[med-svn] [Git][med-team/staden-io-lib][master] 4 commits: Install io_lib_config.h to /usr/include/io_lib/
Michael R. Crusoe
gitlab at salsa.debian.org
Sun Jul 19 16:43:39 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / staden-io-lib
Commits:
2372e63d by Michael R. Crusoe at 2020-07-19T17:00:21+02:00
Install io_lib_config.h to /usr/include/io_lib/
- - - - -
916ee0d9 by Michael R. Crusoe at 2020-07-19T17:02:53+02:00
Add new symbols to debian/libstaden-read14.symbols
- - - - -
fdf2507e by Michael R. Crusoe at 2020-07-19T17:24:47+02:00
forward patches
- - - - -
fa0aad23 by Michael R. Crusoe at 2020-07-19T17:26:04+02:00
release 1.14.13-3
- - - - -
6 changed files:
- debian/changelog
- debian/libstaden-read14.symbols
- debian/patches/fix_fseeko.patch
- debian/patches/pathmax.patch
- debian/patches/spelling
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+staden-io-lib (1.14.13-3) unstable; urgency=medium
+
+ * Install io_lib_config.h to /usr/include/io_lib/
+ * Add new symbols to debian/libstaden-read14.symbols
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sun, 19 Jul 2020 17:25:41 +0200
+
staden-io-lib (1.14.13-2) unstable; urgency=medium
* Don't run dh_missing in for arch independent builds.
=====================================
debian/libstaden-read14.symbols
=====================================
@@ -57,6 +57,7 @@ libstaden-read.so.14 libstaden-read14 #MINVER#
bam_aux_iter at Base 1.14.12
bam_aux_iter_full at Base 1.14.12
bam_aux_size_vec at Base 1.14.12
+ bam_aux_skip at Base 1.14.13
bam_close at Base 1.14.12
bam_construct_seq at Base 1.14.12
bam_copy at Base 1.14.12
@@ -130,6 +131,15 @@ libstaden-read.so.14 libstaden-read14 #MINVER#
cram_codec_decoder2encoder at Base 1.14.12
cram_codec_to_id at Base 1.14.12
cram_compress_block at Base 1.14.12
+ cram_const_decode_byte at Base 1.14.13
+ cram_const_decode_free at Base 1.14.13
+ cram_const_decode_init at Base 1.14.13
+ cram_const_decode_int at Base 1.14.13
+ cram_const_decode_long at Base 1.14.13
+ cram_const_decode_size at Base 1.14.13
+ cram_const_encode at Base 1.14.13
+ cram_const_encode_init at Base 1.14.13
+ cram_const_encode_store at Base 1.14.13
cram_content_type2str at Base 1.14.12
cram_deallocate_encoder at Base 1.14.12
cram_decode_TD at Base 1.14.12
@@ -145,6 +155,7 @@ libstaden-read.so.14 libstaden-read14 #MINVER#
cram_encode_compression_header at Base 1.14.12
cram_encode_container at Base 1.14.12
cram_encode_slice_header at Base 1.14.12
+ cram_encoder_get_fd at Base 1.14.13
cram_encoder_init at Base 1.14.12
cram_encoding2str at Base 1.14.12
cram_enque_compression_block at Base 1.14.12
@@ -256,6 +267,22 @@ libstaden-read.so.14 libstaden-read14 #MINVER#
cram_subexp_decode_init at Base 1.14.12
cram_uncompress_block at Base 1.14.12
cram_update_curr_slice at Base 1.14.12
+ cram_varint_decode_free at Base 1.14.13
+ cram_varint_decode_init at Base 1.14.13
+ cram_varint_decode_int at Base 1.14.13
+ cram_varint_decode_long at Base 1.14.13
+ cram_varint_decode_sint at Base 1.14.13
+ cram_varint_decode_size at Base 1.14.13
+ cram_varint_decode_slong at Base 1.14.13
+ cram_varint_encode_free at Base 1.14.13
+ cram_varint_encode_init at Base 1.14.13
+ cram_varint_encode_int at Base 1.14.13
+ cram_varint_encode_long at Base 1.14.13
+ cram_varint_encode_sint at Base 1.14.13
+ cram_varint_encode_slong at Base 1.14.13
+ cram_varint_encode_store at Base 1.14.13
+ cram_varint_get_block at Base 1.14.13
+ cram_write_SAM_hdr at Base 1.14.12
cram_write_SAM_hdr at Base 1.14.12
cram_write_block at Base 1.14.12
cram_write_container at Base 1.14.12
=====================================
debian/patches/fix_fseeko.patch
=====================================
@@ -3,6 +3,7 @@ Author: James Bonfield <jkb at sanger.ac.uk>,
Last-Update: Thu, 7 Dec 2017 18:09:16 +0000
Bug-Debian: https://bugs.debian.org/876840
Origin: Upstream
+Forwarded: not-needed
Description: Attempt to fix FTBFS on non-i386 32bit for fseeko()
--- staden-io-lib.orig/io_lib/bgzip.c
=====================================
debian/patches/pathmax.patch
=====================================
@@ -1,6 +1,7 @@
Author: Thorsten Alteholz <debian at alteholz.de>
Description: define PATH_MAX in case it is not available
this is needed to compile on hurd_i386
+Forwarded: https://github.com/jkbonfield/io_lib/pull/33
--- staden-io-lib.orig/io_lib/cram_index.c
+++ staden-io-lib/io_lib/cram_index.c
@@ -76,6 +76,14 @@
=====================================
debian/patches/spelling
=====================================
@@ -1,5 +1,6 @@
-From: Michael R. Crusoe <michael.crusoe at gmail.com>
-Subject: Spelling: independant→independent
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Spelling fixes courtesy of Lintian
+Forwarded: https://github.com/jkbonfield/io_lib/pull/32
--- staden-io-lib.orig/io_lib/mach-io.c
+++ staden-io-lib/io_lib/mach-io.c
@@ -81,7 +81,7 @@
=====================================
debian/rules
=====================================
@@ -32,7 +32,8 @@ override_dh_install-arch:
--movedev "debian/tmp/usr/include" usr \
--override s/libhtscodecs2-dev/libhtscodecs-dev/ \
debian/tmp/usr/lib/*/$(libpkg).so
- #
+ mkdir -p $(devpkg)/usr/include/io_lib/
+ cp $(CURDIR)/io_lib_config.h $(devpkg)/usr/include/io_lib/
# make sure io_lib-config --libs will not return -pie (see #825461)
find debian/*/usr/bin -name io_lib-config -exec sed -i -e 's/ *-fPIE//' -e 's/ *-pie//' \{\} \;
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/496d0052f47cd81fc296de2a7f45e41316360d0d...fa0aad23ca50419383469ed5e4b8bbc3c4aed25d
--
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/496d0052f47cd81fc296de2a7f45e41316360d0d...fa0aad23ca50419383469ed5e4b8bbc3c4aed25d
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