Update ncbi-toolkit to version 2002.04.26. Use the new ${REINPLACE_CMD} while I am here. Update patch-aa a) to remove a file that is not actually an executable b) not list all the libraries explicitly, just copy all library files we can find. This simplifies future updates and we already know (or will update) what they are via pkg-plist. Update emails in pkg-descr. Fix typo and unnecessary blank lines in pkg-message.
I notice you mentioned an update to patch-aa which i dont see in your submitted patch. -pat
Sorry, updated a single file and regenerated the patch just before sending but used -u instread of -ruN. Here is patch generated correctly this time (I hope!) thanks -- tonym diff -ruN seaview.orig/Makefile seaview/Makefile --- seaview.orig/Makefile Sat May 18 12:36:56 2002 +++ seaview/Makefile Mon Jun 17 10:05:18 2002 @@ -2,34 +2,61 @@ # Date created: Dec 5 1997 # Whom: frankch@waru.life.nthu.edu.tw # -# $FreeBSD: ports/biology/seaview/Makefile,v 1.18 2002/05/18 02:36:56 kris Exp $ +# $FreeBSD: ports/biology/seaview/Makefile,v 1.17 2000/10/08 10:19:17 asami Exp $ # PORTNAME= seaview -PORTVERSION= 1.0 +PORTVERSION= 2002.04.09 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ DISTNAME= ${PORTNAME} EXTRACT_SUFX= .tar -MAINTAINER= frankch@waru.life.nthu.edu.tw +MAINTAINER= tonym@biolateral.com.au -BROKEN= "Checksum is incorrect" - -LIB_DEPENDS= xforms.0:${PORTSDIR}/x11-toolkits/xforms +LIB_DEPENDS= fltk.1:${PORTSDIR}/x11-toolkits/fltk USE_X_PREFIX= YES +USE_MESA= YES NO_WRKSUBDIR= YES -EXTRACT_CMD= ${TAR} +MAKEFILE= makefile +ALL_TARGET= seaview +EXTRACT_CMD= ${TAR} EXTRACT_BEFORE_ARGS= -xf EXTRACT_AFTER_ARGS= # empty +DOCDIR= ${PREFIX}/share/doc/${PORTNAME} + +pre-extract: +.if !defined(BATCH) && !defined(PACKAGE_BUILDING) && !defined(HAVE_UTAH) + @(/usr/bin/dialog --textbox ${MASTERDIR}/pkg-warning 8 70 || ${TRUE}) +.endif + +pre-patch: +.if defined(HAVE_UTAH) +P_CFLAGS= ${PTHREAD_CFLAGS} +P_LIBS= ${PTHREAD_LIBS} +.endif + +post-patch: + @ ${REINPLACE_CMD} -e 's|../fltk|${X11BASE}|;' \ + -e "s|I(.*)$$|I\\1/include|;" \ + -e 's|-lfltk|-lfltk -lGL -lXext|;' \ + -e 's|^CFLAGS =|CFLAGS += ${P_CFLAGS} |;' \ + -e 's|-lm|-lm ${P_LIBS}|;' \ + ${WRKSRC}/${MAKEFILE} + @ ${REINPLACE_CMD} -e "s|tmpnam|mkstemp|;" \ + -e "s|(<stdlib.h>)|\1\n#include <unistd.h>|;" \ + ${WRKSRC}/align.cxx do-install: @ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin - @ (${MKDIR} ${PREFIX}/lib/X11/seaview) - @ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview + @ ${INSTALL_SCRIPT} ${WRKSRC}/seaview_align.sh ${PREFIX}/bin +.if !defined(NOPORTDOCS) + @ ${MKDIR} ${DOCDIR} + @ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${DOCDIR} +.endif post-install: - @ ${CAT} ${DESCR} + @ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE} .include <bsd.port.mk> diff -ruN seaview.orig/distinfo seaview/distinfo --- seaview.orig/distinfo Mon Apr 24 19:45:46 2000 +++ seaview/distinfo Sun Jun 16 16:12:24 2002 @@ -1 +1 @@ -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab +MD5 (seaview.tar) = 28b96855e50986b7e6ff6a0249b062b7 diff -ruN seaview.orig/files/patch-aa seaview/files/patch-aa --- seaview.orig/files/patch-aa Tue Aug 31 13:57:56 1999 +++ seaview/files/patch-aa Thu Jan 1 10:00:00 1970 @@ -1,20 +0,0 @@ ---- Makefile.orig Mon Aug 30 20:54:56 1999 -+++ Makefile Mon Aug 30 20:55:48 1999 -@@ -0,0 +1,17 @@ -+#matpt.h -+#seaview.h -+CC ?= gcc -+CFLAGS+= -I${X11BASE}/include -+LIBS = -L${X11BASE}/lib -lxforms -lX11 -lm -+SRCS = align.c comlines.c load_seq.c regions.c seaview.c use_mase_files.c xfmatpt.c -+OBJS = align.o comlines.o load_seq.o regions.o seaview.o use_mase_files.o xfmatpt.o -+ -+all: seaview -+ -+seaview: $(OBJS) -+ $(CC) -o seaview $(OBJS) $(LIBS) -+ -+c.o.: $(SRCS) -+ $(CC) $(CFLAGS) -c $(SRCS) -+ -+ diff -ruN seaview.orig/pkg-descr seaview/pkg-descr --- seaview.orig/pkg-descr Mon May 3 07:37:59 1999 +++ seaview/pkg-descr Sun Jun 16 18:27:38 2002 @@ -2,14 +2,6 @@ You can align DNA sequences from several organisms, and find out their relative postions in phylogenic tree. -File test.mase can be used as an example file. -Open the on-line help window through button 'Help' to learn seaview usage. +An example file test.mase can be obtained from the ftp site. -WWW: http://acnuc.univ-lyon1.fr/phylogeny/seaview.html - -***************************************************************************** -* The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ . -* Add an entry in your Xresources or Xdefaults file with: -* -* seaview*helpfile: /usr/X11R6/lib/X11/seaview/seaview.help -***************************************************************************** +WWW: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ diff -ruN seaview.orig/pkg-message seaview/pkg-message --- seaview.orig/pkg-message Thu Jan 1 10:00:00 1970 +++ seaview/pkg-message Sun Jun 16 18:31:49 2002 @@ -0,0 +1,6 @@ +***************************************************************************** +* The help file (seaview.help) is located in %%PREFIX%%/share/doc/seaview/ * +* Add an entry in your Xresources or Xdefaults file with: * +* * +* seaview*helpfile: %%PREFIX%%/share/doc/seaview/seaview.help * +***************************************************************************** diff -ruN seaview.orig/pkg-plist seaview/pkg-plist --- seaview.orig/pkg-plist Mon Dec 22 09:04:39 1997 +++ seaview/pkg-plist Sun Jun 16 18:26:13 2002 @@ -1,3 +1,4 @@ bin/seaview -lib/X11/seaview/seaview.help -@dirrm lib/X11/seaview +bin/seaview_align.sh +%%PORTDOCS%%share/doc/seaview/seaview.help +%%PORTDOCS%%@dirrm share/doc/seaview/ diff -ruN seaview.orig/pkg-warning seaview/pkg-warning --- seaview.orig/pkg-warning Thu Jan 1 10:00:00 1970 +++ seaview/pkg-warning Mon Jun 17 08:53:42 2002 @@ -0,0 +1,3 @@ +If you are using XFree86 version 3 with utah-glx hit Ctrl-C now +and use 'make -DHAVE_UTAH' +Otherwise hit OK and continue.
On Mon, Jun 17, 2002 at 10:13:47AM +1000, Tony Maher wrote: > Sorry, updated a single file and regenerated the patch just before sending > but used -u instread of -ruN. > > Here is patch generated correctly this time (I hope!) seaview? i believe you sent the wrong patch.
Pat, ok here it is patch created with -ruN sorry for confusion thanks -- tonym diff -ruN ncbi-toolkit.orig/Makefile ncbi-toolkit/Makefile --- ncbi-toolkit.orig/Makefile Sat Jun 8 10:40:10 2002 +++ ncbi-toolkit/Makefile Sun Jun 16 11:56:45 2002 @@ -6,7 +6,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2001.12.20 +PORTVERSION= 2002.04.26 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -36,7 +36,7 @@ pre-configure: @${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC} @${CP} ${FILESDIR}/freebsd.ncbi.mk ${PLATFORMDIR} - @${PERL} -pi.orig -e 's#NetBSD#FreeBSD#;' -e 's#netbsd#freebsd#' ${BUILDSCRIPT} + @${REINPLACE_CMD} -e 's#NetBSD#FreeBSD#;' -e 's#netbsd#freebsd#' ${BUILDSCRIPT} post-install: @${MKDIR} ${DATADIR} diff -ruN ncbi-toolkit.orig/distinfo ncbi-toolkit/distinfo --- ncbi-toolkit.orig/distinfo Fri Feb 22 18:57:05 2002 +++ ncbi-toolkit/distinfo Sat Jun 15 09:57:51 2002 @@ -1 +1 @@ -MD5 (ncbi.tar.gz) = 8038afb3f5502b3b8ade4f221eebe46e +MD5 (ncbi.tar.gz) = 7278c10b227b0298f00a5ed5dde58bc4 diff -ruN ncbi-toolkit.orig/files/patch-aa ncbi-toolkit/files/patch-aa --- ncbi-toolkit.orig/files/patch-aa Fri Feb 22 18:57:07 2002 +++ ncbi-toolkit/files/patch-aa Sat Jun 15 09:57:51 2002 @@ -1,12 +1,12 @@ ---- make/makeall.unx.orig Thu Apr 5 09:24:30 2001 -+++ make/makeall.unx Tue Sep 18 14:49:24 2001 -@@ -851,3 +851,51 @@ +--- make/makeall.unx.orig Thu Mar 21 06:01:20 2002 ++++ make/makeall.unx Sat Jun 8 20:16:09 2002 +@@ -859,3 +859,46 @@ #load $(LDFLAGS) getmuid.c medutil.c \ $(SRC11) $(SRC8) $(SRC7) $(SRC6) $(SRC5) $(SRC3) \ $(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl + +EXE= Nentrez Psequin \ -+ asn2fast asn2ff asn2xml asndhuff asntool \ ++ asn2ff asn2xml asndhuff asntool \ + bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \ + cdscan checksub copymat \ + ddv dosimple \ @@ -21,13 +21,6 @@ + udv vecscreen + + -+LIB= libncbi.a libncbicdr.a libncbimla.a libncbitxc2.a \ -+ libnetentr.a libncbiCacc.a libncbicn3d.a libncbimmdb.a \ -+ libnetblast.a libvibgif.a libncbiNacc.a libncbidesk.a \ -+ libncbiobj.a libnetcli.a libvibnet.a libncbiacc.a \ -+ libncbiid1.a libncbitool.a libnetcli_.a libvibrant.a -+ -+ +MKDIR= /bin/mkdir -p +INSTALL_PROGRAM= /usr/bin/install -c + @@ -37,7 +30,9 @@ + +linstall: $(LIB) + ${MKDIR} ${PREFIX}/lib/ncbi -+ ${INSTALL_PROGRAM} $? ${PREFIX}/lib/ncbi ++ for file in *.a; do \ ++ ${INSTALL_PROGRAM} $$file ${PREFIX}/lib/ncbi; \ ++ done + +iinstall:: + ${MKDIR} ${PREFIX}/include/ncbi/connect diff -ruN ncbi-toolkit.orig/pkg-descr ncbi-toolkit/pkg-descr --- ncbi-toolkit.orig/pkg-descr Thu Jun 21 00:25:54 2001 +++ ncbi-toolkit/pkg-descr Sat Jun 15 09:57:51 2002 @@ -16,5 +16,4 @@ have found it a useful and stable basis for a number of tools and applications. --- Tony Maher <tony.maher@ebioinformatics.com> - FreeBSD bio-porters <bio@freebsd.net> +-- Tony Maher <tonym@biolateral.com.au> diff -ruN ncbi-toolkit.orig/pkg-message ncbi-toolkit/pkg-message --- ncbi-toolkit.orig/pkg-message Fri Feb 22 18:57:05 2002 +++ ncbi-toolkit/pkg-message Sat Jun 15 09:57:51 2002 @@ -1,8 +1,6 @@ - -The data files are installed in "%%PREFIX%%/share/ncbi-tookit". +The data files are installed in "%%PREFIX%%/share/ncbi-toolkit". To use them you need to create a .ncbirc file in your home directory with the following lines: [NCBI] Data=%%PREFIX%%/share/ncbi-toolkit/ - diff -ruN ncbi-toolkit.orig/pkg-plist ncbi-toolkit/pkg-plist --- ncbi-toolkit.orig/pkg-plist Fri Feb 22 18:57:05 2002 +++ ncbi-toolkit/pkg-plist Sat Jun 15 09:57:51 2002 @@ -37,12 +37,12 @@ %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn19.gif %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn20.gif %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn21.gif +%%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn22.gif %%PORTDOCS%%share/doc/ncbi-toolkit/ncbixml.txt %%PORTDOCS%%share/doc/ncbi-toolkit/sdk.doc %%PORTDOCS%%share/doc/ncbi-toolkit/sequin.htm bin/Nentrez bin/Psequin -bin/asn2fast bin/asn2ff bin/asn2xml bin/asndhuff @@ -87,6 +87,7 @@ bin/testval bin/udv bin/vecscreen +lib/ncbi/libddvlib.a lib/ncbi/libncbi.a lib/ncbi/libncbiCacc.a lib/ncbi/libncbiNacc.a @@ -102,7 +103,6 @@ lib/ncbi/libncbitxc2.a lib/ncbi/libnetblast.a lib/ncbi/libnetcli.a -lib/ncbi/libnetcli_.a lib/ncbi/libnetentr.a lib/ncbi/libvibgif.a lib/ncbi/libvibnet.a @@ -110,6 +110,7 @@ include/ncbi/connect/ncbi_ansi_ext.h include/ncbi/connect/ncbi_buffer.h include/ncbi/connect/ncbi_comm.h +include/ncbi/connect/ncbi_config.h include/ncbi/connect/ncbi_connection.h include/ncbi/connect/ncbi_connector.h include/ncbi/connect/ncbi_connutil.h @@ -117,6 +118,7 @@ include/ncbi/connect/ncbi_file_connector.h include/ncbi/connect/ncbi_heapmgr.h include/ncbi/connect/ncbi_http_connector.h +include/ncbi/connect/ncbi_memory_connector.h include/ncbi/connect/ncbi_priv.h include/ncbi/connect/ncbi_sendmail.h include/ncbi/connect/ncbi_server_info.h
State Changed From-To: open->closed committed, thanks