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.org
diff -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>
