| Subject: | Patch to resolve clinker on Ubuntu |
Hi Lincoln,
Please see below for a patch that resolves installation issues when installing under Ubuntu (precise, and probably others).
The issue is seen with the following errors during installation:
t/01.bigwig.t ....... Can't load '.../.cpan/build/Bio-BigFile-1.07-LEz6Mw/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so' for module Bio::DB::BigFile: .../.cpan/build/Bio-BigFile-1.07-LEz6Mw/t/../blib/arch/auto/Bio/DB/BigFile/BigFile.so: undefined symbol: pthread_detach at /software/perl-5.16.2/lib/5.16.2/x86_64-linux/DynaLoader.pm line 190.
Patch to resolve:
--- Build.PL.orig 2013-07-25 10:51:33.862829348 +0100
+++ Build.PL 2013-07-25 10:46:08.225179802 +0100
@@ -16,7 +16,7 @@
dist_abstract => "Manipulate Jim Kent's BigWig and BigBed index files for genomic features.",
license => 'perl',
include_dirs => [$jk_include],
- extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl'],
+ extra_linker_flags => ["$jk_lib/$LibFile",'-lz','-lssl', '-lpthread'],
extra_compiler_flags=>[
# turn off warnings originating in Perl's Newx* calls