diff -Nru samtools-1.13/debian/changelog samtools-1.13/debian/changelog --- samtools-1.13/debian/changelog 2021-08-30 14:32:37.000000000 +0000 +++ samtools-1.13/debian/changelog 2021-10-25 18:53:03.000000000 +0000 @@ -1,3 +1,22 @@ +samtools (1.13-4) unstable; urgency=medium + + * [650b7a7] d/rules: only disable executable bit if test package is built. + (Closes: #997834) + + -- Étienne Mollier Mon, 25 Oct 2021 20:53:03 +0200 + +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 Sun, 24 Oct 2021 20:25:10 +0200 + samtools (1.13-2) unstable; urgency=medium [ Étienne Mollier ] diff -Nru samtools-1.13/debian/patches/fix-ftbfs-mvprintw.patch samtools-1.13/debian/patches/fix-ftbfs-mvprintw.patch --- samtools-1.13/debian/patches/fix-ftbfs-mvprintw.patch 1970-01-01 00:00:00.000000000 +0000 +++ samtools-1.13/debian/patches/fix-ftbfs-mvprintw.patch 2021-10-24 18:28:37.000000000 +0000 @@ -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 +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); + } + diff -Nru samtools-1.13/debian/patches/samtools-fasta-q-whatis.patch samtools-1.13/debian/patches/samtools-fasta-q-whatis.patch --- samtools-1.13/debian/patches/samtools-fasta-q-whatis.patch 1970-01-01 00:00:00.000000000 +0000 +++ samtools-1.13/debian/patches/samtools-fasta-q-whatis.patch 2021-10-24 18:24:06.000000000 +0000 @@ -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 +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. diff -Nru samtools-1.13/debian/patches/series samtools-1.13/debian/patches/series --- samtools-1.13/debian/patches/series 2021-08-30 14:32:37.000000000 +0000 +++ samtools-1.13/debian/patches/series 2021-10-24 18:24:06.000000000 +0000 @@ -1 +1,3 @@ reproducible.patch +fix-ftbfs-mvprintw.patch +samtools-fasta-q-whatis.patch diff -Nru samtools-1.13/debian/rules samtools-1.13/debian/rules --- samtools-1.13/debian/rules 2021-08-30 14:32:37.000000000 +0000 +++ samtools-1.13/debian/rules 2021-10-24 22:08:12.000000000 +0000 @@ -28,6 +28,15 @@ 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$$/.EX 8/' debian/*/usr/share/man/man*/*.* + override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) ifeq (,$(filter $(DEB_HOST_ARCH),mipsel)) @@ -48,6 +57,10 @@ for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' $${pscript} ; \ done + # Disable the executable bit on a dataset. + if [ -d debian/samtools-test ] \ + ; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \ + ; fi override_dh_installchangelogs: dh_installchangelogs NEWS diff -Nru samtools-1.13/debian/samtools.lintian-overrides samtools-1.13/debian/samtools.lintian-overrides --- samtools-1.13/debian/samtools.lintian-overrides 2021-08-30 14:32:37.000000000 +0000 +++ samtools-1.13/debian/samtools.lintian-overrides 2021-10-24 18:24:06.000000000 +0000 @@ -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