I updated biology/chemtool. Recent version is availble at http://ruby.chemie.uni-freiburg.de/~martin/chemtool/, where chemtool are actively maintained. Former site http://www.uni-ulm.de/~s_tvolk/chemtool.html is not maintained. Please see revision history, massive enhancement, many many bug fixes are already done.
Hi, I'm very sorry, please insert GNU_CONFIGURE= yes in Makefile. I made a mistake. Thanks, Nakata Maho
I updated former patch(please ignore former patch, sorry!) to enable undo and redo. Sorry for trouble. Again, please ignore former patch!! diff -urN /work/cvsup/ports/science/chemtool/Makefile chemtool/Makefile --- /work/cvsup/ports/science/chemtool/Makefile Tue Sep 11 16:46:02 2001 +++ chemtool/Makefile Thu Aug 15 11:28:11 2002 @@ -1,21 +1,42 @@ -# ex:ts=8 # New ports collection makefile for: chemtool # Date created: Mar 31, 2001 # Whom: Ying-Chieh Liao <ijliao@FreeBSD.org> # -# $FreeBSD: ports/science/chemtool/Makefile,v 1.2 2001/09/11 07:46:02 ijliao Exp $ +# $FreeBSD$ PORTNAME= chemtool -PORTVERSION= 1.3.1 +PORTVERSION= 1.6 CATEGORIES= science -MASTER_SITES= http://www.uni-ulm.de/~s_tvolk/chemtool/src/ +MASTER_SITES= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ +DISTNAME= ct16a6 +EXTRACT_SUFX= .tgz MAINTAINER= ports@FreeBSD.org RUN_DEPENDS= transfig:${PORTSDIR}/print/transfig +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}alpha6 +USE_REINPLACE= yes USE_GTK= yes +GNU_CONFIGURE= yes +USE_GMAKE= yes +MAN1= chemtool.1 cht.1 -MAN1= chemtool.1 +do-build: + @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${GMAKE}) + +pre-patch: + @${REINPLACE_CMD} -e 's|gtk-config|${GTK_CONFIG}|g;' \ + ${WRKSRC}/configure + @${REINPLACE_CMD} -e 's|gtk-config|${GTK_CONFIG}|g; s|-lgtk|-lgtk12|g;' \ + ${WRKSRC}/Makefile.in + +do-install: + @(cd ${WRKSRC}; ${GMAKE} install) + @(cd ${WRKSRC}; \ + ${MKDIR} ${PREFIX}/share/examples/chemtool/; \ + cd ${WRKSRC}/examples/; \ + ${INSTALL_DATA} * ${PREFIX}/share/examples/chemtool; \ + ) .include <bsd.port.mk> diff -urN /work/cvsup/ports/science/chemtool/distinfo chemtool/distinfo --- /work/cvsup/ports/science/chemtool/distinfo Tue Sep 11 16:46:02 2001 +++ chemtool/distinfo Mon Jul 15 16:37:42 2002 @@ -1 +1 @@ -MD5 (chemtool-1.3.1.tar.gz) = 1b61a19a9757292b9b9a827b798f0320 +MD5 (ct16a6.tgz) = a3297b3f6512897a02e1b99f829b7ada diff -urN /work/cvsup/ports/science/chemtool/files/patch-Makefile chemtool/files/patch-Makefile --- /work/cvsup/ports/science/chemtool/files/patch-Makefile Fri Sep 21 23:18:28 2001 +++ chemtool/files/patch-Makefile Thu Jan 1 09:00:00 1970 @@ -1,39 +0,0 @@ -$FreeBSD: ports/science/chemtool/files/patch-Makefile,v 1.4 2001/09/21 14:18:28 sf Exp $ - ---- Makefile.orig Thu May 3 08:31:00 2001 -+++ Makefile Fri Sep 21 23:15:06 2001 -@@ -1,7 +1,5 @@ --PREFIX=/usr/local --LOCALEDIR=/usr/share/locale --CFLAGS=-O2 -Wall `gtk-config --cflags` # -DDISABLE_NLS --CC=gcc -+LOCALEDIR=${PREFIX}/share/locale -+CFLAGS+=`${GTK_CONFIG} --cflags` # -DDISABLE_NLS - CP=/bin/cp - RM=/bin/rm -f - -@@ -9,7 +7,7 @@ - OBJS = main.o chemproc.o graph.o draw.o inout.o - - --SYS_LIBRARIES = `gtk-config --libs` -lm -+SYS_LIBRARIES = `${GTK_CONFIG} --libs` -lm - - all: chemtool cht - -@@ -25,9 +23,12 @@ - # ${CC} ${CFLAGS} ${EXTRA_INCLUDES} -c ${SRCS} - - install: chemtool src-cht/cht -- ${CP} chemtool src-cht/cht ${PREFIX}/bin -- ${CP} chemtool.1 ${PREFIX}/man/man1 -- for L in `ls locales`; do ${CP} locales/$$L/chemtool.mo ${LOCALEDIR}/$$L/LC_MESSAGES;done -+ ${BSD_INSTALL_PROGRAM} chemtool src-cht/cht ${PREFIX}/bin -+ ${BSD_INSTALL_MAN} chemtool.1 ${PREFIX}/man/man1 -+ for L in `ls locales`; do \ -+ mkdir -p ${LOCALEDIR}/$$L/LC_MESSAGES; \ -+ ${BSD_INSTALL_DATA} locales/$$L/chemtool.mo ${LOCALEDIR}/$$L/LC_MESSAGES; \ -+ done - - clean: - ${RM} *.o *~ src-cht/*.o src-cht/*~ chemtool src-cht/cht diff -urN /work/cvsup/ports/science/chemtool/files/patch-aa chemtool/files/patch-aa --- /work/cvsup/ports/science/chemtool/files/patch-aa Thu Jan 1 09:00:00 1970 +++ chemtool/files/patch-aa Thu Aug 15 11:29:11 2002 @@ -0,0 +1,11 @@ +--- undo.c.orig Mon Jul 15 16:41:57 2002 ++++ undo.c Mon Jul 15 16:43:17 2002 +@@ -61,7 +61,7 @@ + #define MAP_NEW_ANON_AT_FLAGS(pos, size, flags) \ + (mmap((pos), (size), \ + PROT_READ | PROT_WRITE | PROT_EXEC, \ +- MAP_PRIVATE | MAP_ANONYMOUS | (flags), 0, 0)) ++ MAP_PRIVATE | MAP_ANON | (flags), -1, 0)) + #define MAP_NEW_ANON(size) MAP_NEW_ANON_AT_FLAGS(0, (size), 0) + #define MAP_NEW_ANON_AT(pos, size) \ + MAP_NEW_ANON_AT_FLAGS((pos), (size), MAP_FIXED) diff -urN /work/cvsup/ports/science/chemtool/files/patch-ab chemtool/files/patch-ab --- /work/cvsup/ports/science/chemtool/files/patch-ab Thu Jan 1 09:00:00 1970 +++ chemtool/files/patch-ab Thu Aug 15 11:29:17 2002 @@ -0,0 +1,11 @@ +--- Makefile.in.orig Wed Aug 14 12:36:43 2002 ++++ Makefile.in Wed Aug 14 12:37:10 2002 +@@ -5,7 +5,7 @@ + mandir=@mandir@ + kdedir=@kdemimedir@ + gnomedir=@gnomemimedir@ +-CFLAGS=-O2 -Wall -Wunused -Wuninitialized -I. `/usr/X11R6/bin/gtk12-config --cflags` @DEFS@ -DLOCALEDIR=\"${localedir}\" ++CFLAGS+= -Wall -Wunused -Wuninitialized -I. `/usr/X11R6/bin/gtk12-config --cflags` @DEFS@ -DLOCALEDIR=\"${localedir}\" + + CC=@CC@ + CP=/bin/cp diff -urN /work/cvsup/ports/science/chemtool/files/patch-src-cht::Makefile chemtool/files/patch-src-cht::Makefile --- /work/cvsup/ports/science/chemtool/files/patch-src-cht::Makefile Tue Sep 11 16:46:02 2001 +++ chemtool/files/patch-src-cht::Makefile Thu Jan 1 09:00:00 1970 @@ -1,8 +0,0 @@ ---- src-cht/Makefile.orig Wed Feb 7 03:38:54 2001 -+++ src-cht/Makefile Sat Apr 14 02:13:38 2001 -@@ -1,4 +1,4 @@ - default: cht - - cht: cht-1.7.c -- gcc -O cht-1.7.c -lm -o cht -+ ${CC} ${CFLAGS} cht-1.7.c -lm -o cht diff -urN /work/cvsup/ports/science/chemtool/pkg-descr chemtool/pkg-descr --- /work/cvsup/ports/science/chemtool/pkg-descr Sat Mar 31 04:22:59 2001 +++ chemtool/pkg-descr Wed Aug 14 13:12:45 2002 @@ -1,4 +1,4 @@ Chemtool is a program for drawing organic molecules easily and store them as a X bitmap file. -WWW: http://www.uni-ulm.de/~s_tvolk/chemtool.html +WWW: http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ diff -urN /work/cvsup/ports/science/chemtool/pkg-plist chemtool/pkg-plist --- /work/cvsup/ports/science/chemtool/pkg-plist Tue Sep 11 16:46:02 2001 +++ chemtool/pkg-plist Wed Aug 14 13:06:04 2002 @@ -1,5 +1,39 @@ bin/chemtool bin/cht +share/examples/chemtool/14263232.mol +share/examples/chemtool/AMP.cht +share/examples/chemtool/Adenosine.cht +share/examples/chemtool/Dehydrotubifolin.cht +share/examples/chemtool/G-host.pdb +share/examples/chemtool/Indolizomycin.cht +share/examples/chemtool/Lepicidin-A-Aglycon.cht +share/examples/chemtool/Neu2 +share/examples/chemtool/amine.mol +share/examples/chemtool/bcarotin.pdb +share/examples/chemtool/breve.cht +share/examples/chemtool/breve.mol +share/examples/chemtool/byrostatin1.cht +share/examples/chemtool/c70.cht +share/examples/chemtool/camphor +share/examples/chemtool/claisen.cht +share/examples/chemtool/dodecahedran.cht +share/examples/chemtool/example1 +share/examples/chemtool/example2 +share/examples/chemtool/example3 +share/examples/chemtool/example4 +share/examples/chemtool/example5 +share/examples/chemtool/example7 +share/examples/chemtool/indigo +share/examples/chemtool/kdo +share/examples/chemtool/krebs.cht +share/examples/chemtool/pagodan.cht +share/examples/chemtool/penicillin_v.cht +share/examples/chemtool/pteridin +share/examples/chemtool/reaction.cht +share/examples/chemtool/rutamycin_b.cht +share/examples/chemtool/tcdd.cht +share/examples/chemtool/viagra.cht share/locale/cs/LC_MESSAGES/chemtool.mo share/locale/de/LC_MESSAGES/chemtool.mo share/locale/ru/LC_MESSAGES/chemtool.mo +@dirrm share/examples/chemtool -- Sincerely, Nakata Maho
In article <200208150250.g7F2o37e005234@freefall.freebsd.org> you write: > PORTNAME= chemtool > -PORTVERSION= 1.3.1 > +PORTVERSION= 1.6 No... > CATEGORIES= science > -MASTER_SITES= http://www.uni-ulm.de/~s_tvolk/chemtool/src/ > +MASTER_SITES= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ > +DISTNAME= ct16a6 This is not version 1.6, this is some alpha version. Either fix PORTVERSION, or better yet wait for the next release. > +do-build: > + @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${GMAKE}) Why introduce a do-build target here? General note: Each command line in a Makefile is executed in a separate shell invocation. Adding an extra subshell (...) is usless. -- Christian "naddy" Weisgerber naddy@mips.inka.de
Hello, Mr. Christian Weisgerber, thank you very much for your comment. > > PORTNAME= chemtool > > -PORTVERSION= 1.3.1 > > +PORTVERSION= 1.6 > > No... > > > CATEGORIES= science > > -MASTER_SITES= http://www.uni-ulm.de/~s_tvolk/chemtool/src/ > > +MASTER_SITES= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ > > +DISTNAME= ct16a6 > > This is not version 1.6, this is some alpha version. > Either fix PORTVERSION, or better yet wait for the next release. Next release may be later, but many useful features are available in these development series. Many templates, useful import mode from BABEL, MDL molfile... everything is good for chemist. I'm currently using this one but I don't have serious problems. If it is possible, what PORTVERSION should be set? 16a6? 1.6.0.6? > > +do-build: > > + @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${GMAKE}) > > Why introduce a do-build target here? CFLAGS are ignored, so that I set ${SETENV} ${MAKE_ENV}. > General note: Each command line in a Makefile is executed in a > separate shell invocation. Adding an extra subshell (...) is usless. Thank you very much for your advice. Sincerely yours, Nakata Maho
Hello, Naddy, We recieved an e-mail from Dr. Martin Kroeker<martin@ruby.chemie.uni-freiburg.de>, and I decided to make an upgrade for chemtool-1.5 not 1.6alpha. My recognition was wrong, 1.6alpha is not stable as you told. Sorry for your trouble. Here is a patch to, # $FreeBSD: ports/science/chemtool/Makefile,v 1.2 2001/09/11 07:46:02 ijliao Exp$ -- cut here ---- cut here ---- cut here ---- cut here ---- cut here -- diff -urN /work/cvsup/ports/science/chemtool/Makefile chemtool/Makefile --- /work/cvsup/ports/science/chemtool/Makefile Tue Sep 11 16:46:02 2001 +++ chemtool/Makefile Thu Aug 22 10:43:09 2002 @@ -1,21 +1,35 @@ -# ex:ts=8 # New ports collection makefile for: chemtool # Date created: Mar 31, 2001 # Whom: Ying-Chieh Liao <ijliao@FreeBSD.org> # -# $FreeBSD: ports/science/chemtool/Makefile,v 1.2 2001/09/11 07:46:02 ijliao Exp $ +# $FreeBSD$ PORTNAME= chemtool -PORTVERSION= 1.3.1 +PORTVERSION= 1.5 CATEGORIES= science -MASTER_SITES= http://www.uni-ulm.de/~s_tvolk/chemtool/src/ +MASTER_SITES= http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ MAINTAINER= ports@FreeBSD.org RUN_DEPENDS= transfig:${PORTSDIR}/print/transfig +USE_REINPLACE= yes USE_GTK= yes +GNU_CONFIGURE= yes +USE_GMAKE= yes +MAN1= chemtool.1 cht.1 -MAN1= chemtool.1 +pre-patch: + @${REINPLACE_CMD} -e 's|gtk-config|${GTK_CONFIG}|g;' \ + ${WRKSRC}/configure + @${REINPLACE_CMD} -e 's|gtk-config|${GTK_CONFIG}|g; s|-lgtk|-lgtk12|g;' \ + ${WRKSRC}/Makefile.in + +do-install: + @cd ${WRKSRC}; ${GMAKE} install + @cd ${WRKSRC}; \ + ${MKDIR} ${PREFIX}/share/examples/chemtool/; \ + cd ${WRKSRC}/examples/; \ + ${INSTALL_DATA} * ${PREFIX}/share/examples/chemtool .include <bsd.port.mk> diff -urN /work/cvsup/ports/science/chemtool/distinfo chemtool/distinfo --- /work/cvsup/ports/science/chemtool/distinfo Tue Sep 11 16:46:02 2001 +++ chemtool/distinfo Thu Aug 22 10:29:16 2002 @@ -1 +1 @@ -MD5 (chemtool-1.3.1.tar.gz) = 1b61a19a9757292b9b9a827b798f0320 +MD5 (chemtool-1.5.tar.gz) = 093b68e032b2c5611c2f83315764bd40 diff -urN /work/cvsup/ports/science/chemtool/files/patch-Makefile chemtool/files/patch-Makefile --- /work/cvsup/ports/science/chemtool/files/patch-Makefile Fri Sep 21 23:18:28 2001 +++ chemtool/files/patch-Makefile Thu Jan 1 09:00:00 1970 @@ -1,39 +0,0 @@ -$FreeBSD: ports/science/chemtool/files/patch-Makefile,v 1.4 2001/09/21 14:18:28 sf Exp $ - ---- Makefile.orig Thu May 3 08:31:00 2001 -+++ Makefile Fri Sep 21 23:15:06 2001 -@@ -1,7 +1,5 @@ --PREFIX=/usr/local --LOCALEDIR=/usr/share/locale --CFLAGS=-O2 -Wall `gtk-config --cflags` # -DDISABLE_NLS --CC=gcc -+LOCALEDIR=${PREFIX}/share/locale -+CFLAGS+=`${GTK_CONFIG} --cflags` # -DDISABLE_NLS - CP=/bin/cp - RM=/bin/rm -f - -@@ -9,7 +7,7 @@ - OBJS = main.o chemproc.o graph.o draw.o inout.o - - --SYS_LIBRARIES = `gtk-config --libs` -lm -+SYS_LIBRARIES = `${GTK_CONFIG} --libs` -lm - - all: chemtool cht - -@@ -25,9 +23,12 @@ - # ${CC} ${CFLAGS} ${EXTRA_INCLUDES} -c ${SRCS} - - install: chemtool src-cht/cht -- ${CP} chemtool src-cht/cht ${PREFIX}/bin -- ${CP} chemtool.1 ${PREFIX}/man/man1 -- for L in `ls locales`; do ${CP} locales/$$L/chemtool.mo ${LOCALEDIR}/$$L/LC_MESSAGES;done -+ ${BSD_INSTALL_PROGRAM} chemtool src-cht/cht ${PREFIX}/bin -+ ${BSD_INSTALL_MAN} chemtool.1 ${PREFIX}/man/man1 -+ for L in `ls locales`; do \ -+ mkdir -p ${LOCALEDIR}/$$L/LC_MESSAGES; \ -+ ${BSD_INSTALL_DATA} locales/$$L/chemtool.mo ${LOCALEDIR}/$$L/LC_MESSAGES; \ -+ done - - clean: - ${RM} *.o *~ src-cht/*.o src-cht/*~ chemtool src-cht/cht diff -urN /work/cvsup/ports/science/chemtool/files/patch-aa chemtool/files/patch-aa --- /work/cvsup/ports/science/chemtool/files/patch-aa Thu Jan 1 09:00:00 1970 +++ chemtool/files/patch-aa Thu Aug 15 11:29:11 2002 @@ -0,0 +1,11 @@ +--- undo.c.orig Mon Jul 15 16:41:57 2002 ++++ undo.c Mon Jul 15 16:43:17 2002 +@@ -61,7 +61,7 @@ + #define MAP_NEW_ANON_AT_FLAGS(pos, size, flags) \ + (mmap((pos), (size), \ + PROT_READ | PROT_WRITE | PROT_EXEC, \ +- MAP_PRIVATE | MAP_ANONYMOUS | (flags), 0, 0)) ++ MAP_PRIVATE | MAP_ANON | (flags), -1, 0)) + #define MAP_NEW_ANON(size) MAP_NEW_ANON_AT_FLAGS(0, (size), 0) + #define MAP_NEW_ANON_AT(pos, size) \ + MAP_NEW_ANON_AT_FLAGS((pos), (size), MAP_FIXED) diff -urN /work/cvsup/ports/science/chemtool/files/patch-ab chemtool/files/patch-ab --- /work/cvsup/ports/science/chemtool/files/patch-ab Thu Jan 1 09:00:00 1970 +++ chemtool/files/patch-ab Thu Aug 15 11:29:17 2002 @@ -0,0 +1,11 @@ +--- Makefile.in.orig Wed Aug 14 12:36:43 2002 ++++ Makefile.in Wed Aug 14 12:37:10 2002 +@@ -5,7 +5,7 @@ + mandir=@mandir@ + kdedir=@kdemimedir@ + gnomedir=@gnomemimedir@ +-CFLAGS=-O2 -Wall -Wunused -Wuninitialized -I. `/usr/X11R6/bin/gtk12-config --cflags` @DEFS@ -DLOCALEDIR=\"${localedir}\" ++CFLAGS+= -Wall -Wunused -Wuninitialized -I. `/usr/X11R6/bin/gtk12-config --cflags` @DEFS@ -DLOCALEDIR=\"${localedir}\" + + CC=@CC@ + CP=/bin/cp diff -urN /work/cvsup/ports/science/chemtool/files/patch-src-cht::Makefile chemtool/files/patch-src-cht::Makefile --- /work/cvsup/ports/science/chemtool/files/patch-src-cht::Makefile Tue Sep 11 16:46:02 2001 +++ chemtool/files/patch-src-cht::Makefile Thu Jan 1 09:00:00 1970 @@ -1,8 +0,0 @@ ---- src-cht/Makefile.orig Wed Feb 7 03:38:54 2001 -+++ src-cht/Makefile Sat Apr 14 02:13:38 2001 -@@ -1,4 +1,4 @@ - default: cht - - cht: cht-1.7.c -- gcc -O cht-1.7.c -lm -o cht -+ ${CC} ${CFLAGS} cht-1.7.c -lm -o cht diff -urN /work/cvsup/ports/science/chemtool/pkg-descr chemtool/pkg-descr --- /work/cvsup/ports/science/chemtool/pkg-descr Sat Mar 31 04:22:59 2001 +++ chemtool/pkg-descr Wed Aug 14 13:12:45 2002 @@ -1,4 +1,4 @@ Chemtool is a program for drawing organic molecules easily and store them as a X bitmap file. -WWW: http://www.uni-ulm.de/~s_tvolk/chemtool.html +WWW: http://ruby.chemie.uni-freiburg.de/~martin/chemtool/ diff -urN /work/cvsup/ports/science/chemtool/pkg-plist chemtool/pkg-plist --- /work/cvsup/ports/science/chemtool/pkg-plist Tue Sep 11 16:46:02 2001 +++ chemtool/pkg-plist Thu Aug 22 10:28:35 2002 @@ -1,5 +1,36 @@ bin/chemtool bin/cht +share/examples/chemtool/14263232.mol +share/examples/chemtool/AMP.cht +share/examples/chemtool/Adenosine.cht +share/examples/chemtool/Dehydrotubifolin.cht +share/examples/chemtool/G-host.pdb +share/examples/chemtool/Indolizomycin.cht +share/examples/chemtool/Lepicidin-A-Aglycon.cht +share/examples/chemtool/Neu2 +share/examples/chemtool/amine.mol +share/examples/chemtool/bcarotin.pdb +share/examples/chemtool/breve.cht +share/examples/chemtool/breve.mol +share/examples/chemtool/byrostatin1.cht +share/examples/chemtool/camphor +share/examples/chemtool/claisen.cht +share/examples/chemtool/example1 +share/examples/chemtool/example2 +share/examples/chemtool/example3 +share/examples/chemtool/example4 +share/examples/chemtool/example5 +share/examples/chemtool/example7 +share/examples/chemtool/indigo +share/examples/chemtool/kdo +share/examples/chemtool/krebs.cht +share/examples/chemtool/penicillin_v.cht +share/examples/chemtool/pteridin +share/examples/chemtool/reaction.cht +share/examples/chemtool/rutamycin_b.cht +share/examples/chemtool/tcdd.cht +share/examples/chemtool/viagra.cht share/locale/cs/LC_MESSAGES/chemtool.mo share/locale/de/LC_MESSAGES/chemtool.mo share/locale/ru/LC_MESSAGES/chemtool.mo +@dirrm share/examples/chemtool -- cut here ---- cut here ---- cut here ---- cut here ---- cut here -- I tested with (make clean ; make install ; make deinstall ) and portlint and got no errors. If you think it is worth, would you please commit my update patch? Sincerely yours, Nakata Maho
Responsible Changed From-To: freebsd-ports->naddy I'll look at this.
State Changed From-To: open->closed There were lots of problems with this. I committed a fixed version.