Summary: | dev-perl/Bio-DB-HTS-2.10: htslib detection fails on SYMLINK_LIB=no systems | ||
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Product: | Gentoo Linux | Reporter: | Kent Fredric (IRC: kent\n) (RETIRED) <kentnl> |
Component: | Current packages | Assignee: | Marek Szuba <marecki> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | perl, sci-biology |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- |
Description
Kent Fredric (IRC: kent\n) (RETIRED)
2018-05-01 03:09:08 UTC
Following a discussion on IRC, it turns out Kent uses a profile with SYMLINK_LIB disabled. Considering upstream build script always looks for htslib.a in *lib*, it is not surprising this fails. I'll come up with a workaround but in general, this really should be addressed upstream. Furtheremore, there is now a dependency on sci-biology/bioperl. The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f7bdf03a3823e8156f7e31aea55948702f4882e2 commit f7bdf03a3823e8156f7e31aea55948702f4882e2 Author: Marek Szuba <marecki@gentoo.org> AuthorDate: 2018-05-01 08:45:02 +0000 Commit: Marek Szuba <marecki@gentoo.org> CommitDate: 2018-05-01 08:45:33 +0000 dev-perl/Bio-DB-HTS: allow explicit specification of htslib directories Upstream build script takes a single directory as htslib prefix, then appends "include/htslib" while looking for header files and "lib" while looking for library. Unsurprisingly, the latter fails to locate the htslib library on SYMLINK_LIB=no systems. I have patched the build script to allow both htslib-includedir and htslib-libdir to be provided explicitly, thus letting the ebuild take care of choosing the correct libdir name for the specified architecture/ABI. Closes: https://bugs.gentoo.org/654460 Package-Manager: Portage-2.3.24, Repoman-2.3.6 dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild | 3 +- .../files/2.10-build_split_htslib_opts.patch | 48 ++++++++++++++++++++++ 2 files changed, 50 insertions(+), 1 deletion(-) |