the objects which reference them, otherwise they will be discarded by the linker, resulting in errors such as the above. I have uploaded the attached patch to psortb in Ubuntu. Please consider applying it in Debian as well. -- 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.orgdiff -Nru psortb-3.0.5+dfsg/debian/patches/remove-bundled-party-libsvm.patch psortb-3.0.5+dfsg/debian/patches/remove-bundled-party-libsvm.patch --- psortb-3.0.5+dfsg/debian/patches/remove-bundled-party-libsvm.patch 2018-02-20 09:25:29.000000000 -0800 +++ psortb-3.0.5+dfsg/debian/patches/remove-bundled-party-libsvm.patch 2018-04-09 23:09:22.000000000 -0700 @@ -1,17 +1,23 @@ Description: Remove source from bundled libsvm and adjust build system. Author: Carnë Draug <carandraug+...@gmail.com> -Last-Update: 2017-04-20 ---- a/bio-tools-psort-svmloc/MANIFEST -+++ b/bio-tools-psort-svmloc/MANIFEST -@@ -8,5 +8,4 @@ bindings.h +Author: Steve Langasek <steve.langa...@ubuntu.com> +Last-Update: 2018-04-09 + +Index: psortb-3.0.5+dfsg/bio-tools-psort-svmloc/MANIFEST +=================================================================== +--- psortb-3.0.5+dfsg.orig/bio-tools-psort-svmloc/MANIFEST ++++ psortb-3.0.5+dfsg/bio-tools-psort-svmloc/MANIFEST +@@ -8,5 +8,4 @@ lib/Bio/Tools/PSort/SVMLoc.pm sample.model fre_patterns.txt -libsvm.h typemap ---- a/bio-tools-psort-svmloc/Makefile.PL -+++ b/bio-tools-psort-svmloc/Makefile.PL -@@ -9,7 +9,7 @@ $CC = 'g++'; +Index: psortb-3.0.5+dfsg/bio-tools-psort-svmloc/Makefile.PL +=================================================================== +--- psortb-3.0.5+dfsg.orig/bio-tools-psort-svmloc/Makefile.PL ++++ psortb-3.0.5+dfsg/bio-tools-psort-svmloc/Makefile.PL +@@ -9,7 +9,7 @@ @libs = qw/svmloc/; %paths = (); @@ -20,8 +26,19 @@ $defaults_file = '../psortb.defaults'; if( -f $defaults_file ) { ---- a/bio-tools-psort-svmloc/bindings.h -+++ b/bio-tools-psort-svmloc/bindings.h +@@ -24,7 +24,7 @@ + if($additional_libpath) { + $libpath .= ' ' . $additional_libpath . ' ' . join(' ', map { '-l' . $_ } @libs); + } else { +- $libpath .= Bio::Tools::PSort::Install->makeLibPath(@libs); ++ $libpath = Bio::Tools::PSort::Install->makeLibPath(@libs) . " " . $libpath; + } + + if($^O eq 'cygwin') { +Index: psortb-3.0.5+dfsg/bio-tools-psort-svmloc/bindings.h +=================================================================== +--- psortb-3.0.5+dfsg.orig/bio-tools-psort-svmloc/bindings.h ++++ psortb-3.0.5+dfsg/bio-tools-psort-svmloc/bindings.h @@ -9,7 +9,9 @@ #include <set> #include <assert.h>
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--- Begin Message ---Source: psortb Source-Version: 3.0.5+dfsg-2 We believe that the bug you reported is fixed in the latest version of psortb, 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 895...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated psortb 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: Tue, 10 Apr 2018 09:01:11 +0200 Source: psortb Binary: psortb Architecture: source Version: 3.0.5+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: psortb - bacterial localization prediction tool Closes: 895344 Changes: psortb (3.0.5+dfsg-2) unstable; urgency=medium . [ Steve Langasek ] * Enable build with -Wl, --as-needed Closes: #895344 . [ Andreas Tille ] * Standards-Version: 4.1.4 * Point Vcs fields to salsa.debian.org Checksums-Sha1: 7efab19992fa87420b3632e69591bc5478105838 2090 psortb_3.0.5+dfsg-2.dsc 04c8c9dc24c2f02ee4aa7c4ab7da85b2f10c3c38 6320 psortb_3.0.5+dfsg-2.debian.tar.xz Checksums-Sha256: 6340548bc2b2a855d7a0ca3d281a5ffdcad4d0df900f86fd86a39d851237b90d 2090 psortb_3.0.5+dfsg-2.dsc d5dda1e7a00e26c3f498e8ea3c5fa5e6a8d1940126cbd85b5f82b2b45b078a01 6320 psortb_3.0.5+dfsg-2.debian.tar.xz Files: 0abddb68cc50bf4f18de2f4eb1eb27d2 2090 science optional psortb_3.0.5+dfsg-2.dsc 4e87d447f1bd6ab46fb7df056bd765cb 6320 science optional psortb_3.0.5+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlrMZHQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH7aA/+PCfMl0+EBnNAlxnq0DrDALk9raN0pm4p ou5FTLQ4aKF+bVOdaZMqXXgxTMKpYW9/dfIh4fSJyyTr3ThpUsYMpR+NlzA2tlCV bdXACaQc/k+1RgF1Vo0S3GuYJbMPp9Dh2MdVEyyujMrQe30kVw1FC8mwKOFHyYOK KtGPYW4P2ijpgDHCFd9mQYGy5nqL1sXzKhq85SAco/26fyqEgwq8Jd/8vaDlF55M U/XhkAun8lDHefttKl1JSnX0pAzlZ7kxNAWZSPEcgL/UlH7TO+v622/GdfjTeVBf 48n2mGVB+Etpdm3GE+owBVGGAkZzCvXpDvOfOY3BFgbyoH2JcUBi7HIWpytt57Dp 4AjJH05WoF4SXzzPWPUTLh/ET/cV8zMv0BIhtuxDL3QtUBFx4lpPjn7KvIt/bWmf 5G9TGC0QNUMCELS5PitvUn6TfpJsPJx9OmvY4CDwZX81K0umtpRc5RZzeXKE8dJl 3x0rur+dGIVDpdatLiAQNn2Nv8Uhv7VP0Ao9AMmJjVWZvK30e2DpyxyRw8hFavkR iO8/5q8bw0UD0n5xNPIJgI6VtMIMoPconY9ZjuSJdAEWw0A466y0OzhOMliwliU1 Sn2gksVd9EkhR71Y/dxfSUvIXiGnvpZrpkA8SRRKlzMY9I3lOP13Mw432meDOqQn T4MBdY5fxIA= =OY2J -----END PGP SIGNATURE-----
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