From owner-freebsd-ports-bugs@FreeBSD.ORG Fri May 2 19:30:14 2003 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id AC50F37B404 for ; Fri, 2 May 2003 19:30:14 -0700 (PDT) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id BEA0F43F93 for ; Fri, 2 May 2003 19:30:12 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.12.9/8.12.9) with ESMTP id h432UCUp035480 for ; Fri, 2 May 2003 19:30:12 -0700 (PDT) (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.12.9/8.12.9/Submit) id h432UCAj035479; Fri, 2 May 2003 19:30:12 -0700 (PDT) Resent-Date: Fri, 2 May 2003 19:30:12 -0700 (PDT) Resent-Message-Id: <200305030230.h432UCAj035479@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Tony Maher Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 8F86937B401 for ; Fri, 2 May 2003 19:20:51 -0700 (PDT) Received: from c17443.thorn1.nsw.optusnet.com.au (c17443.thorn1.nsw.optusnet.com.au [210.49.151.50]) by mx1.FreeBSD.org (Postfix) with ESMTP id 4B83143F3F for ; Fri, 2 May 2003 19:20:50 -0700 (PDT) (envelope-from tonymaher@optushome.com.au) Received: from dt.home (localhost [127.0.0.1])h432KiFl046022 for ; Sat, 3 May 2003 12:20:44 +1000 (EST) (envelope-from tonym@dt.home) Received: (from tonym@localhost) by dt.home (8.12.9/8.12.9/Submit) id h432Kdkm045981; Sat, 3 May 2003 12:20:39 +1000 (EST) (envelope-from tonym) Message-Id: <200305030220.h432Kdkm045981@dt.home> Date: Sat, 3 May 2003 12:20:39 +1000 (EST) From: Tony Maher To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Subject: ports/51709: Port update (maintainer): biology/ncbi-toolkit X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list Reply-To: Tony Maher List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 03 May 2003 02:30:15 -0000 >Number: 51709 >Category: ports >Synopsis: Port update (maintainer): biology/ncbi-toolkit >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Fri May 02 19:30:12 PDT 2003 >Closed-Date: >Last-Modified: >Originator: Tony Maher >Release: FreeBSD 4.8-STABLE i386 >Organization: >Environment: System: FreeBSD dt.home 4.8-STABLE FreeBSD 4.8-STABLE #2: Wed Apr 16 13:00:01 EST 2003 root@dt.home:/usr/obj/usr/src/sys/DT i386 >Description: Update port to version 2003.04.21 Thanks to Brad Chapman who alerted me to the new version and supplied patches though I did not apply them directly. o compiles on 4-stable *and* now on 5-current (Brad's fixes) o NCBI now support FreeBSD (4-stable) directly therefore no longer require files/freebsd.ncbi.mk files/patch-ab and files/patch-ac o now link against the thread library (but I am not sure if it helps) Tested a single blastn and get identical results on 5.0-current (02-05-03) and 4.8-stable (16-04-03). I do not currently have access to large/varied data sets so testing is very limited. Please delete files/freebsd.ncbi.mk files/patch-ab and files/patch-ac >How-To-Repeat: >Fix: diff -ruN ncbi-toolkit.orig/Makefile ncbi-toolkit/Makefile --- ncbi-toolkit.orig/Makefile Tue Feb 25 18:50:46 2003 +++ ncbi-toolkit/Makefile Thu May 1 14:54:58 2003 @@ -6,7 +6,7 @@ # PORTNAME= ncbi-toolkit -PORTVERSION= 2002.04.26 +PORTVERSION= 2003.04.21 CATEGORIES= biology MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/ DISTNAME= ncbi @@ -15,16 +15,12 @@ COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support USE_MOTIF= yes -USE_REINPLACE= yes # # In the files directory we have: # DUMMYMAKE= Makefile -PLATFORMDIR= ${WRKSRC}/platform -BUILDSCRIPT= ${WRKSRC}/make/makedis.csh - DOCDIR= ${PREFIX}/share/doc/${PORTNAME} CPIO= cpio --quiet -pdum -R @@ -37,8 +33,6 @@ pre-configure: @${CP} ${FILESDIR}/${DUMMYMAKE} ${WRKSRC} - @${CP} ${FILESDIR}/freebsd.ncbi.mk ${PLATFORMDIR} - @${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 Sat Sep 21 21:11:22 2002 +++ ncbi-toolkit/distinfo Thu May 1 11:23:11 2003 @@ -1 +1 @@ -MD5 (ncbi.tar.gz) = 7278c10b227b0298f00a5ed5dde58bc4 +MD5 (ncbi.tar.gz) = 96208e10f92b2163f5dcc3c5cf74dd44 diff -ruN ncbi-toolkit.orig/files/freebsd.ncbi.mk ncbi-toolkit/files/freebsd.ncbi.mk --- ncbi-toolkit.orig/files/freebsd.ncbi.mk Fri Feb 22 18:57:07 2002 +++ ncbi-toolkit/files/freebsd.ncbi.mk Thu Jan 1 10:00:00 1970 @@ -1,31 +0,0 @@ -# -# $Id$ freebsd.ncbi.mk -# -# That platform is not supported and is contributed to NCBI by -# freebsd-bio@freebsd.net -# -NCBI_DEFAULT_LCL = bsd -NCBI_MAKE_SHELL = /bin/sh -NCBI_CC = cc -NCBI_CFLAGS1 = ${CFLAGS} -c -NCBI_LDFLAGS1 = -O -NCBI_OPTFLAG = -NCBI_BIN_MASTER = /home/coremake/ncbi/bin -NCBI_BIN_COPY = /home/coremake/ncbi/bin -NCBI_INCDIR = /home/coremake/ncbi/include -NCBI_LIBDIR = /home/coremake/ncbi/lib -NCBI_ALTLIB = /home/coremake/ncbi/altlib -#will work only when you have Motif installed! -NCBI_VIBFLAG = -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF -NCBI_VIBLIBS = -lXm -lXmu -lXp -lXpm -lXt -lX11 -lXext -NCBI_DISTVIBLIBS = -L/usr/X11R6/lib /usr/X11R6/lib/libXm.a /usr/X11R6/lib/libXp.a /usr/X11R6/lib/libXpm.a -lXmu -lXt -lX11 -lXext -NCBI_OTHERLIBS = -lm -NCBI_RANLIB = ranlib -# Used by makedis.csh -NCBI_MT_OTHERLIBS = -NCBI_THREAD_OBJ = ncbithr.o -NETENTREZVERSION = 2.02c2ASN1SPEC6 - -NCBI_LBSM_SRC = ncbi_service_lbsmd_stub.c -NCBI_LBSM_OBJ = ncbi_service_lbsmd_stub.o - diff -ruN ncbi-toolkit.orig/files/patch-aa ncbi-toolkit/files/patch-aa --- ncbi-toolkit.orig/files/patch-aa Sat Sep 21 21:11:22 2002 +++ ncbi-toolkit/files/patch-aa Thu May 1 12:02:23 2003 @@ -6,11 +6,11 @@ $(SRC2) $(SRC1) $(OTHERLIBS) -lsocket -lnsl + +EXE= Nentrez Psequin \ -+ asn2ff asn2xml asndhuff asntool \ -+ bl2seq blast.REAL blastall blastcl3 blastclust blastpgp \ ++ asn2ff asn2gb asn2xml asndhuff asntool \ ++ blastall blastcl3 blastclust blastpgp \ + cdscan checksub copymat \ -+ ddv dosimple \ -+ entrcmd errhdr fa2htgs fastacmd findspl fmerge formatdb \ ++ ddv demo_regexp demo_regexp_grep dosimple \ ++ entrcmd entrez2 errhdr fa2htgs fastacmd findspl fmerge formatdb \ + getfeat getmesh getpub getseq gil2bin \ + idfetch impala indexpub \ + makemat makeset megablast \ diff -ruN ncbi-toolkit.orig/files/patch-ab ncbi-toolkit/files/patch-ab --- ncbi-toolkit.orig/files/patch-ab Mon Oct 30 00:56:24 2000 +++ ncbi-toolkit/files/patch-ab Thu Jan 1 10:00:00 1970 @@ -1,19 +0,0 @@ ---- corelib/ncbilcl.bsd.orig Mon Apr 3 08:50:57 2000 -+++ corelib/ncbilcl.bsd Mon Apr 3 08:51:55 2000 -@@ -74,7 +74,6 @@ - #include - #include - #include --#include - #include - #include - #include -@@ -84,7 +83,7 @@ - - /* Check if there are POSIX threads available */ - #ifdef _POSIX_THREADS --#define POSIX_THREADS_AVAIL -+#define POSIX_THREADS_AVAIL_broken - #endif - - diff -ruN ncbi-toolkit.orig/files/patch-ac ncbi-toolkit/files/patch-ac --- ncbi-toolkit.orig/files/patch-ac Mon Oct 30 00:56:24 2000 +++ ncbi-toolkit/files/patch-ac Thu Jan 1 10:00:00 1970 @@ -1,11 +0,0 @@ ---- corelib/ncbienv.c.orig Tue Jan 25 08:16:49 2000 -+++ corelib/ncbienv.c Mon Apr 3 08:56:02 2000 -@@ -183,6 +183,8 @@ - - #ifdef OS_UNIX - #include -+#include -+#define LOGNAME_MAX MAXLOGNAME - #endif /* OS_UNIX */ - #ifdef OS_MAC - #include diff -ruN ncbi-toolkit.orig/files/patch-ncbilcl.fbd ncbi-toolkit/files/patch-ncbilcl.fbd --- ncbi-toolkit.orig/files/patch-ncbilcl.fbd Thu Jan 1 10:00:00 1970 +++ ncbi-toolkit/files/patch-ncbilcl.fbd Sat May 3 11:11:19 2003 @@ -0,0 +1,18 @@ +--- corelib/ncbilcl.fbd.orig Sat Nov 23 07:05:04 2002 ++++ corelib/ncbilcl.fbd Sat May 3 10:06:18 2003 +@@ -67,6 +67,7 @@ + /*----------------------------------------------------------------------*/ + #define SYSV_IPC_AVAIL /* System V Interprocess Communication available */ + #define _POSIX_C_SOURCE 199309L ++#define _XOPEN_SOURCE 600 /* req. for 5.0 */ + #define HAVE_STRCASECMP 1 + #define HAVE_STRDUP 1 + +@@ -87,6 +88,7 @@ + #include + #include + #include ++#include /* req. for 5.0. fd_set def. moved from types.h */ + + /* Check if there are POSIX threads available */ + #ifdef _POSIX_THREADS diff -ruN ncbi-toolkit.orig/pkg-plist ncbi-toolkit/pkg-plist --- ncbi-toolkit.orig/pkg-plist Sat Sep 21 21:11:22 2002 +++ ncbi-toolkit/pkg-plist Thu May 1 13:55:15 2003 @@ -1,7 +1,9 @@ %%PORTDOCS%%share/doc/ncbi-toolkit/FAQ.txt +%%PORTDOCS%%share/doc/ncbi-toolkit/README-qm %%PORTDOCS%%share/doc/ncbi-toolkit/README.asn2xml %%PORTDOCS%%share/doc/ncbi-toolkit/README.bcl %%PORTDOCS%%share/doc/ncbi-toolkit/README.bls +%%PORTDOCS%%share/doc/ncbi-toolkit/README.fastacmd %%PORTDOCS%%share/doc/ncbi-toolkit/README.formatdb %%PORTDOCS%%share/doc/ncbi-toolkit/README.imp %%PORTDOCS%%share/doc/ncbi-toolkit/README.mbl @@ -9,11 +11,13 @@ %%PORTDOCS%%share/doc/ncbi-toolkit/README.pbl %%PORTDOCS%%share/doc/ncbi-toolkit/README.rps %%PORTDOCS%%share/doc/ncbi-toolkit/README.sdk +%%PORTDOCS%%share/doc/ncbi-toolkit/asn2gb.txt +%%PORTDOCS%%share/doc/ncbi-toolkit/asn2gph.txt +%%PORTDOCS%%share/doc/ncbi-toolkit/dispatcher.html %%PORTDOCS%%share/doc/ncbi-toolkit/fa2htgs/README %%PORTDOCS%%share/doc/ncbi-toolkit/fa2htgs/updateHtgsDoc %%PORTDOCS%%share/doc/ncbi-toolkit/firedialog.gif %%PORTDOCS%%share/doc/ncbi-toolkit/firewall.html -%%PORTDOCS%%share/doc/ncbi-toolkit/firewall.txt %%PORTDOCS%%share/doc/ncbi-toolkit/fwd_check.sh %%PORTDOCS%%share/doc/ncbi-toolkit/images/ncbi_sequin.css %%PORTDOCS%%share/doc/ncbi-toolkit/images/seqn01.gif @@ -41,14 +45,14 @@ %%PORTDOCS%%share/doc/ncbi-toolkit/ncbixml.txt %%PORTDOCS%%share/doc/ncbi-toolkit/sdk.doc %%PORTDOCS%%share/doc/ncbi-toolkit/sequin.htm +%%PORTDOCS%%share/doc/ncbi-toolkit/tbl2asn.txt bin/Nentrez bin/Psequin bin/asn2ff +bin/asn2gb bin/asn2xml bin/asndhuff bin/asntool -bin/bl2seq -bin/blast.REAL bin/blastall bin/blastcl3 bin/blastclust @@ -57,8 +61,11 @@ bin/checksub bin/copymat bin/ddv +bin/demo_regexp +bin/demo_regexp_grep bin/dosimple bin/entrcmd +bin/entrez2 bin/errhdr bin/fa2htgs bin/fastacmd @@ -104,9 +111,11 @@ lib/ncbi/libnetblast.a lib/ncbi/libnetcli.a lib/ncbi/libnetentr.a +lib/ncbi/libregexp.a lib/ncbi/libvibgif.a lib/ncbi/libvibnet.a lib/ncbi/libvibrant.a +include/ncbi/connect/connect_export.h include/ncbi/connect/ncbi_ansi_ext.h include/ncbi/connect/ncbi_buffer.h include/ncbi/connect/ncbi_comm.h @@ -115,9 +124,14 @@ include/ncbi/connect/ncbi_connector.h include/ncbi/connect/ncbi_connutil.h include/ncbi/connect/ncbi_core.h +include/ncbi/connect/ncbi_core_c.h +include/ncbi/connect/ncbi_dispd.h include/ncbi/connect/ncbi_file_connector.h include/ncbi/connect/ncbi_heapmgr.h +include/ncbi/connect/ncbi_host_info.h +include/ncbi/connect/ncbi_host_infop.h include/ncbi/connect/ncbi_http_connector.h +include/ncbi/connect/ncbi_lbsmd.h include/ncbi/connect/ncbi_memory_connector.h include/ncbi/connect/ncbi_priv.h include/ncbi/connect/ncbi_sendmail.h @@ -126,12 +140,17 @@ include/ncbi/connect/ncbi_service.h include/ncbi/connect/ncbi_service_connector.h include/ncbi/connect/ncbi_servicep.h -include/ncbi/connect/ncbi_servicep_dispd.h -include/ncbi/connect/ncbi_servicep_lbsmd.h include/ncbi/connect/ncbi_socket.h include/ncbi/connect/ncbi_socket_connector.h include/ncbi/connect/ncbi_types.h include/ncbi/connect/ncbi_util.h +include/ncbi/FSpCompat.h +include/ncbi/FullPath.h +include/ncbi/MoreCarbonAccessors.h +include/ncbi/MoreFilesExtras.h +include/ncbi/MoreFilesX.h +include/ncbi/Optimization.h +include/ncbi/OptimizationEnd.h include/ncbi/PubStructAsn.h include/ncbi/a2ferr.h include/ncbi/a2ferrdf.h @@ -161,7 +180,11 @@ include/ncbi/asn2graphic.h include/ncbi/asn2graphicp.h include/ncbi/asnacces.h +include/ncbi/asngbseq.h +include/ncbi/asntseq.h include/ncbi/blast.h +include/ncbi/blastconcat.h +include/ncbi/blastconcatdef.h include/ncbi/asnalign.h include/ncbi/asnbibli.h include/ncbi/asnblock.h @@ -382,6 +405,7 @@ include/ncbi/objentr.h include/ncbi/objfdef.h include/ncbi/objfeat.h +include/ncbi/objgbseq.h include/ncbi/objgen.h include/ncbi/objloc.h include/ncbi/objmdrs.h @@ -404,9 +428,14 @@ include/ncbi/objsset.h include/ncbi/objsub.h include/ncbi/objtax1.h +include/ncbi/objtseq.h include/ncbi/odlbox.h include/ncbi/panels.h include/ncbi/parsegb.h +include/ncbi/pcre.h +include/ncbi/pcre_config.h +include/ncbi/pcre_internal.h +include/ncbi/pcreposix.h include/ncbi/pdiagnos.h include/ncbi/pgppop.h include/ncbi/pictur3d.h @@ -457,6 +486,7 @@ include/ncbi/seqgrphx.h include/ncbi/seqmgr.h include/ncbi/seqmtrx.h +include/ncbi/seqpanel.h include/ncbi/seqpcc.h include/ncbi/seqport.h include/ncbi/seqscrl.h @@ -552,7 +582,6 @@ include/ncbi/vsmutil.h include/ncbi/wrpsb.h include/ncbi/wrpsbtool.h -include/ncbi/wwwblast.h include/ncbi/xmlblast.h share/ncbi-toolkit/BLOSUM45 share/ncbi-toolkit/BLOSUM62 >Release-Note: >Audit-Trail: >Unformatted: