[med-svn] [Git][med-team/samtools][master] 9 commits: d/rules: fix several issues in manual pages
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Oct 24 22:40:57 BST 2021
Étienne Mollier pushed to branch master at Debian Med / samtools
Commits:
ee4c97ec by Étienne Mollier at 2021-10-24T19:24:53+02:00
d/rules: fix several issues in manual pages
Most of these were reported by lintian as bad-whatis-entry or
groff-message. Some are still under the radar though.
- - - - -
488881b3 by Étienne Mollier at 2021-10-24T19:29:15+02:00
Add fix-ftbfs-mvprintw.patch
Closes: #997180
- - - - -
d9a87518 by Étienne Mollier at 2021-10-24T19:35:17+02:00
d/rules: prudent pattern to fix whatis entries
Gbp-Dcp: ignore
- - - - -
da4dc4ae by Étienne Mollier at 2021-10-24T19:50:10+02:00
d/rules: disable executable bit on ac_test.bed
- - - - -
fbfd6c99 by Étienne Mollier at 2021-10-24T19:52:33+02:00
Add samtools-fasta-q-whatis.patch
- - - - -
06566462 by Étienne Mollier at 2021-10-24T19:56:34+02:00
update changelog
- - - - -
4cfbf2b4 by Étienne Mollier at 2021-10-24T20:00:08+02:00
d/samtools.lintian-overrides removed *.py pattern
Apparently, the samtools do not ship python scripts anymore.
- - - - -
015d4162 by Étienne Mollier at 2021-10-24T20:28:55+02:00
Adjust fix-ftbfs-mvprintw.patch metainformations
Thanks: John Marshall
This is done in the light of information forwarded upstream and
existing patch with minimum change.
- - - - -
a35323b7 by Étienne Mollier at 2021-10-24T20:31:11+02:00
ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- + debian/patches/fix-ftbfs-mvprintw.patch
- + debian/patches/samtools-fasta-q-whatis.patch
- debian/patches/series
- debian/rules
- debian/samtools.lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+samtools (1.13-3) unstable; urgency=medium
+
+ * [ee4c97e] d/rules: fix several issues in manual pages.
+ * [488881b] Add fix-ftbfs-mvprintw.patch (Closes: #997180)
+ * [da4dc4a] d/rules: disable executable bit on ac_test.bed.
+ * [fbfd6c9] Add samtools-fasta-q-whatis.patch.
+ * [4cfbf2b] d/samtools.lintian-overrides: remove *.py pattern.
+ * [015d416] Adjust fix-ftbfs-mvprintw.patch metainformations.
+ Thanks to John Marshall for the forward upstream!
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 24 Oct 2021 20:25:10 +0200
+
samtools (1.13-2) unstable; urgency=medium
[ Étienne Mollier ]
=====================================
debian/patches/fix-ftbfs-mvprintw.patch
=====================================
@@ -0,0 +1,23 @@
+Description: fix format not a string literal in mvprintw call
+ The idea is to use an equivalent function that does not do the format
+ parsing, since it does not seem to be the intent.
+ .
+ Thanks John Marshall for the forward of the elegant solution!
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997180
+Forwarded: https://github.com/samtools/samtools/pull/1509
+Applied-Upstream: 1.14
+Last-Update: 2021-10-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- samtools.orig/bam_tview_curses.c
++++ samtools/bam_tview_curses.c
+@@ -85,7 +85,7 @@
+ va_start(argptr, fmt);
+ vsnprintf(str,size, fmt, argptr);
+ va_end(argptr);
+- mvprintw(y,x,str);
++ mvprintw(y,x,"%s",str);
+ free(str);
+ }
+
=====================================
debian/patches/samtools-fasta-q-whatis.patch
=====================================
@@ -0,0 +1,19 @@
+Description: fix bad whatis entry for samtools-fasta and samtools-fastq manual
+ The format is inspired from printf(3) to fit automatically several commands
+ with same purpose in one page, while keeping the whatis entries parse happy.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2021-10-24
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- samtools.orig/doc/samtools-fasta.1
++++ samtools/doc/samtools-fasta.1
+@@ -1,7 +1,7 @@
+ '\" t
+ .TH samtools-fasta 1 "7 July 2021" "samtools-1.13" "Bioinformatics tools"
+ .SH NAME
+-samtools fasta / fastq \- converts a SAM/BAM/CRAM file to FASTA or FASTQ
++samtools-fasta, samtools-fastq \- converts a SAM/BAM/CRAM file to FASTA or FASTQ
+ .\"
+ .\" Copyright (C) 2008-2011, 2013-2020 Genome Research Ltd.
+ .\" Portions copyright (C) 2010, 2011 Broad Institute.
=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
reproducible.patch
+fix-ftbfs-mvprintw.patch
+samtools-fasta-q-whatis.patch
=====================================
debian/rules
=====================================
@@ -28,6 +28,15 @@ override_dh_auto_build:
CPPFLAGS="\$$(DFLAGS) \$$(INCLUDES) $$(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$$(dpkg-buildflags --get LDFLAGS)"
+# Fix several issues in the manual pages.
+execute_before_dh_installman:
+ # Fix whatis entries for subcommands; "samtools subcommand \- desc."
+ # will confuse the lexer, but "samtools-subcommand \- desc." will work.
+ sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \
+ debian/*/usr/share/man/man*/*.*
+ # .EX expects a indentation width.
+ sed -i 's/^.EX$$/.EX 8/' debian/*/usr/share/man/man*/*.*
+
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
ifeq (,$(filter $(DEB_HOST_ARCH),mipsel))
@@ -48,6 +57,8 @@ override_dh_install:
for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \
sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' $${pscript} ; \
done
+ # Disable the executable bit on a dataset.
+ chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed
override_dh_installchangelogs:
dh_installchangelogs NEWS
=====================================
debian/samtools.lintian-overrides
=====================================
@@ -1,4 +1,3 @@
# Even if there is a conflict with Debian policy samtools internally
# relies on these extensions (see #799698)
samtools: script-with-language-extension usr/bin/*.pl
-samtools: script-with-language-extension usr/bin/*.py
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/fc228655e35308a3cb76a0ba97ff167edc2a75df...a35323b79a488fda60725883670bf9fe132dec9b
--
View it on GitLab: https://salsa.debian.org/med-team/samtools/-/compare/fc228655e35308a3cb76a0ba97ff167edc2a75df...a35323b79a488fda60725883670bf9fe132dec9b
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