[med-svn] [Git][med-team/soapaligner][master] 4 commits: Architecture: any-amd64 x32
Andreas Tille
gitlab at salsa.debian.org
Thu Jul 5 13:00:53 BST 2018
Andreas Tille pushed to branch master at Debian Med / soapaligner
Commits:
0a7d7482 by Andreas Tille at 2018-07-05T13:04:53+02:00
Architecture: any-amd64 x32
- - - - -
191005b3 by Andreas Tille at 2018-07-05T13:44:02+02:00
Force propagation of hardening options (no idea why this is necessary)
- - - - -
296ab910 by Andreas Tille at 2018-07-05T13:50:45+02:00
Fix spelling
- - - - -
7e8bd159 by Andreas Tille at 2018-07-05T13:51:57+02:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/linkerror.patch
- debian/patches/series
- + debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+soapaligner (2.20-3) unstable; urgency=medium
+
+ * Team upload.
+ * Architecture: any-amd64 x32
+ Closes: #903003
+ * More sensible date for reproducible builds (SOURCE_DATE_EPOCH)
+ * Force propagation of hardening options
+ * Fix spelling
+
+ -- Andreas Tille <tille at debian.org> Thu, 05 Jul 2018 13:51:03 +0200
+
soapaligner (2.20-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -10,7 +10,7 @@ Vcs-Git: https://salsa.debian.org/med-team/soapaligner.git
Homepage: http://soap.genomics.org.cn/soapaligner.html
Package: soapaligner
-Architecture: any
+Architecture: any-amd64 x32
Depends: ${shlibs:Depends},
${misc:Depends}
Description: aligner of short reads of next generation sequencers
=====================================
debian/patches/linkerror.patch
=====================================
--- a/debian/patches/linkerror.patch
+++ b/debian/patches/linkerror.patch
@@ -2,11 +2,9 @@ Author: Steffen Moeller
Last-Update: 2018-05-04 18:33:03 +0200
Description: Fix build
-Index: soapaligner/Makefile
-===================================================================
---- soapaligner.orig/Makefile
-+++ soapaligner/Makefile
-@@ -32,8 +32,8 @@ ifeq (YES, $(PROFILE))
+--- a/Makefile
++++ b/Makefile
+@@ -37,8 +37,8 @@ ifeq (YES, $(PROFILE))
CFLAGS += $(PROFILE_FLAGS)
endif
@@ -17,16 +15,14 @@ Index: soapaligner/Makefile
.SUFFIX: .c .o
.c.o:
-@@ -65,3 +65,5 @@ kstring.o:kstring.h
+@@ -70,3 +70,5 @@ kstring.o:kstring.h
clean:
rm -f *.o $(PROG)
+
+.PHONY: clean
-Index: soapaligner/Match.c
-===================================================================
---- soapaligner.orig/Match.c
-+++ soapaligner/Match.c
+--- a/Match.c
++++ b/Match.c
@@ -74,7 +74,8 @@
} \
}
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
compiler_options.patch
linkerror.patch
UsageDoublette.patch
+spelling.patch
=====================================
debian/patches/spelling.patch
=====================================
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,46 @@
+Description: Fix spelling
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 05 Jul 2018 13:04:29 +0200
+
+--- a/soap.1
++++ b/soap.1
+@@ -69,7 +69,7 @@ Totally allowed mismatches in one read,
+ Allow gap size in one read, [0]
+ .TP
+ .B -M INT
+-Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
++Match mode for each read or the seed part of read, which shouldn't contain more than 2 mismatches, [4]
+ .RS
+ .TP
+ 0: exact match only
+@@ -88,7 +88,7 @@ SOAP2 output format contains following c
+ .PP
+ 1. reads name / reads ID (if -t is available)
+ .P
+-2. reads sequence (if read align to reverse strand, here is the reverse sequence of orignal read)
++2. reads sequence (if read align to reverse strand, here is the reverse sequence of original read)
+ .P
+ 3. quality sequence (if input is fasta reads, the column will be all 'h', and the sequence is backward if reads mapping reverse )
+ .P
+--- a/soap.c
++++ b/soap.c
+@@ -119,7 +119,7 @@ static void Usage(void) {
+ fprintf(stdout, "\t-b <str> query b file\n");
+ fprintf(stdout, "\t-D <str> reference sequences indexing table, *.index format\n");
+ fprintf(stdout, "\t-o <str> output alignment file(txt)\n");
+- fprintf(stdout, "\t-M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]\n"
++ fprintf(stdout, "\t-M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismatches, [4]\n"
+ "\t 0: exact match only\n"
+ "\t 1: 1 mismatch match only\n"
+ "\t 2: 2 mismatch match only\n"
+--- a/soap.man
++++ b/soap.man
+@@ -71,7 +71,7 @@ CCOOMMMMAANNDD AANNDD OOPPT
+ --gg IINNTT Allow gap size in one read, [0]
+
+ --MM IINNTT Match mode for each read or the seed part of read, which
+- shouldn't contain more than 2 mismaches, [4]
++ shouldn't contain more than 2 mismatches, [4]
+
+ 0: exact match only
+
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -2,14 +2,13 @@
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
export DH_VERBOSE=1
-export DFLAGS = -DMAKE_TIME=\""be reproducible"\"
-
-export CFLAGS += -flto
-export CXXFLAGS += -flto
-export LDFLAGS += -Wl,-flto
+export DFLAGS = -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\"
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export CFLAGS:=-flto $(shell dpkg-buildflags --get CFLAGS)
+export CXXFLAGS:=-flto $(shell dpkg-buildflags --get CXXFLAGS)
+export LDFLAGS:=-Wl,-flto $(shell dpkg-buildflags --get LDFLAGS)
%:
dh $@
View it on GitLab: https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16
--
View it on GitLab: https://salsa.debian.org/med-team/soapaligner/compare/e56a4867dbe574f42d2aa418ce8c3e515bdb36ae...7e8bd159fa492b883bdea5adefabda1eb67aaf16
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