[med-svn] r258 - in trunk/packages/sigma-align/trunk: . debian src
Charles Plessy
charles-guest at alioth.debian.org
Sun Apr 8 11:31:07 UTC 2007
Author: charles-guest
Date: 2007-04-08 11:31:07 +0000 (Sun, 08 Apr 2007)
New Revision: 258
Added:
trunk/packages/sigma-align/trunk/sigma.1
trunk/packages/sigma-align/trunk/sigma.1.xml
Modified:
trunk/packages/sigma-align/trunk/ChangeLog
trunk/packages/sigma-align/trunk/Makefile.am
trunk/packages/sigma-align/trunk/Makefile.in
trunk/packages/sigma-align/trunk/NOTES
trunk/packages/sigma-align/trunk/README
trunk/packages/sigma-align/trunk/configure
trunk/packages/sigma-align/trunk/configure.ac
trunk/packages/sigma-align/trunk/debian/
trunk/packages/sigma-align/trunk/debian/changelog
trunk/packages/sigma-align/trunk/debian/control
trunk/packages/sigma-align/trunk/debian/rules
trunk/packages/sigma-align/trunk/src/printhelp.c
Log:
New upstream release, which adopts my manpages
Modified: trunk/packages/sigma-align/trunk/ChangeLog
===================================================================
--- trunk/packages/sigma-align/trunk/ChangeLog 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/ChangeLog 2007-04-08 11:31:07 UTC (rev 258)
@@ -1,3 +1,8 @@
+Version 1.1.1:
+ * fix compilation error on powerpc (and maybe other platforms)
+ * include manpage contributed by Charles Plessy
+ * document -l option in NOTES and printhelp.c
+
Version 1.1: rewrite in C, a few bugfixes and improvements
described in README
Modified: trunk/packages/sigma-align/trunk/Makefile.am
===================================================================
--- trunk/packages/sigma-align/trunk/Makefile.am 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/Makefile.am 2007-04-08 11:31:07 UTC (rev 258)
@@ -1,3 +1,3 @@
SUBDIRS=src
-#man_MANS= sigma.1
-EXTRA_DIST= COMPILING NOTES Background/*
+man_MANS= sigma.1
+EXTRA_DIST= $(man_MANS) COMPILING NOTES sigma.1.xml Background/*
Modified: trunk/packages/sigma-align/trunk/Makefile.in
===================================================================
--- trunk/packages/sigma-align/trunk/Makefile.in 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/Makefile.in 2007-04-08 11:31:07 UTC (rev 258)
@@ -56,6 +56,10 @@
install-recursive installcheck-recursive installdirs-recursive \
pdf-recursive ps-recursive uninstall-info-recursive \
uninstall-recursive
+man1dir = $(mandir)/man1
+am__installdirs = "$(DESTDIR)$(man1dir)"
+NROFF = nroff
+MANS = $(man_MANS)
ETAGS = etags
CTAGS = ctags
DIST_SUBDIRS = $(SUBDIRS)
@@ -153,8 +157,8 @@
sysconfdir = @sysconfdir@
target_alias = @target_alias@
SUBDIRS = src
-#man_MANS= sigma.1
-EXTRA_DIST = COMPILING NOTES Background/*
+man_MANS = sigma.1
+EXTRA_DIST = $(man_MANS) COMPILING NOTES sigma.1.xml Background/*
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-recursive
@@ -210,6 +214,51 @@
distclean-hdr:
-rm -f config.h stamp-h1
uninstall-info-am:
+install-man1: $(man1_MANS) $(man_MANS)
+ @$(NORMAL_INSTALL)
+ test -z "$(man1dir)" || $(mkdir_p) "$(DESTDIR)$(man1dir)"
+ @list='$(man1_MANS) $(dist_man1_MANS) $(nodist_man1_MANS)'; \
+ l2='$(man_MANS) $(dist_man_MANS) $(nodist_man_MANS)'; \
+ for i in $$l2; do \
+ case "$$i" in \
+ *.1*) list="$$list $$i" ;; \
+ esac; \
+ done; \
+ for i in $$list; do \
+ if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
+ else file=$$i; fi; \
+ ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+ case "$$ext" in \
+ 1*) ;; \
+ *) ext='1' ;; \
+ esac; \
+ inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+ inst=`echo $$inst | sed -e 's/^.*\///'`; \
+ inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+ echo " $(INSTALL_DATA) '$$file' '$(DESTDIR)$(man1dir)/$$inst'"; \
+ $(INSTALL_DATA) "$$file" "$(DESTDIR)$(man1dir)/$$inst"; \
+ done
+uninstall-man1:
+ @$(NORMAL_UNINSTALL)
+ @list='$(man1_MANS) $(dist_man1_MANS) $(nodist_man1_MANS)'; \
+ l2='$(man_MANS) $(dist_man_MANS) $(nodist_man_MANS)'; \
+ for i in $$l2; do \
+ case "$$i" in \
+ *.1*) list="$$list $$i" ;; \
+ esac; \
+ done; \
+ for i in $$list; do \
+ ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+ case "$$ext" in \
+ 1*) ;; \
+ *) ext='1' ;; \
+ esac; \
+ inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+ inst=`echo $$inst | sed -e 's/^.*\///'`; \
+ inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+ echo " rm -f '$(DESTDIR)$(man1dir)/$$inst'"; \
+ rm -f "$(DESTDIR)$(man1dir)/$$inst"; \
+ done
# This directory's subdirectories are mostly independent; you can cd
# into them and run `make' without going through this Makefile.
@@ -487,9 +536,12 @@
exit 1; } >&2
check-am: all-am
check: check-recursive
-all-am: Makefile config.h
+all-am: Makefile $(MANS) config.h
installdirs: installdirs-recursive
installdirs-am:
+ for dir in "$(DESTDIR)$(man1dir)"; do \
+ test -z "$$dir" || $(mkdir_p) "$$dir"; \
+ done
install: install-recursive
install-exec: install-exec-recursive
install-data: install-data-recursive
@@ -533,13 +585,13 @@
info-am:
-install-data-am:
+install-data-am: install-man
install-exec-am:
install-info: install-info-recursive
-install-man:
+install-man: install-man1
installcheck-am:
@@ -561,10 +613,12 @@
ps-am:
-uninstall-am: uninstall-info-am
+uninstall-am: uninstall-info-am uninstall-man
uninstall-info: uninstall-info-recursive
+uninstall-man: uninstall-man1
+
.PHONY: $(RECURSIVE_TARGETS) CTAGS GTAGS all all-am am--refresh check \
check-am clean clean-generic clean-recursive ctags \
ctags-recursive dist dist-all dist-bzip2 dist-gzip dist-shar \
@@ -573,12 +627,13 @@
distcleancheck distdir distuninstallcheck dvi dvi-am html \
html-am info info-am install install-am install-data \
install-data-am install-exec install-exec-am install-info \
- install-info-am install-man install-strip installcheck \
- installcheck-am installdirs installdirs-am maintainer-clean \
- maintainer-clean-generic maintainer-clean-recursive \
- mostlyclean mostlyclean-generic mostlyclean-recursive pdf \
- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
- uninstall-info-am
+ install-info-am install-man install-man1 install-strip \
+ installcheck installcheck-am installdirs installdirs-am \
+ maintainer-clean maintainer-clean-generic \
+ maintainer-clean-recursive mostlyclean mostlyclean-generic \
+ mostlyclean-recursive pdf pdf-am ps ps-am tags tags-recursive \
+ uninstall uninstall-am uninstall-info-am uninstall-man \
+ uninstall-man1
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
Modified: trunk/packages/sigma-align/trunk/NOTES
===================================================================
--- trunk/packages/sigma-align/trunk/NOTES 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/NOTES 2007-04-08 11:31:07 UTC (rev 258)
@@ -26,7 +26,10 @@
-F, --fasta_output
(multi-fasta output; compare -A option. Default is mixed-case;
for upper-case only, specify -C)
- -n, --ncorrel
+ -l, --maxfraglength
+ (very long sequences are "pre-fragmented" into pieces of this
+ average length, or less, for efficiency; default 4000)
+ -n, --ncorrel
(background correlation order; 2=dinucleotide is the default,
1=single-site basecounts, 0=0.25 per base. Higher than 2 not
implemented at present.)
Modified: trunk/packages/sigma-align/trunk/README
===================================================================
--- trunk/packages/sigma-align/trunk/README 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/README 2007-04-08 11:31:07 UTC (rev 258)
@@ -1,5 +1,5 @@
Sigma: Simple greedy multiple alignment
-Version 1.1, (C) 2007, Rahul Siddharthan <rsidd at imsc.res.in>
+Version 1.1.1, (C) 2007, Rahul Siddharthan <rsidd at imsc.res.in>
This is a port to C of Sigma, which was originally (version 1.0)
written in ocaml. A paper describing the algorithm was published in
@@ -8,6 +8,8 @@
version. It does everything that the ocaml version did, but more
correctly (and faster).
+1.1.1 is a minor update (see ChangeLog) with no new features.
+
Changes since version 1.0:
1. Mismatches in previously-aligned sequence fragments are treated
@@ -40,12 +42,12 @@
legitimate alignments (but, I believe, did not cause incorrect
alignments).
-For help on compiling, see the file COMPILING. For command-line
-options, see the file NOTES or simply run the program without options.
-(A manual page may be written for future versions, but there is not
-really much to describe.) For discussion of background models and a
-sample file, see the Background directory. For a detailed description
-of the algorithm, see BMC Bioinformatics 7:143 (2006).
+For help on compiling, see the file COMPILING. For command-line options, see
+the file NOTES or simply run the program without options. A unix manual page,
+contributed by Charles Plessy, is in "sigma.1" and will be installed with "make
+install". The docbook source is in "sigma.1.xml". For discussion of
+background models and a sample file, see the Background directory. For a
+detailed description of the algorithm, see BMC Bioinformatics 7:143 (2006).
The program is distributed under the GNU General Public License, version 2.
For copyright and licensing information, see COPYING.
Modified: trunk/packages/sigma-align/trunk/configure
===================================================================
--- trunk/packages/sigma-align/trunk/configure 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/configure 2007-04-08 11:31:07 UTC (rev 258)
@@ -1724,7 +1724,7 @@
PACKAGE=sigma
-VERSION=1.1
+VERSION=1.1.1
am__api_version="1.9"
ac_aux_dir=
for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
Modified: trunk/packages/sigma-align/trunk/configure.ac
===================================================================
--- trunk/packages/sigma-align/trunk/configure.ac 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/configure.ac 2007-04-08 11:31:07 UTC (rev 258)
@@ -2,7 +2,7 @@
AM_CONFIG_HEADER(config.h)
PACKAGE=sigma
-VERSION=1.1
+VERSION=1.1.1
AM_INIT_AUTOMAKE([$PACKAGE], [$VERSION])
# Checks for programs.
Property changes on: trunk/packages/sigma-align/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
- 1
Modified: trunk/packages/sigma-align/trunk/debian/changelog
===================================================================
--- trunk/packages/sigma-align/trunk/debian/changelog 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/debian/changelog 2007-04-08 11:31:07 UTC (rev 258)
@@ -1,10 +1,12 @@
-sigma-align (1.1-1) unstable; urgency=low
+sigma-align (1.1.1-1) unstable; urgency=low
* New upstream release.
- * Manpage enhanced by the upstream author of sigma.
+ - 1.1 : complete rewrite in C.
+ - 1.1.1 : fixes a building problem on powerpc.
+ * Manpage adopted and updated by the upstream author of Sigma.
* Add Subversion repository URL to debian/control.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 4 Mar 2007 22:54:45 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 8 Apr 2007 15:26:34 +0900
sigma-align (1.0-1) unstable; urgency=low
Modified: trunk/packages/sigma-align/trunk/debian/control
===================================================================
--- trunk/packages/sigma-align/trunk/debian/control 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/debian/control 2007-04-08 11:31:07 UTC (rev 258)
@@ -3,7 +3,7 @@
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), xsltproc, docbook-xsl, docbook-xml
+Build-Depends: debhelper (>= 5), xsltproc, docbook-xsl, docbook-xml, libglib2.0-dev
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
Modified: trunk/packages/sigma-align/trunk/debian/rules
===================================================================
--- trunk/packages/sigma-align/trunk/debian/rules 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/debian/rules 2007-04-08 11:31:07 UTC (rev 258)
@@ -11,24 +11,26 @@
./configure --prefix=$(CURDIR)/debian/sigma-align/usr
touch configure-stamp
-build: configure-stamp src/sigma debian/sigma.1
+build: configure src/sigma manpage
-src/sigma:
+src/sigma: configure
$(MAKE)
-debian/sigma.1: debian/sigma.1.xml
- xsltproc -o debian/ \
- -''-nonet \
+manpage: manpage-stamp
+
+manpage-stamp:
+ xsltproc -''-nonet \
-''-param man.charmap.use.subset "0" \
-''-param make.year.ranges "1" \
-''-param make.single.year.ranges "1" \
- debian/sigma.1.xml
+ sigma.1.xml
+ touch manpage-stamp
clean: configure-stamp
dh_testdir
dh_testroot
$(MAKE) distclean
- dh_clean debian/sigma.1 configure-stamp
+ dh_clean configure-stamp manpage-stamp
install: build
dh_testdir
@@ -45,7 +47,7 @@
dh_installchangelogs ChangeLog
dh_installdocs README NOTES
dh_installexamples Background
- dh_installman debian/sigma.1
+ dh_installman sigma.1
dh_link
dh_strip
dh_compress
@@ -58,4 +60,4 @@
binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure Makefile
+.PHONY: build clean binary-indep binary-arch binary install configure
Copied: trunk/packages/sigma-align/trunk/sigma.1 (from rev 257, trunk/packages/sigma-align/branches/upstream/current/sigma.1)
Copied: trunk/packages/sigma-align/trunk/sigma.1.xml (from rev 257, trunk/packages/sigma-align/branches/upstream/current/sigma.1.xml)
Modified: trunk/packages/sigma-align/trunk/src/printhelp.c
===================================================================
--- trunk/packages/sigma-align/trunk/src/printhelp.c 2007-04-08 06:27:40 UTC (rev 257)
+++ trunk/packages/sigma-align/trunk/src/printhelp.c 2007-04-08 11:31:07 UTC (rev 258)
@@ -1,8 +1,3 @@
-/* Sigma - Simple greedy multiple alignment */
-/* Copyright (C) 2007 Rahul Siddharthan */
-/* Licensed under the GNU GPL, version 2 */
-/* See file COPYING in source distribution */
-
#include <stdio.h>
void printhelp() {
printf("Sigma, version 1.1: simple greedy multiple alignment\n");
@@ -33,7 +28,10 @@
printf(" -F, --fasta_output \n");
printf(" (multi-fasta output; compare -A option. Default is mixed-case;\n");
printf(" for upper-case only, specify -C)\n");
- printf(" -n, --ncorrel\n");
+ printf(" -l, --maxfraglength \n");
+ printf(" (very long sequences are \"pre-fragmented\" into pieces of this \n");
+ printf(" average length, or less, for efficiency; default 4000)\n");
+ printf(" -n, --ncorrel \n");
printf(" (background correlation order; 2=dinucleotide is the default,\n");
printf(" 1=single-site basecounts, 0=0.25 per base. Higher than 2 not\n");
printf(" implemented at present.)\n");
More information about the debian-med-commit
mailing list