>>> Emerging (3 of 20) dev-perl/Bio-SamTools-1.420.0::gentoo * Bio-SamTools-1.42.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking Bio-SamTools-1.42.tar.gz to /apps/gentoo/var/tmp/portage/dev-perl/Bio-SamTools-1.420.0/work >>> Source unpacked in /apps/gentoo/var/tmp/portage/dev-perl/Bio-SamTools-1.420.0/work >>> Preparing source in /apps/gentoo/var/tmp/portage/dev-perl/Bio-SamTools-1.420.0/work/Bio-SamTools-1.42 ... * Applying Bio-SamTools-1.390.0-samtools-1.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /apps/gentoo/var/tmp/portage/dev-perl/Bio-SamTools-1.420.0/work/Bio-SamTools-1.42 ... * Using Module::Build * perl Build.PL --installdirs=vendor --libdoc= --destdir=/apps/gentoo/var/tmp/portage/dev-perl/Bio-SamTools-1.420.0/image/ --create_packlist=1 This module requires samtools 0.1.10 or higher (samtools.sourceforge.net). Please enter the location of the bam.h and compiled libbam.a files: Huh? Probably: ${EPREFIX}/usr/include/bam-0.1-legacy/ ${EPREFIX}/usr/lib64/libbam-0.1-legacy.so
sci-biology/samtools doe snot provided a static libbam.a but only libbam.so. Bio-SamTools needs a fix to use the any "-lbam" library.
Bug has been closed via the following commit: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=29bb345f1ea0a356c7e7e4eca3ab3bc405a7d846 commit 29bb345f1ea0a356c7e7e4eca3ab3bc405a7d846 Author: Kent Fredric <kentnl@gentoo.org> AuthorDate: 2017-09-10 03:20:29 +0000 Commit: Kent Fredric <kentnl@gentoo.org> CommitDate: 2017-09-10 03:22:39 +0000 dev-perl/Bio-SamTools: Bump to version 1.430.0 - Links against samtools:0.1-legacy series, as even though this code previously attempted to use 1.0+, closer inspection indicated incomplete linking, missing symbols, and failing tests introduced by this attempt. Additionally, upstream EXPLICITLY STATE the lack of current support for samtools 1.0 - Restores DIST_TEST as I can now test they work - Fold swathe of sed commands into patch Upstream: - Ship some test files requried for tests to pass Closes: https://bugs.gentoo.org/611970 Closes: https://bugs.gentoo.org/604950 Package-Manager: Portage-2.3.6, Repoman-2.3.2 dev-perl/Bio-SamTools/Bio-SamTools-1.430.0.ebuild | 33 ++++++++ dev-perl/Bio-SamTools/Manifest | 1 + .../files/Bio-SamTools-1.430.0-legacy.patch | 88 ++++++++++++++++++++++ 3 files changed, 122 insertions(+)
