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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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