[med-svn] r6840 - in trunk/packages/smile/trunk: . debian debian/patches debian/source
Thorsten Alteholz
alteholz-guest at alioth.debian.org
Thu May 19 18:12:35 UTC 2011
Author: alteholz-guest
Date: 2011-05-19 18:12:13 +0000 (Thu, 19 May 2011)
New Revision: 6840
Added:
trunk/packages/smile/trunk/debian/patches/Makefile.patch
trunk/packages/smile/trunk/debian/patches/although.patch
trunk/packages/smile/trunk/debian/patches/misc.patch
trunk/packages/smile/trunk/debian/patches/series
trunk/packages/smile/trunk/debian/source/
trunk/packages/smile/trunk/debian/source/format
Removed:
trunk/packages/smile/trunk/README
trunk/packages/smile/trunk/debian/patches/xyz.diff
Modified:
trunk/packages/smile/trunk/debian/
trunk/packages/smile/trunk/debian/README.Debian
trunk/packages/smile/trunk/debian/changelog
trunk/packages/smile/trunk/debian/compat
trunk/packages/smile/trunk/debian/control
trunk/packages/smile/trunk/debian/copyright
trunk/packages/smile/trunk/debian/dirs
trunk/packages/smile/trunk/debian/manpages
trunk/packages/smile/trunk/debian/rules
Log:
renamed package to biosmile and made it lintian clean
Deleted: trunk/packages/smile/trunk/README
===================================================================
--- trunk/packages/smile/trunk/README 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/README 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1,3 +0,0 @@
-Work on this project was started by Steffen Möller but has stalled.
-Feel free to take it over.
-
Property changes on: trunk/packages/smile/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Modified: trunk/packages/smile/trunk/debian/README.Debian
===================================================================
--- trunk/packages/smile/trunk/debian/README.Debian 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/README.Debian 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1,6 +1,11 @@
smile for Debian
----------------
+ As there is a multimedia package with the same name, I renamed this package
+ to biosmile.
+
+ -- Thorsten Alteholz <debian at alteholz.de>, Wed, 18 May 2011 18:20:05 +0200
+
Renamed SMILE to smile in file names.
The upstream author Laurent Marsan is very supportive of this package
Modified: trunk/packages/smile/trunk/debian/changelog
===================================================================
--- trunk/packages/smile/trunk/debian/changelog 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/changelog 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1,12 +1,24 @@
-smile (1.47-1) unstable; urgency=low
+biosmile (1.47-2) unstable; urgency=low
+ * renamed package to biosmile
+ * Lintian clean
+ * already prepared patches from Steffen Moeller applied
+ * debian/source/format added
+ * debian/compat changed to 8
+ * debian/copyright: new address of FSF, added version to licenses
+ * debian/rules: errors in manpage corrected
+
+ -- Thorsten Alteholz <debian at alteholz.de> Tue, 18 May 2011 18:17:00 +0200
+
+biosmile (1.47-1) unstable; urgency=low
+
* New upstream release.
* GPL license stated in upstream release.
* Sponsored by Aaron M. Ucko <ucko at debian.org>
-- Steffen Moeller <moeller at pzr.uni-rostock.de> Tue, 05 Apr 2004 13:17:00 +0200
-smile (1.46-1) unstable; urgency=low
+biosmile (1.46-1) unstable; urgency=low
* Initial Release (Closes: #221492).
* Upstream author contributed man page.
Modified: trunk/packages/smile/trunk/debian/compat
===================================================================
--- trunk/packages/smile/trunk/debian/compat 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/compat 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1 +1 @@
-4
+8
Modified: trunk/packages/smile/trunk/debian/control
===================================================================
--- trunk/packages/smile/trunk/debian/control 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/control 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1,11 +1,15 @@
-Source: smile
+Source: biosmile
Section: science
Priority: optional
-Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
-Build-Depends: debhelper (>= 4.0.0)
-Standards-Version: 3.6.1.1
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.2
+Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
-Package: smile
+Package: biosmile
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, perl
Description: [Biology] Find statistically significant patterns in sequences
@@ -24,5 +28,3 @@
.
* Introduction of a set of sequences with negative controls
that should not match automatically determined motifs.
- .
- Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Modified: trunk/packages/smile/trunk/debian/copyright
===================================================================
--- trunk/packages/smile/trunk/debian/copyright 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/copyright 2011-05-19 18:12:13 UTC (rev 6840)
@@ -3,7 +3,7 @@
It was downloaded from http://www-igm.univ-mlv.fr/~marsan/smile_english.html
-Upstream Author: Laurent Marsan <marsan at univ-mlv.fr>
+Upstream Author: Copyright 2005 Laurent Marsan <marsan at univ-mlv.fr>
Copyright:
@@ -19,15 +19,15 @@
You should have received a copy of the GPL and the LGPL
along with this package; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
- 02111-1307, USA.
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ 02110-1301, USA.
On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'
+Public License can be found in `/usr/share/common-licenses/GPL-2'
and the full text of the Lesser General Public License in
-'/usr/share/common-licenses/LGPL'.
+'/usr/share/common-licenses/LGPL-2.1'.
-Upstream copyrigh notice from the file COPYING, the Free Software
+Upstream copyright notice from the file COPYING, the Free Software
Foundation's license files COPYING.gpl and COPYING.lgpl are
omitted from the packaging:
Modified: trunk/packages/smile/trunk/debian/dirs
===================================================================
--- trunk/packages/smile/trunk/debian/dirs 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/dirs 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1,4 +1,4 @@
usr/bin
usr/lib
-usr/lib/smile
-usr/lib/smile/bin
+usr/lib/biosmile
+usr/lib/biosmile/bin
Modified: trunk/packages/smile/trunk/debian/manpages
===================================================================
--- trunk/packages/smile/trunk/debian/manpages 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/manpages 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1 +1 @@
-smile.1
+biosmile.1
Added: trunk/packages/smile/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/smile/trunk/debian/patches/Makefile.patch (rev 0)
+++ trunk/packages/smile/trunk/debian/patches/Makefile.patch 2011-05-19 18:12:13 UTC (rev 6840)
@@ -0,0 +1,121 @@
+Add install target to Makefiles
+--- smile-1.47.orig/P_BLOCS/Makefile
++++ smile-1.47/P_BLOCS/Makefile
+@@ -124,4 +124,12 @@
+ depend:
+ makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
+
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/biosmile/
++
++install: all
++ -mkdir -p $(DESTLIBDIR)/bin
++ cp $(BIN_DIR)$(PROG_NAME) $(DESTLIBDIR)/bin
++
++
+ # DO NOT DELETE
+--- smile-1.47.orig/Makefile
++++ smile-1.47/Makefile
+@@ -8,19 +8,26 @@
+
+ all: clean
+ @echo "**** Making P_BLOCS..."
+- (cd $(P_DIR) && $(MAKE) all)
++ $(MAKE) -C $(P_DIR) all
+ @echo "==> P_BLOCS OK."
+ @echo "**** Making P_BLOCS+DELTA..."
+- (cd $(PD_DIR) && $(MAKE) all)
++ $(MAKE) -C $(PD_DIR) all
+ @echo "==> P_BLOCS+DELTA OK."
+ @echo "**** Making SigStat..."
+- (cd $(S_DIR) && $(MAKE) all)
++ $(MAKE) -C $(S_DIR) all
+ @echo "==> SigStat OK."
+
+ clean:
+ @echo Cleaning...
+- (cd $(P_DIR) && $(MAKE) clean)
+- (cd $(PD_DIR) && $(MAKE) clean)
+- (cd $(S_DIR) && $(MAKE) clean)
++ $(MAKE) -C $(P_DIR) clean
++ $(MAKE) -C $(PD_DIR) clean
++ $(MAKE) -C $(S_DIR) clean
+ @echo Clean OK.
+
++DESTDIR=""
++
++install:
++ $(MAKE) -C $(P_DIR) install
++ $(MAKE) -C $(PD_DIR) install
++ $(MAKE) -C $(S_DIR) install
++ cp Lanceur/smile $(DESTDIR)/usr/bin/biosmile
+--- smile-1.47.orig/P_BLOCS+DELTA/Makefile
++++ smile-1.47/P_BLOCS+DELTA/Makefile
+@@ -124,4 +124,12 @@
+ depend:
+ makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
+
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/biosmile/
++
++install: all
++ -mkdir -p $(DESTLIBDIR)/bin
++ cp $(BIN_DIR)$(PROG_NAME) $(DESTLIBDIR)/bin
++
++
+ # DO NOT DELETE
+--- smile-1.47.orig/SigStat/Makefile
++++ smile-1.47/SigStat/Makefile
+@@ -50,7 +50,7 @@
+
+ grep+::
+ @echo Making grep+...
+- (cd $(GREP_DIR) && $(MAKE) obj)
++ $(MAKE) -C $(GREP_DIR) obj
+ @echo Fin du Make de grep+.
+
+ $(SIG_BIN_DIR)$(PROG_NAME): $(SIG_OBJ)
+@@ -86,7 +86,7 @@
+
+
+ clean: clean_emacs clean_obj
+- (cd $(GREP_DIR) && $(MAKE) clean)
++ $(MAKE) -C $(GREP_DIR) clean
+ @echo CLEAN OK!!!
+
+ clean_emacs:
+@@ -102,3 +102,10 @@
+ tgz: clean
+ tar -zcvf $(ARCHIVE_NAME) ./*
+
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/biosmile/
++
++install: all
++ -mkdir -p $(DESTLIBDIR)/bin
++ cp $(SIG_BIN_DIR)$(PROG_NAME) $(SIG_BIN_DIR)$(PROG_NAME2) $(DESTLIBDIR)/bin
++ $(MAKE) -C $(GREP_DIR) install
+--- smile-1.47.orig/SigStat/grep+/Makefile
++++ smile-1.47/SigStat/grep+/Makefile
+@@ -36,7 +36,7 @@
+
+ SPELL_OBJ=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o
+
+-SPELL_OBJ_DEB=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)main.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o
++SPELL_OBJ_DEB=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)main.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o $(SPELL_OBJ_DIR)/sub_suffix_tree.o
+
+ OBJ_FILE=$(TREE_OBJ) $(SPELL_OBJ)
+
+@@ -132,4 +132,12 @@
+
+ depend:
+ makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
++
++DESTDIR=""
++DESTLIBDIR=$(DESTDIR)/usr/lib/biosmile/
++
++install: obj
++ #-mkdir -p $(DESTLIBDIR)/bin
++ #cp $(PROG_NAME) $(DESTLIBDIR)/bin
++
+ # DO NOT DELETE
Added: trunk/packages/smile/trunk/debian/patches/although.patch
===================================================================
--- trunk/packages/smile/trunk/debian/patches/although.patch (rev 0)
+++ trunk/packages/smile/trunk/debian/patches/although.patch 2011-05-19 18:12:13 UTC (rev 6840)
@@ -0,0 +1,12 @@
+Spelling error altough -> although
+--- smile-1.47.orig/SigStat/src/io.c 2011-05-16 18:18:45.000000000 +0200
++++ smile-1.47/SigStat/src/io.c 2011-05-16 18:20:30.000000000 +0200
+@@ -132,7 +132,7 @@
+ fprintf(stderr,
+ "Error: output file contains no occurrences number,\n");
+ fprintf(stderr,
+- " altough statistics on total number of occurrences have been requested.\n");
++ " although statistics on total number of occurrences have been requested.\n");
+ return (NULL);
+ }
+ else
Added: trunk/packages/smile/trunk/debian/patches/misc.patch
===================================================================
--- trunk/packages/smile/trunk/debian/patches/misc.patch (rev 0)
+++ trunk/packages/smile/trunk/debian/patches/misc.patch 2011-05-19 18:12:13 UTC (rev 6840)
@@ -0,0 +1,99 @@
+Different patches for Debian.
+--- smile-1.47.orig/P_BLOCS/src/allocateurs.c
++++ smile-1.47/P_BLOCS/src/allocateurs.c
+@@ -17,6 +17,7 @@
+ /* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */
+ /******************************************************************************/
+
++#include<unistd.h>
+ #include<allocateurs.h>
+
+ Allocateur Noeud_Alloc;
+--- smile-1.47.orig/Lanceur/smile
++++ smile-1.47/Lanceur/smile
+@@ -34,10 +34,22 @@
+ # et symb_compo[i][j] le nb max de ce symbole j apparaissant ds une boite i
+
+ # Chemin des programmes executable ##############################################
+-$prog1 = "../P_BLOCS/bin/x-smile";
+-$prog2 = "../P_BLOCS+DELTA/bin/x-smile_delta";
+-$progstat = "../SigStat/bin/e-smile_shuffling";
+-$progfaux = "../SigStat/bin/e-smile_against";
++
++my $prefix="..";
++if ( -x "/usr/lib/biosmile/bin") {
++ $prefix="/usr/lib/biosmile/bin";
++ $prog1 = "$prefix/x-smile";
++ $prog2 = "$prefix/x-smile_delta";
++ $progstat = "$prefix/e-smile_shuffling";
++ $progfaux = "$prefix/e-smile_against";
++}
++else {
++ $prog1 = "$prefix/P_BLOCS/bin/x-smile";
++ $prog2 = "$prefix/P_BLOCS+DELTA/bin/x-smile_delta";
++ $progstat = "$prefix/SigStat/bin/e-smile_shuffling";
++ $progfaux = "$prefix/SigStat/bin/e-smile_against";
++}
++print STDERR "Using binaries in $prefix\n\n";
+
+ # Fichier de noms de fichiers generes ##########################################
+ $namefile = ".namefile";
+--- smile-1.47.orig/SigStat/grep+/Spell/src/grep+.c
++++ smile-1.47/SigStat/grep+/Spell/src/grep+.c
+@@ -892,14 +892,14 @@
+
+
+
+-
++#ifdef GREPWITHMAIN
+
+ /******************************************************************************/
+ /******************************************************************************/
+ /********************************** MAIN **************************************/
+ /******************************************************************************/
+ /******************************************************************************/
+-/*
++
+ int main(int argc, char **argv)
+ {
+ Criteres criteres, cr;
+@@ -948,4 +948,4 @@
+
+ return(0);
+ }
+-*/
++#endif
+--- smile-1.47.orig/COPYING
++++ smile-1.47/COPYING
+@@ -1,5 +1,5 @@
+ All the source files of this package are distributed according to the GPL
+-License (see COPYING.gpl), excepted
++License (see COPYING.gpl), except
+ libfasta.h
+ libsysk.h
+ Gtypes.h
+--- smile-1.47.orig/t.paam
++++ smile-1.47/t.paam
+@@ -0,0 +1,22 @@
++
++*********************
++ O o
++ ^ SMILE! v1.47
++ \_/
++*********************
++
++EXTRACTION (Step 1) =======================================================
++FASTA file t.fas
++Output file t.fas_out
++
++GLOBAL PARAMETERS =============
++Alphabet file t.fas_alphabet
++Quorum 90
++Total min length 2
++Total max length 10
++Total substitutions 2
++Boxes 1
++
++Composition in ? 0
++
++
Added: trunk/packages/smile/trunk/debian/patches/series
===================================================================
--- trunk/packages/smile/trunk/debian/patches/series (rev 0)
+++ trunk/packages/smile/trunk/debian/patches/series 2011-05-19 18:12:13 UTC (rev 6840)
@@ -0,0 +1,3 @@
+Makefile.patch
+although.patch
+misc.patch
Deleted: trunk/packages/smile/trunk/debian/patches/xyz.diff
===================================================================
--- trunk/packages/smile/trunk/debian/patches/xyz.diff 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/patches/xyz.diff 2011-05-19 18:12:13 UTC (rev 6840)
@@ -1,218 +0,0 @@
---- smile-1.47.orig/P_BLOCS/src/allocateurs.c
-+++ smile-1.47/P_BLOCS/src/allocateurs.c
-@@ -17,6 +17,7 @@
- /* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. */
- /******************************************************************************/
-
-+#include<unistd.h>
- #include<allocateurs.h>
-
- Allocateur Noeud_Alloc;
---- smile-1.47.orig/P_BLOCS/Makefile
-+++ smile-1.47/P_BLOCS/Makefile
-@@ -124,4 +124,12 @@
- depend:
- makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
-
-+DESTDIR=""
-+DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
-+
-+install: all
-+ -mkdir -p $(DESTLIBDIR)/bin
-+ cp $(BIN_DIR)$(PROG_NAME) $(DESTLIBDIR)/bin
-+
-+
- # DO NOT DELETE
---- smile-1.47.orig/Makefile
-+++ smile-1.47/Makefile
-@@ -8,19 +8,26 @@
-
- all: clean
- @echo "**** Making P_BLOCS..."
-- (cd $(P_DIR) && $(MAKE) all)
-+ $(MAKE) -C $(P_DIR) all
- @echo "==> P_BLOCS OK."
- @echo "**** Making P_BLOCS+DELTA..."
-- (cd $(PD_DIR) && $(MAKE) all)
-+ $(MAKE) -C $(PD_DIR) all
- @echo "==> P_BLOCS+DELTA OK."
- @echo "**** Making SigStat..."
-- (cd $(S_DIR) && $(MAKE) all)
-+ $(MAKE) -C $(S_DIR) all
- @echo "==> SigStat OK."
-
- clean:
- @echo Cleaning...
-- (cd $(P_DIR) && $(MAKE) clean)
-- (cd $(PD_DIR) && $(MAKE) clean)
-- (cd $(S_DIR) && $(MAKE) clean)
-+ $(MAKE) -C $(P_DIR) clean
-+ $(MAKE) -C $(PD_DIR) clean
-+ $(MAKE) -C $(S_DIR) clean
- @echo Clean OK.
-
-+DESTDIR=""
-+
-+install:
-+ $(MAKE) -C $(P_DIR) install
-+ $(MAKE) -C $(PD_DIR) install
-+ $(MAKE) -C $(S_DIR) install
-+ cp Lanceur/smile $(DESTDIR)/usr/bin
---- smile-1.47.orig/P_BLOCS+DELTA/Makefile
-+++ smile-1.47/P_BLOCS+DELTA/Makefile
-@@ -124,4 +124,12 @@
- depend:
- makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
-
-+DESTDIR=""
-+DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
-+
-+install: all
-+ -mkdir -p $(DESTLIBDIR)/bin
-+ cp $(BIN_DIR)$(PROG_NAME) $(DESTLIBDIR)/bin
-+
-+
- # DO NOT DELETE
---- smile-1.47.orig/Lanceur/smile
-+++ smile-1.47/Lanceur/smile
-@@ -34,10 +34,22 @@
- # et symb_compo[i][j] le nb max de ce symbole j apparaissant ds une boite i
-
- # Chemin des programmes executable ##############################################
--$prog1 = "../P_BLOCS/bin/x-smile";
--$prog2 = "../P_BLOCS+DELTA/bin/x-smile_delta";
--$progstat = "../SigStat/bin/e-smile_shuffling";
--$progfaux = "../SigStat/bin/e-smile_against";
-+
-+my $prefix="..";
-+if ( -x "/usr/lib/smile/bin") {
-+ $prefix="/usr/lib/smile/bin";
-+ $prog1 = "$prefix/x-smile";
-+ $prog2 = "$prefix/x-smile_delta";
-+ $progstat = "$prefix/e-smile_shuffling";
-+ $progfaux = "$prefix/e-smile_against";
-+}
-+else {
-+ $prog1 = "$prefix/P_BLOCS/bin/x-smile";
-+ $prog2 = "$prefix/P_BLOCS+DELTA/bin/x-smile_delta";
-+ $progstat = "$prefix/SigStat/bin/e-smile_shuffling";
-+ $progfaux = "$prefix/SigStat/bin/e-smile_against";
-+}
-+print STDERR "Using binaries in $prefix\n\n";
-
- # Fichier de noms de fichiers generes ##########################################
- $namefile = ".namefile";
---- smile-1.47.orig/SigStat/Makefile
-+++ smile-1.47/SigStat/Makefile
-@@ -50,7 +50,7 @@
-
- grep+::
- @echo Making grep+...
-- (cd $(GREP_DIR) && $(MAKE) obj)
-+ $(MAKE) -C $(GREP_DIR) obj
- @echo Fin du Make de grep+.
-
- $(SIG_BIN_DIR)$(PROG_NAME): $(SIG_OBJ)
-@@ -86,7 +86,7 @@
-
-
- clean: clean_emacs clean_obj
-- (cd $(GREP_DIR) && $(MAKE) clean)
-+ $(MAKE) -C $(GREP_DIR) clean
- @echo CLEAN OK!!!
-
- clean_emacs:
-@@ -102,3 +102,10 @@
- tgz: clean
- tar -zcvf $(ARCHIVE_NAME) ./*
-
-+DESTDIR=""
-+DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
-+
-+install: all
-+ -mkdir -p $(DESTLIBDIR)/bin
-+ cp $(SIG_BIN_DIR)$(PROG_NAME) $(SIG_BIN_DIR)$(PROG_NAME2) $(DESTLIBDIR)/bin
-+ $(MAKE) -C $(GREP_DIR) install
---- smile-1.47.orig/SigStat/grep+/Makefile
-+++ smile-1.47/SigStat/grep+/Makefile
-@@ -36,7 +36,7 @@
-
- SPELL_OBJ=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o
-
--SPELL_OBJ_DEB=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)main.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o
-+SPELL_OBJ_DEB=$(SPELL_OBJ_DIR)global.o $(SPELL_OBJ_DIR)pile_occ.o $(SPELL_OBJ_DIR)grep+.o $(SPELL_OBJ_DIR)occ.o $(SPELL_OBJ_DIR)criteres.o $(SPELL_OBJ_DIR)barre.o $(SPELL_OBJ_DIR)main.o $(SPELL_OBJ_DIR)alphabet.o $(SPELL_OBJ_DIR)model.o $(SPELL_OBJ_DIR)/sub_suffix_tree.o
-
- OBJ_FILE=$(TREE_OBJ) $(SPELL_OBJ)
-
-@@ -132,4 +132,12 @@
-
- depend:
- makedepend -o.o $(SPELL_INCL_DIR)*.h $(INCL_DIR)*.h $(SPELL_SRC_DIR)*.c $(SRC_DIR)*.c -I$(INCL_DIR) -I$(SPELL_INCL_DIR)
-+
-+DESTDIR=""
-+DESTLIBDIR=$(DESTDIR)/usr/lib/smile/
-+
-+install: obj
-+ #-mkdir -p $(DESTLIBDIR)/bin
-+ #cp $(PROG_NAME) $(DESTLIBDIR)/bin
-+
- # DO NOT DELETE
---- smile-1.47.orig/SigStat/grep+/Spell/src/grep+.c
-+++ smile-1.47/SigStat/grep+/Spell/src/grep+.c
-@@ -892,14 +892,14 @@
-
-
-
--
-+#ifdef GREPWITHMAIN
-
- /******************************************************************************/
- /******************************************************************************/
- /********************************** MAIN **************************************/
- /******************************************************************************/
- /******************************************************************************/
--/*
-+
- int main(int argc, char **argv)
- {
- Criteres criteres, cr;
-@@ -948,4 +948,4 @@
-
- return(0);
- }
--*/
-+#endif
---- smile-1.47.orig/COPYING
-+++ smile-1.47/COPYING
-@@ -1,5 +1,5 @@
- All the source files of this package are distributed according to the GPL
--License (see COPYING.gpl), excepted
-+License (see COPYING.gpl), except
- libfasta.h
- libsysk.h
- Gtypes.h
---- smile-1.47.orig/t.paam
-+++ smile-1.47/t.paam
-@@ -0,0 +1,22 @@
-+
-+*********************
-+ O o
-+ ^ SMILE! v1.47
-+ \_/
-+*********************
-+
-+EXTRACTION (Step 1) =======================================================
-+FASTA file t.fas
-+Output file t.fas_out
-+
-+GLOBAL PARAMETERS =============
-+Alphabet file t.fas_alphabet
-+Quorum 90
-+Total min length 2
-+Total max length 10
-+Total substitutions 2
-+Boxes 1
-+
-+Composition in ? 0
-+
-+
Modified: trunk/packages/smile/trunk/debian/rules
===================================================================
--- trunk/packages/smile/trunk/debian/rules 2011-05-16 13:13:27 UTC (rev 6839)
+++ trunk/packages/smile/trunk/debian/rules 2011-05-19 18:12:13 UTC (rev 6840)
@@ -35,7 +35,13 @@
# Add here commands to compile the package.
$(MAKE)
- zcat smile.1.gz > smile.1
+ # some spellings in compressed man page corrected
+ zcat smile.1.gz |sed "s/\.\.\.which/which/g"|\
+ sed "s/allows to/allows one to/g"|\
+ sed "s/algorithmical/algorithmically/g"|\
+ sed "s/smile \-g/smile \\\-g/g"|\
+ sed "s/smile/biosmile/g"|\
+ sed "s/Smile/Biosmile/g" > biosmile.1
touch build-stamp
@@ -43,20 +49,20 @@
dh_testdir
dh_testroot
rm -f build-stamp configure-stamp
- -rm -r $(CURDIR)/debian/smile
+ -rm -r $(CURDIR)/debian/biosmile
# Add here commands to clean up after the build process.
- -$(MAKE) clean
- dh_clean smile.1
+ [ ! -f Makefile ] || $(MAKE) clean
+ dh_clean biosmile.1
install: build
dh_testdir
dh_testroot
- dh_clean -k
+ dh_prep
dh_installdirs
- # Add here commands to install the package into debian/smile.
- $(MAKE) install DESTDIR=$(CURDIR)/debian/smile
+ # Add here commands to install the package into debian/biosmile.
+ $(MAKE) install DESTDIR=$(CURDIR)/debian/biosmile
# Build architecture-independent files here.
binary-indep: build install
@@ -66,7 +72,7 @@
binary-arch: build install
dh_testdir
dh_testroot
- dh_installchangelogs
+ dh_installchangelogs READ_ME
dh_installdocs
dh_installexamples
dh_installman
Added: trunk/packages/smile/trunk/debian/source/format
===================================================================
--- trunk/packages/smile/trunk/debian/source/format (rev 0)
+++ trunk/packages/smile/trunk/debian/source/format 2011-05-19 18:12:13 UTC (rev 6840)
@@ -0,0 +1 @@
+3.0 (quilt)
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