commit: f7bdf03a3823e8156f7e31aea55948702f4882e2 Author: Marek Szuba <marecki <AT> gentoo <DOT> org> AuthorDate: Tue May 1 08:45:02 2018 +0000 Commit: Marek Szuba <marecki <AT> gentoo <DOT> org> CommitDate: Tue May 1 08:45:33 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f7bdf03a
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(-) diff --git a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild index 1490c3fe5ed..0a150300213 100644 --- a/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild +++ b/dev-perl/Bio-DB-HTS/Bio-DB-HTS-2.10.ebuild @@ -23,9 +23,10 @@ DEPEND="${RDEPEND} PATCHES=( "${FILESDIR}/2.10-build_search_for_so.patch" + "${FILESDIR}/2.10-build_split_htslib_opts.patch" ) src_configure() { - local myconf="--htslib=${EPREFIX}/usr" + local myconf="--htslib-includedir=${EPREFIX}/usr/include/htslib --htslib-libdir=${EPREFIX}/usr/$(get_libdir)" perl-module_src_configure } diff --git a/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch b/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch new file mode 100644 index 00000000000..d68bc54e40d --- /dev/null +++ b/dev-perl/Bio-DB-HTS/files/2.10-build_split_htslib_opts.patch @@ -0,0 +1,48 @@ +--- a/Build.PL ++++ b/Build.PL +@@ -68,7 +68,13 @@ + # If either of these are set, we expect to find the htslib files there: + # (They're explicitly set by the user, so we shouldn't fall back to + # finding another copy somewhere else.) +- if (my $dir = $self->args('htslib')) { ++ if (my ($incdir, $libdir) = ($self->args('htslib-includedir'), $self->args('htslib-libdir'))) { ++ return 1 if $self->find_hts_in_split_install_dirs($incdir, $libdir); ++ $self->die_hts_not_found( ++ "--htslib-includedir '$incdir' or --htslib-libdir '$libdir' command line parameters do not contain expected files\n" ++ ); ++ } ++ elsif (my $dir = $self->args('htslib')) { + return 1 if $self->find_hts_in_build_dir($dir); + return 1 if $self->find_hts_in_install_dir($dir); + $self->die_hts_not_found( +@@ -155,6 +161,22 @@ + } + } + ++sub find_hts_in_split_install_dirs { ++ my ($self, $hts_include, $hts_lib) = @_; ++ ++ chomp($hts_include); ++ chomp($hts_lib); ++ ++ if ((-f "$hts_lib/libhts.so" || -f "$hts_lib/libhts.a") && -f "$hts_include/hts.h") { ++ $self->config_data('hts_lib' => $hts_lib); ++ $self->config_data('hts_include' => $hts_include); ++ return 1; ++ } ++ else { ++ return 0; ++ } ++} ++ + sub die_hts_not_found { + my ($self, $msg) = @_; + +@@ -166,6 +188,7 @@ + + This script will attempt to locate htslib by looking for hts.h and libhts.so/libhts.a in: + ++ 0. --htslib-includedir and --htslib-libdir command line arguments + 1. --htslib command line argument + 2. HTSLIB_DIR environment variable + 3. --prefix command line argument (which also sets installation location)
