[med-svn] [Git][med-team/libbio-db-hts-perl][master] 5 commits: d/rules: nudge configure steps to find htslib.

[Étienne Mollier (@emollier)]

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 <emollier at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Étienne Mollier <emollier at debian.org>
 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
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