Date: Sun, 16 Jun 2002 18:00:14 -0700 (PDT) From: Tony Maher <tonym@biolateral.com.au> To: freebsd-ports@FreeBSD.org Subject: Re: ports/39357: Maintainer update: biology/ncbi-toolkit Message-ID: <200206170100.g5H10EN85352@freefall.freebsd.org>
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The following reply was made to PR ports/39357; it has been noted by GNATS. From: Tony Maher <tonym@biolateral.com.au> To: pat@FreeBSD.ORG Cc: freebsd-gnats-submit@FreeBSD.ORG Subject: Re: ports/39357: Maintainer update: biology/ncbi-toolkit Date: Mon, 17 Jun 2002 10:54:24 +1000 (EST) 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 To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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