[med-svn] [Git][med-team/htslib][master] 5 commits: disable_plugin_loading_test.patch: remove; test is supposed to pass.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Oct 19 21:27:20 BST 2022
Étienne Mollier pushed to branch master at Debian Med / htslib
Commits:
8801e313 by Étienne Mollier at 2022-10-19T19:05:29+02:00
disable_plugin_loading_test.patch: remove; test is supposed to pass.
- - - - -
9b013cdd by Étienne Mollier at 2022-10-19T22:16:35+02:00
d/rules: do not erase LDFLAGS.
The build procedure requires some specific flags such as -rdynamic
to make plugins usable. There is probably more room for improvement
but that should be sufficient for now.
- - - - -
6e307027 by Étienne Mollier at 2022-10-19T22:19:18+02:00
d/patches/: remove unused patches.
- - - - -
d211e8e6 by Étienne Mollier at 2022-10-19T22:25:35+02:00
trim-file-prefix.patch: add; improve reproducible build.
- - - - -
e317c719 by Étienne Mollier at 2022-10-19T22:26:50+02:00
ready to upload to unstable.
- - - - -
7 changed files:
- debian/changelog
- − debian/patches/big-endian
- − debian/patches/disable_plugin_loading_test.patch
- − debian/patches/plugins_to_lib.patch
- debian/patches/series
- + debian/patches/trim-file-prefix.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,17 @@
-htslib (1.16+ds-3) UNRELEASED; urgency=medium
+htslib (1.16+ds-3) unstable; urgency=medium
* d/rules: make sure libdir and plugindir are defined.
Thanks to James Bonfield
* d/libhts3.install: relocate plugins following fix at configure step.
* d/*.install: remove dh-exec shebang.
* d/control: remove build-dependency to dh-exec.
+ * disable_plugin_loading_test.patch: remove; test is supposed to pass.
+ * d/rules: do not erase LDFLAGS; fix the aforementioned test failure
+ by restoring -rdynamic flag supposed to be passed to the linker.
+ * d/patches/: remove unused patches.
+ * trim-file-prefix.patch: add; improve reproducible build.
- -- Étienne Mollier <emollier at debian.org> Wed, 19 Oct 2022 17:01:44 +0200
+ -- Étienne Mollier <emollier at debian.org> Wed, 19 Oct 2022 22:25:57 +0200
htslib (1.16+ds-2) unstable; urgency=medium
=====================================
debian/patches/big-endian deleted
=====================================
@@ -1,23 +0,0 @@
-From: Rob Davies <rmd+git at sanger.ac.uk>
-Date: Mon, 3 Feb 2020 13:45:20 +0000
-Subject: [PATCH] Add / fix byte swapping code for big-endian platforms
- Properly swap expanded l->n in idx_read_core()
- .
- Fix various places where bcf INFO and FORMAT values were not
- being accessed correctly.
- .
- Seems the original patch was adopted upstream. This last remaining
- taken over from the original patch is probably not needed any more
- and thus the patch is deactivated.
-
---- a/hts.c
-+++ b/hts.c
-@@ -2206,7 +2206,7 @@ static int idx_read_core(hts_idx_t *idx,
- bins_t *p;
- h = idx->bidx[i] = kh_init(bin);
- if (bgzf_read(fp, &n, 4) != 4) return -1;
-- if (is_be) ed_swap_4p(&n);
-+ if (is_be) ed_swap_8p(&n);
- if (n < 0) return -3;
- for (j = 0; j < n; ++j) {
- khint_t k;
=====================================
debian/patches/disable_plugin_loading_test.patch deleted
=====================================
@@ -1,13 +0,0 @@
-Author: Steffen Moeller <moeller at debian.org>
-Description: This test contacts a localhost, which fails, like all networking should fail during testing? Unsure.
---- a/test/test.pl
-+++ b/test/test.pl
-@@ -58,7 +58,7 @@ test_command($opts,cmd=>'test-bcf-transl
- test_convert_padded_header($opts);
- test_rebgzip($opts);
- test_logging($opts);
--test_plugin_loading($opts);
-+#test_plugin_loading($opts);
- test_realn($opts);
- test_bcf_set_variant_type($opts);
-
=====================================
debian/patches/plugins_to_lib.patch deleted
=====================================
@@ -1,23 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 02 Oct 2020 11:35:21 +0200
-Description: Debian has no libexecdir - plugins should go to libdir
-FIXME: Deactivated since
- --with-plugin-dir='$(libdir)/htslib' --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:$(plugindir)'
- should be sufficient
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -115,11 +115,11 @@ AC_ARG_WITH([libdeflate],
-
- AC_ARG_WITH([plugin-dir],
- [AS_HELP_STRING([--with-plugin-dir=DIR],
-- [plugin installation location [LIBEXECDIR/htslib]])],
-+ [plugin installation location [LIBDIR/htslib]])],
- [case $withval in
- yes|no) MSG_ERROR([no directory specified for --with-plugin-dir]) ;;
- esac],
-- [with_plugin_dir='$(libexecdir)/htslib'])
-+ [with_plugin_dir='$(libdir)/htslib'])
- AC_SUBST([plugindir], $with_plugin_dir)
-
- AC_ARG_WITH([plugin-path],
=====================================
debian/patches/series
=====================================
@@ -3,8 +3,6 @@ define_PATH_MAX.patch
fPIC.patch
testShebang.patch
fix_float_precision
-# big-endian
cram_to_bam_export.patch
-# plugins_to_lib.patch - can probably be removed
-disable_plugin_loading_test.patch
fix_sequence_of_linked_libs.patch
+trim-file-prefix.patch
=====================================
debian/patches/trim-file-prefix.patch
=====================================
@@ -0,0 +1,20 @@
+Description: trim build path from config_vars.
+ This is done in hope to improve build reproducibility.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2022-10-19
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- htslib.orig/Makefile
++++ htslib/Makefile
+@@ -163,7 +163,9 @@
+ config_vars.h:
+ echo '#define HTS_CC "$(CC)"' > $@
+ echo '#define HTS_CPPFLAGS "$(CPPFLAGS)"' >> $@
+- echo '#define HTS_CFLAGS "$(CFLAGS)"' >> $@
++ echo '#define HTS_CFLAGS "$(CFLAGS)"' \
++ | sed 's/-ffile-prefix-map=[^ ]*=.//' \
++ >> $@
+ echo '#define HTS_LDFLAGS "$(LDFLAGS)"' >> $@
+ echo '#define HTS_LIBS "$(LIBS)"' >> $@
+
=====================================
debian/rules
=====================================
@@ -49,7 +49,6 @@ override_dh_auto_build-arch:
dh_auto_build -- \
CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="$(UPSTREAM_VERSION)" \
libdir=$(libdir)
# re-try later LDLIBS=-lhts \
@@ -63,7 +62,6 @@ override_dh_auto_install-arch:
dh_auto_install -- prefix=/usr \
CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="$(UPSTREAM_VERSION)" \
libdir=$(libdir)
# restore clean copy of test dir before dh_install is run
@@ -82,7 +80,6 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
dh_auto_test -- \
CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="-I. -DSAMTOOLS=1 $$(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)" \
PACKAGE_VERSION="$(UPSTREAM_VERSION)" \
libdir=$(libdir) \
|| \
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/94dbb268188a476d7afc6fea80d00376879e67cb...e317c71930b3248d0ba927d48ab5f8e39f50fb5e
--
View it on GitLab: https://salsa.debian.org/med-team/htslib/-/compare/94dbb268188a476d7afc6fea80d00376879e67cb...e317c71930b3248d0ba927d48ab5f8e39f50fb5e
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