>>> Configuring source in /var/tmp/portage/dev-perl/Bio-DB-HTS-2.10/work/Bio-DB-HTS-2.10 ... * Using Module::Build * perl Build.PL --installdirs=vendor --libdoc= --destdir=/var/tmp/portage/dev-perl/Bio-DB-HTS-2.10/image/ --create_packlist=1 --htslib=/usr Checking prerequisites... requires: ! Bio::Root::Version is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. --htslib '/usr' command line parameter does not contain expected files This module requires htslib (http://htslib/org) Install it if you have not done so already. This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in: 1. --htslib command line argument 2. HTSLIB_DIR environment variable 3. --prefix command line argument (which also sets installation location) 4. Alien::HTSlib dependency resolver 5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable) 6. common library locations: /usr /usr/local, /usr/share, /opt/local * ERROR: dev-perl/Bio-DB-HTS-2.10::gentoo failed (configure phase): * Unable to build! * * Call stack: * ebuild.sh, line 124: Called src_configure * environment, line 872: Called perl-module_src_configure * environment, line 441: Called die * The specific snippet of code:
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(-)
