Étienne Mollier pushed to branch master at Debian Med / libbio-db-hts-perl
Commits: c5bc276b by Étienne Mollier at 2024-10-31T22:29:10+01:00 d/rules: nudge configure steps to find htslib. Closes: #1086359 - - - - - dcd49798 by Étienne Mollier at 2024-10-31T22:31:49+01:00 find_htslib.patch: remove DT_RUNPATH injection. - - - - - 01be5e2a by Étienne Mollier at 2024-10-31T22:32:48+01:00 d/control: declare myself as uploader. - - - - - 5af395f6 by Étienne Mollier at 2024-10-31T22:33:14+01:00 d/control: declare compliance to standards version 4.7.0. - - - - - 6e618e69 by Étienne Mollier at 2024-10-31T22:34:15+01:00 d/changelog: ready for sid upload. - - - - - 4 changed files: - debian/changelog - debian/control - debian/patches/find_htslib.patch - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +libbio-db-hts-perl (3.01-5) unstable; urgency=medium + + * d/rules: nudge configure steps to find htslib. (Closes: #1086359) + * find_htslib.patch: remove DT_RUNPATH injection. + * d/control: declare myself as uploader. + * d/control: declare compliance to standards version 4.7.0. + + -- Étienne Mollier <[email protected]> Thu, 31 Oct 2024 22:33:43 +0100 + libbio-db-hts-perl (3.01-4) unstable; urgency=medium * Packaging update ===================================== debian/control ===================================== @@ -1,6 +1,7 @@ Source: libbio-db-hts-perl Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: Andreas Tille <[email protected]>, + Étienne Mollier <[email protected]> Section: science Testsuite: autopkgtest-pkg-perl Priority: optional @@ -11,7 +12,7 @@ Build-Depends: debhelper-compat (= 13), libhts-dev, libmodule-build-perl, perl -Standards-Version: 4.6.1 +Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-hts-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-db-hts-perl.git Homepage: https://metacpan.org/release/Bio-DB-HTS ===================================== debian/patches/find_htslib.patch ===================================== @@ -39,7 +39,7 @@ Description: Take over changes in Build.PL from commit 83c9327 to make sure htsl $self->die_hts_not_found(); } -@@ -114,12 +125,15 @@ sub set_include_and_compiler_flags { +@@ -114,12 +125,14 @@ sub set_include_and_compiler_flags { my $hts_include = $self->config_data('hts_include'); my $hts_lib = $self->config_data('hts_lib'); my $static = $self->args('static'); @@ -54,13 +54,12 @@ Description: Take over changes in Build.PL from commit 83c9327 to make sure htsl + my @linker_dirflags; + if ($hts_lib) { + push @linker_dirflags, "-L$hts_lib"; -+ push @linker_dirflags, "-Wl,-rpath,$hts_lib" unless $static; } + $self->extra_linker_flags(@linker_dirflags, '-lhts', '-lpthread', '-lz'); } sub hts_dev_files_exist { -@@ -165,6 +179,48 @@ sub find_hts_in_install_dir { +@@ -165,6 +178,48 @@ sub find_hts_in_install_dir { } } @@ -109,7 +108,7 @@ Description: Take over changes in Build.PL from commit 83c9327 to make sure htsl sub die_hts_not_found { my ($self, $msg) = @_; -@@ -177,12 +233,17 @@ Install it if you have not done so alrea +@@ -177,12 +232,17 @@ Install it if you have not done so alrea This script will attempt to locate HTSlib by looking for htslib/hts.h and libhts.a / libhts.so in: ===================================== debian/rules ===================================== @@ -4,3 +4,13 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all %: dh $@ + +override_dh_auto_configure: + # Nudge configure steps to locate htslib, as for some reason it + # fails to find the htslb on its own with the logic provided in + # Build.PL. + dh_auto_configure -- \ + --htslib-includedir \ + $(shell pkgconf htslib --variable includedir) \ + --htslib-libdir \ + $(shell pkgconf htslib --variable libdir) View it on GitLab: https://salsa.debian.org/med-team/libbio-db-hts-perl/-/compare/c3da7a5a8fe393e12b90a9f8ce34ac6a0cf572a5...6e618e699de1264c75c39e0dca8fce55232551ef -- View it on GitLab: https://salsa.debian.org/med-team/libbio-db-hts-perl/-/compare/c3da7a5a8fe393e12b90a9f8ce34ac6a0cf572a5...6e618e699de1264c75c39e0dca8fce55232551ef You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
