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 M�ller 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 <[email protected]>, 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 <[email protected]> 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 <[email protected]> -- Steffen Moeller <[email protected]> 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 <[email protected]> -Build-Depends: debhelper (>= 4.0.0) -Standards-Version: 3.6.1.1 +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller <[email protected]>, + Thorsten Alteholz <[email protected]> +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 <[email protected]> +Upstream Author: Copyright 2005 Laurent Marsan <[email protected]> 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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