Étienne Mollier pushed to branch master at Debian Med / lastz
Commits: 36002308 by Étienne Mollier at 2021-11-02T22:21:52+01:00 Add gcc11.patch Closes: #984081 - - - - - 4b80d632 by Étienne Mollier at 2021-11-02T22:56:51+01:00 Edit propagate_cflags.patch to propagate CPPFLAGS - - - - - 872a1c7c by Étienne Mollier at 2021-11-02T23:08:46+01:00 d/control: lastz-examples depends on python3 The initial setting about depending on the dynamic python3:Depends substvar does not seem to provide python3 anymore, so using a hardcoded dependency instead. - - - - - 6fa527dd by Étienne Mollier at 2021-11-02T23:13:59+01:00 ready to upload to unstable - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/gcc11.patch - debian/patches/propagate_cflags.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +lastz (1.04.15-2) unstable; urgency=medium + + * Team upload. + * Add gcc11.patch. (Closes: #984081) + * Edit propagate_cflags.patch to propagate CPPFLAGS as well. + * d/control: lastz-examples explicitly depends on python3:any. + + -- Étienne Mollier <[email protected]> Tue, 02 Nov 2021 23:12:52 +0100 + lastz (1.04.15-1) unstable; urgency=medium [ Steffen Moeller ] ===================================== debian/control ===================================== @@ -23,7 +23,7 @@ Description: pairwise aligning DNA sequences Package: lastz-examples Architecture: all -Depends: ${python3:Depends}, ${misc:Depends} +Depends: python3:any, ${python3:Depends}, ${misc:Depends} Multi-Arch: foreign Description: pairwise aligning DNA sequences (examples and test scripts) LASTZ is a drop-in replacement for BLASTZ, and is backward compatible with ===================================== debian/patches/gcc11.patch ===================================== @@ -0,0 +1,31 @@ +Description: fix ftbfs with gcc 11 + Inspired from upstream commit d00249da148a011a8c2d819f702356908859c51c. +Author: Étienne Mollier <[email protected]> +Bug: https://github.com/lastz/lastz/issues/42 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984081 +Applied-Upstream: d00249da148a011a8c2d819f702356908859c51c +Last-Update: 2021-11-02 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- lastz.orig/src/sequences.c ++++ lastz/src/sequences.c +@@ -3621,7 +3621,7 @@ + //---------- + + static int find_2bit_sequence (seq* _seq, char* name); +-static u32 read_2bit_index_entry (seq* _seq, char seqName[256], u32 seqNum); ++static u32 read_2bit_index_entry (seq* _seq, char seqName[maxSequenceName+1], u32 seqNum); + + //--- read_2bit_header --- + +--- lastz.orig/src/sequences.h ++++ lastz/src/sequences.h +@@ -192,7 +192,7 @@ + // + //---------- + +-#define maxSequenceName 100 ++#define maxSequenceName 255 + #define maxSequenceHeader 992 + #define seqBufferSize (maxSequenceHeader+32) + #define maxFastqSequenceLen 10000 ===================================== debian/patches/propagate_cflags.patch ===================================== @@ -1,11 +1,14 @@ Author: Andreas Tille <[email protected]> -Last-Update: Mon, 15 Jun 2020 11:47:45 +0200 Description: Propagate DEB_CFLAGS_MAINT_APPEND = -Wno-stringop-truncation - Also LDFLAGS is added to propagate remaining hardening options + Also LDFLAGS is added to propagate remaining hardening options. + . + Later edited to add support for preprocessor flags (CPPFLAGS). +Reviewed-By: Étienne Mollier <[email protected]> +Last-Update: 2021-11-02 ---- a/src/Makefile -+++ b/src/Makefile -@@ -71,7 +71,7 @@ VERSION_FLAGS= \ +--- lastz.orig/src/Makefile ++++ lastz/src/Makefile +@@ -71,7 +71,7 @@ -DSUBVERSION_REV="\"${SUBVERSION_REV}"\" @@ -14,7 +17,20 @@ Description: Propagate DEB_CFLAGS_MAINT_APPEND = -Wno-stringop-truncation srcFiles = lastz infer_scores \ -@@ -101,13 +101,13 @@ incFiles = lastz.h infer_scores.h \ +@@ -91,23 +91,23 @@ + utilities.h dna_utilities.h sequences.h capsule.h + + %.o: %.c version.mak ${incFiles} +- ${CC} -c ${CFLAGS} -Dscore_type=\'I\' $< -o $@ ++ ${CC} ${CPPFLAGS} -c ${CFLAGS} -Dscore_type=\'I\' $< -o $@ + + %_D.o: %.c version.mak ${incFiles} +- ${CC} -c ${CFLAGS} -Dscore_type=\'D\' $< -o $@ ++ ${CC} ${CPPFLAGS} -c ${CFLAGS} -Dscore_type=\'D\' $< -o $@ + + %_32.o: %.c version.mak ${incFiles} +- ${CC} -c ${CFLAGS} ${flagsFor32} $< -o $@ ++ ${CC} ${CPPFLAGS} -c ${CFLAGS} ${flagsFor32} $< -o $@ lastz: $(foreach part,${srcFiles},${part}.o) ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ propagate_cflags.patch fix_signed_char.patch spelling.patch +gcc11.patch View it on GitLab: https://salsa.debian.org/med-team/lastz/-/compare/e0920a8745831a26441c142d85c830be8d189982...6fa527dd3b0dedb41579461eb41ec832a79e26d9 -- View it on GitLab: https://salsa.debian.org/med-team/lastz/-/compare/e0920a8745831a26441c142d85c830be8d189982...6fa527dd3b0dedb41579461eb41ec832a79e26d9 You're receiving this email because of your account on salsa.debian.org.
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