[med-svn] r18725 - in trunk/packages/vsearch/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon Feb 2 09:01:35 UTC 2015
Author: tille
Date: 2015-02-02 09:01:35 +0000 (Mon, 02 Feb 2015)
New Revision: 18725
Added:
trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch
trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
Modified:
trunk/packages/vsearch/trunk/debian/changelog
trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
trunk/packages/vsearch/trunk/debian/patches/hardening.patch
trunk/packages/vsearch/trunk/debian/patches/series
trunk/packages/vsearch/trunk/debian/rules
Log:
Hopefully fix #776812, start polishing manpage
Modified: trunk/packages/vsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/vsearch/trunk/debian/changelog 2015-02-02 06:56:55 UTC (rev 18724)
+++ trunk/packages/vsearch/trunk/debian/changelog 2015-02-02 09:01:35 UTC (rev 18725)
@@ -3,6 +3,9 @@
* New upstream version
* debian/README.source: Add proper information for data files
* drop -msse2 flag
+ * conditional use of -mtune flag
+ Closes: #776812
+ * Polishing manpage
-- Andreas Tille <tille at debian.org> Mon, 02 Feb 2015 07:40:07 +0100
Modified: trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch 2015-02-02 06:56:55 UTC (rev 18724)
+++ trunk/packages/vsearch/trunk/debian/patches/fix_optimisation_flags.patch 2015-02-02 09:01:35 UTC (rev 18725)
@@ -25,3 +25,14 @@
LINKFLAGS=$(PROFILING)
LIBS=-lpthread -lz
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -27,7 +27,7 @@ WARN=-Wall -Wsign-compare
+ #WARN=-Weverything
+
+ CXX=g++
+-CXXFLAGS=-O3 -msse2 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
++CXXFLAGS=-O3 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
+ LINKFLAGS=$(PROFILING)
+ LIBS=-lpthread
+
Modified: trunk/packages/vsearch/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/hardening.patch 2015-02-02 06:56:55 UTC (rev 18724)
+++ trunk/packages/vsearch/trunk/debian/patches/hardening.patch 2015-02-02 09:01:35 UTC (rev 18725)
@@ -4,10 +4,10 @@
--- a/src/Makefile.BZLIB
+++ b/src/Makefile.BZLIB
-@@ -28,7 +28,7 @@ WARN=-Wall
+@@ -34,7 +34,7 @@ endif
CXX=g++
- CXXFLAGS=-O3 -DHAVE_BZLIB -msse2 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
+ CXXFLAGS=-O3 -DHAVE_BZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
-LINKFLAGS=$(PROFILING)
+LINKFLAGS=$(PROFILING) $(LDFLAGS)
LIBS=-lpthread -lbz2
@@ -15,21 +15,21 @@
PROG=vsearch-bz
--- a/src/Makefile.ZLIB
+++ b/src/Makefile.ZLIB
-@@ -29,7 +29,7 @@ WARN=-Wall
+@@ -34,7 +34,7 @@ endif
+
CXX=g++
- CXXFLAGS=-O3 -DHAVE_ZLIB -msse2 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
- LINKFLAGS=$(PROFILING)
--LIBS=-lpthread -lz
-+LIBS=-lpthread -lz $(LDFLAGS)
+ CXXFLAGS=-O3 -DHAVE_ZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
+-LINKFLAGS=$(PROFILING)
++LINKFLAGS=$(PROFILING) $(LDFLAGS)
+ LIBS=-lpthread -lz
PROG=vsearch-gz
-
--- a/src/Makefile
+++ b/src/Makefile
-@@ -28,7 +28,7 @@ WARN=-Wall
+@@ -34,7 +34,7 @@ endif
CXX=g++
- CXXFLAGS=-O3 -msse2 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
+ CXXFLAGS=-O3 $(MTUNE) -Icityhash $(WARN) $(PROFILING)
-LINKFLAGS=$(PROFILING)
+LINKFLAGS=$(PROFILING) $(LDFLAGS)
LIBS=-lpthread
Added: trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch (rev 0)
+++ trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch 2015-02-02 09:01:35 UTC (rev 18725)
@@ -0,0 +1,81 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
+Description: Suppress some lintian warnings
+
+--- a/doc/vsearch.1
++++ b/doc/vsearch.1
+@@ -9,58 +9,58 @@ vsearch \(em chimera detection, clusteri
+ .ad l
+ Chimera detection:
+ .RS
+-\fBvsearch\fR --uchime_denovo \fIfastafile\fR (--chimeras |
+---nonchimeras | --uchimealns | --uchimeout) \fIoutputfile\fR
++\fBvsearch\fR \-\-uchime_denovo \fIfastafile\fR (\-\-chimeras |
++\-\-nonchimeras | \-\-uchimealns | \-\-uchimeout) \fIoutputfile\fR
+ [\fIoptions\fR]
+ .PP
+-\fBvsearch\fR --uchime_ref \fIfastafile\fR (--chimeras | --nonchimeras
+-| --uchimealns | --uchimeout) \fIoutputfile\fR --db \fIfastafile\fR
++\fBvsearch\fR \-\-uchime_ref \fIfastafile\fR (\-\-chimeras | \-\-nonchimeras
++| \-\-uchimealns | \-\-uchimeout) \fIoutputfile\fR \-\-db \fIfastafile\fR
+ [\fIoptions\fR]
+ .PP
+ .RE
+ Clustering:
+ .RS
+-\fBvsearch\fR (--cluster_fast | --cluster_size | --cluster_smallmem)
+-\fIfastafile\fR (--alnout | --blast6out | --centroids | --clusters |
+---msaout | --uc | --userout) \fIoutputfile\fR --id \fIreal\fR
++\fBvsearch\fR (\-\-cluster_fast | \-\-cluster_size | \-\-cluster_smallmem)
++\fIfastafile\fR (\-\-alnout | \-\-blast6out | \-\-centroids | \-\-clusters |
++\-\-msaout | \-\-uc | \-\-userout) \fIoutputfile\fR \-\-id \fIreal\fR
+ [\fIoptions\fR]
+ .PP
+ .RE
+ Dereplication:
+ .RS
+-\fBvsearch\fR --derep_fulllength \fIfastafile\fR (--output | --uc)
++\fBvsearch\fR \-\-derep_fulllength \fIfastafile\fR (\-\-output | \-\-uc)
+ \fIoutputfile\fR [\fIoptions\fR]
+ .PP
+ .RE
+ Masking:
+ .RS
+-\fBvsearch\fR --maskfasta \fIfastafile\fR --output \fIoutputfile\fR
++\fBvsearch\fR \-\-maskfasta \fIfastafile\fR \-\-output \fIoutputfile\fR
+ [\fIoptions\fR]
+ .PP
+ .RE
+ Pairwise alignment:
+ .RS
+-\fBvsearch\fR --allpairs_global \fIfastafile\fR (--alnout |
+---blast6out | --matched | --notmatched | --uc | --userout)
+-\fIoutputfile\fR (--acceptall | --id \fIreal\fR) [\fIoptions\fR]
++\fBvsearch\fR \-\-allpairs_global \fIfastafile\fR (\-\-alnout |
++\-\-blast6out | \-\-matched | \-\-notmatched | \-\-uc | \-\-userout)
++\fIoutputfile\fR (\-\-acceptall | \-\-id \fIreal\fR) [\fIoptions\fR]
+ .PP
+ .RE
+ Searching:
+ .RS
+-\fBvsearch\fR --usearch_global \fIfastafile\fR --db \fIfastafile\fR
+-(--alnout | --blast6out | --uc | --userout) \fIoutputfile\fR --id
++\fBvsearch\fR \-\-usearch_global \fIfastafile\fR \-\-db \fIfastafile\fR
++(\-\-alnout | \-\-blast6out | \-\-uc | \-\-userout) \fIoutputfile\fR \-\-id
+ \fIreal\fR [\fIoptions\fR]
+ .PP
+ .RE
+ Shuffling:
+ .RS
+-\fBvsearch\fR --shuffle \fIfastafile\fR --output \fIoutputfile\fR
++\fBvsearch\fR \-\-shuffle \fIfastafile\fR \-\-output \fIoutputfile\fR
+ [\fIoptions\fR]
+ .PP
+ .RE
+ Sorting:
+ .RS
+-\fBvsearch\fR (--sortbylength | --sortbysize) \fIfastafile\fR --output
++\fBvsearch\fR (\-\-sortbylength | \-\-sortbysize) \fIfastafile\fR \-\-output
+ \fIoutputfile\fR [\fIoptions\fR]
+ .PP
+ .RE
Modified: trunk/packages/vsearch/trunk/debian/patches/series
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/series 2015-02-02 06:56:55 UTC (rev 18724)
+++ trunk/packages/vsearch/trunk/debian/patches/series 2015-02-02 09:01:35 UTC (rev 18725)
@@ -1,2 +1,4 @@
fix_optimisation_flags.patch
+x86_spezific_opts.patch
hardening.patch
+manpage_syntax.patch
Added: trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch (rev 0)
+++ trunk/packages/vsearch/trunk/debian/patches/x86_spezific_opts.patch 2015-02-02 09:01:35 UTC (rev 18725)
@@ -0,0 +1,59 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Mon, 02 Feb 2015 07:40:07 +0100
+Bugs-Debian: http://bugs.debian.org/776812
+Description: Conditional use of -mtune flag
+
+--- a/src/Makefile.BZLIB
++++ b/src/Makefile.BZLIB
+@@ -26,8 +26,14 @@ PROFILING=-g
+ WARN=-Wall -Wsign-compare
+ #WARN=-Weverything
+
++ifeq ($(USEOPT),no)
++ MTUNE:=""
++else
++ MTUNE:=-mtune=core2
++endif
++
+ CXX=g++
+-CXXFLAGS=-O3 -DHAVE_BZLIB -mtune=core2 -Icityhash $(WARN) $(PROFILING)
++CXXFLAGS=-O3 -DHAVE_BZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
+ LINKFLAGS=$(PROFILING)
+ LIBS=-lpthread -lbz2
+
+--- a/src/Makefile.ZLIB
++++ b/src/Makefile.ZLIB
+@@ -26,8 +26,14 @@ PROFILING=-g
+ WARN=-Wall -Wsign-compare
+ #WARN=-Weverything
+
++ifeq ($(USEOPT),no)
++ MTUNE:=""
++else
++ MTUNE:=-mtune=core2
++endif
++
+ CXX=g++
+-CXXFLAGS=-O3 -DHAVE_ZLIB -mtune=core2 -Icityhash $(WARN) $(PROFILING)
++CXXFLAGS=-O3 -DHAVE_ZLIB $(MTUNE) -Icityhash $(WARN) $(PROFILING)
+ LINKFLAGS=$(PROFILING)
+ LIBS=-lpthread -lz
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -26,8 +26,14 @@ PROFILING=-g
+ WARN=-Wall -Wsign-compare
+ #WARN=-Weverything
+
++ifeq ($(USEOPT),no)
++ MTUNE:=""
++else
++ MTUNE:=-mtune=core2
++endif
++
+ CXX=g++
+-CXXFLAGS=-O3 -mtune=core2 -Icityhash $(WARN) $(PROFILING)
++CXXFLAGS=-O3 $(MTUNE) -Icityhash $(WARN) $(PROFILING)
+ LINKFLAGS=$(PROFILING)
+ LIBS=-lpthread
+
Modified: trunk/packages/vsearch/trunk/debian/rules
===================================================================
--- trunk/packages/vsearch/trunk/debian/rules 2015-02-02 06:56:55 UTC (rev 18724)
+++ trunk/packages/vsearch/trunk/debian/rules 2015-02-02 09:01:35 UTC (rev 18725)
@@ -6,14 +6,25 @@
pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
testdir := $(CURDIR)/debian/$(pkg)-data/usr/share/doc/$(pkg)/tests
+HOST:=$(shell dpkg-architecture -qDEB_HOST_GNU_CPU)
+ifeq ($(HOST),x86_64)
+ USEOPT:=yes
+else
+ ifeq ($(HOST),i386)
+ USEOPT:=yes
+ else
+ USEOPT:=no
+ endif
+endif
+
%:
dh $@ --sourcedirectory=src
override_dh_auto_build:
# See notes in README.source
- dh_auto_build -- -f Makefile.BZLIB
+ dh_auto_build -- -f Makefile.BZLIB USEOPT="$(USEOPT)"
dh_auto_clean
- dh_auto_build -- -f Makefile.ZLIB
+ dh_auto_build -- -f Makefile.ZLIB USEOPT="$(USEOPT)"
dh_auto_clean
dh_auto_build
markdown_py -f README.html README.md
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