[med-svn] [Git][med-team/lastz][master] 4 commits: Add gcc11.patch

[Étienne Mollier (@emollier)]

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 <emollier at debian.org>  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 <emollier at debian.org>
+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 <tille at debian.org>
-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 <emollier at debian.org>
+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
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