[med-svn] r253 - in trunk/packages/sigma-align/trunk: debian src
Charles Plessy
charles-guest at alioth.debian.org
Sat Apr 7 12:10:16 UTC 2007
Author: charles-guest
Date: 2007-04-07 12:10:16 +0000 (Sat, 07 Apr 2007)
New Revision: 253
Modified:
trunk/packages/sigma-align/trunk/debian/control
trunk/packages/sigma-align/trunk/debian/copyright
trunk/packages/sigma-align/trunk/debian/rules
trunk/packages/sigma-align/trunk/src/parseopts.c
Log:
adapting to C ; hosting temporarly a patch for building on powerpc
Modified: trunk/packages/sigma-align/trunk/debian/control
===================================================================
--- trunk/packages/sigma-align/trunk/debian/control 2007-04-07 08:26:57 UTC (rev 252)
+++ trunk/packages/sigma-align/trunk/debian/control 2007-04-07 12:10:16 UTC (rev 253)
@@ -3,14 +3,14 @@
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), ocaml-best-compilers, xsltproc, docbook-xsl, docbook-xml
+Build-Depends: debhelper (>= 5), xsltproc, docbook-xsl, docbook-xml
Standards-Version: 3.7.2
XS-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/sigma-align/trunk/
XS-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/sigma-align
Package: sigma-align
Architecture: any
-Depends: ocaml-base-nox-${F:OCamlABI}, ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}
Description: Simple greedy multiple alignment of non-coding DNA sequences
Sigma ("Simple greedy multiple alignment") is an alignment program with a new
algorithm and scoring scheme designed specifically for non-coding DNA
@@ -24,4 +24,4 @@
alignments are superior. It has been published in BMC Bioinformatics. 2006 Mar
16;7:143.
.
- Homepage: http://www.imsc.res.in/~rsidd/sigma/
+ Homepage: http://www.imsc.res.in/~rsidd/sigma/
Modified: trunk/packages/sigma-align/trunk/debian/copyright
===================================================================
--- trunk/packages/sigma-align/trunk/debian/copyright 2007-04-07 08:26:57 UTC (rev 252)
+++ trunk/packages/sigma-align/trunk/debian/copyright 2007-04-07 12:10:16 UTC (rev 253)
@@ -4,7 +4,7 @@
Sigma was downloaded from <http://www.imsc.res.in/~rsidd/sigma/>
-Copyright (C) Rahul Siddharthan, 2006
+Copyright (C) Rahul Siddharthan, 2006-2007
License:
Modified: trunk/packages/sigma-align/trunk/debian/rules
===================================================================
--- trunk/packages/sigma-align/trunk/debian/rules 2007-04-07 08:26:57 UTC (rev 252)
+++ trunk/packages/sigma-align/trunk/debian/rules 2007-04-07 12:10:16 UTC (rev 253)
@@ -1,62 +1,61 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
# dh-make output file, you may use that output file without restriction.
# This special exception was added by Craig Small in version 0.37 of dh-make.
-# Modifications by Charles Plessy during the year 2006
+# Modifications by Charles Plessy during the years 2006-2007
# are hereby released as "public domain".
+configure: configure-stamp
-configure:
+configure-stamp:
+ ./configure --prefix=$(CURDIR)/debian/sigma-align/usr
+ touch configure-stamp
-build: sigma debian/sigma.1
+build: configure-stamp src/sigma debian/sigma.1
-sigma:
- dh_testdir
- if [ -x /usr/bin/ocamlopt ]; then \
- ocamlopt str.cmxa sigma.ml -o sigma ; \
- else \
- ocamlc str.cma sigma.ml -o sigma ; \
- fi
+src/sigma:
+ $(MAKE)
debian/sigma.1: debian/sigma.1.xml
- xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl debian/sigma.1.xml
+ xsltproc -o debian/ \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ debian/sigma.1.xml
-clean:
+clean: configure-stamp
dh_testdir
dh_testroot
- rm -f sigma sigma.cmi sigma.cmx sigma.o
- dh_clean debian/sigma.1 build
+ $(MAKE) distclean
+ dh_clean debian/sigma.1 configure-stamp
install: build
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs /usr/bin
+ $(MAKE) install
binary-indep:
binary-arch: install
dh_testdir
dh_testroot
- dh_installdocs sigma.ml
- dh_install sigma usr/bin
+ dh_installchangelogs ChangeLog
+ dh_installdocs README NOTES
+ dh_installexamples Background
dh_installman debian/sigma.1
- dh_installchangelogs
- mkdir -p debian/sigma-align/usr/share/lintian/overrides/
- cp debian/lintian-override/sigma-align debian/sigma-align/usr/share/lintian/overrides/
dh_link
-# dh_strip
+ dh_strip
dh_compress
dh_fixperms
dh_installdeb
dh_shlibdeps
- dh_gencontrol -s -- -VF:OCamlABI="$(shell ocamlc -version)"
+ dh_gencontrol
dh_md5sums
dh_builddeb
binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+.PHONY: build clean binary-indep binary-arch binary install configure Makefile
Modified: trunk/packages/sigma-align/trunk/src/parseopts.c
===================================================================
--- trunk/packages/sigma-align/trunk/src/parseopts.c 2007-04-07 08:26:57 UTC (rev 252)
+++ trunk/packages/sigma-align/trunk/src/parseopts.c 2007-04-07 12:10:16 UTC (rev 253)
@@ -14,8 +14,8 @@
int parseopts(int argc, char *argv[], params *v)
{
- char ch,Nstr[256],*seqname;
- int n;
+ char Nstr[256],*seqname;
+ int n,ch;
if (argc==0) {
v->printhelp=1;
@@ -38,7 +38,7 @@
while ((ch = getopt_long(argc,argv,"Ab:B:CFhl:n:x:", longopts, NULL)) != -1) {
- switch (ch) {
+ switch ((char) ch) {
case 'A':
n = strlen(v->outtype);
if (n < 255){
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