Attachment 132280 Details for Bug 176544 – biology_ncbi-toolkit.diff

[patch] biology_ncbi-toolkit.diff

biology_ncbi-toolkit.diff (text/x-diff), 23.84 KB, created by tkato432 on 2013-03-06 17:45:06 UTC

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Creator: tkato432

Created: 2013-03-06 17:45:06 UTC

Size: 23.84 KB

patch

obsolete

>diff -urN /usr/ports/biology/ncbi-toolkit/Makefile biology/ncbi-toolkit/Makefile
>--- /usr/ports/biology/ncbi-toolkit/Makefile	2012-11-08 06:53:09.000000000 +0900
>+++ biology/ncbi-toolkit/Makefile	2013-03-02 13:48:33.000000000 +0900
>@@ -2,18 +2,20 @@
> # $FreeBSD: head/biology/ncbi-toolkit/Makefile 305130 2012-10-01 14:45:16Z tabthorpe $
> 
> PORTNAME=	ncbi-toolkit
>-PORTVERSION=	2009.03.01	# containing BLAST v2.2.19
>-PORTREVISION=	1
>+PORTVERSION=	2012.06.20	# containing BLAST v2.2.27
> CATEGORIES=	biology
>-MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
>+MASTER_SITES=	ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
> DISTNAME=	ncbi
> DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
> 
> MAINTAINER=	ports@FreeBSD.org
> COMMENT=	NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
> 
>+OPTIONS_DEFINE=	DOCS
>+
> USE_MOTIF=	yes
>-CPIO_ARGS=	--quiet -pdum -R
>+MAKE_JOBS_UNSAFE=	yes
>+
> SUB_FILES=	pkg-message
> 
> # These are the executables we install.
>@@ -28,32 +30,42 @@
> # change in the future with the addition of selectable knobs or
> # new slave ports
> 
>-TOOLKIT_EXE=	asn2ff asn2gb asn2idx asn2xml asndhuff asntool checksub \
>-		debruijn entrcmd fa2htgs findspl getmesh getpub gil2bin \
>-		idfetch indexpub makeset tbl2asn vecscreen demo_regexp \
>-		demo_regexp_grep errhdr gene2xml ncbisort seqtest test_regexp
>+TOOLKIT_EXE=	asn2ff asn2gb asn2idx asn2xml asndhuff asntool cdscan \
>+		checksub debruijn demo_regexp demo_regexp_grep dosimple \
>+		entrcmd errhdr fa2htgs findspl gene2xml getmesh getpub \
>+		gil2bin idfetch indexpub makeset ncbisort seqtest tbl2asn \
>+		vecscreen
> BLAST_EXE=	bl2seq blastall blastcl3 blastclust blastpgp copymat \
> 		fastacmd formatdb formatrpsdb impala makemat megablast \
> 		rpsblast seedtop taxblast
> X11_EXE=	Nentrez Psequin ddv entrez2 sbtedit udv
> 
> # and these are the man pages we have
>-MAN1=	Psequin.1 asn2all.1 asn2asn.1 asn2ff.1 asn2fsa.1 asn2gb.1 asn2idx.1 \
>-	asn2xml.1 asndhuff.1 asntool.1 asnval.1 blast.1 blastclust.1 \
>-	cdscan.1 checksub.1 copymat.1 ddv.1 \
>-	debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 fastacmd.1 findspl.1 \
>-	fmerge.1 formatdb.1 formatrpsdb.1 getmesh.1 getpub.1 gil2bin.1 \
>-	idfetch.1 indexpub.1 makemat.1 makeset.1 rpsblast.1 sbtedit.1 \
>-	tbl2asn.1 udv.1 vecscreen.1
>-
>-MLINKS=	blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
>-	blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
>-	blast.1 seedtop.1 blast.1 rpsblast.1
>+MAN1=		Psequin.1 asn2ff.1 asn2idx.1 asn2xml.1 asndhuff.1 \
>+		asntool.1 blast.1 blastclust.1 cdscan.1 checksub.1 \
>+		copymat.1 ddv.1 debruijn.1 entrez2.1 errhdr.1 fa2htgs.1 \
>+		fastacmd.1 findspl.1 formatdb.1 formatrpsdb.1 getmesh.1 \
>+		getpub.1 gil2bin.1 idfetch.1 indexpub.1 makemat.1 \
>+		taxblast.1 tbl2asn.1 udv.1 vecscreen.1
>+
>+MLINKS=		blast.1 bl2seq.1 blast.1 blastall.1 blast.1 blastcl3.1 \
>+		blast.1 blastpgp.1 blast.1 impala.1 blast.1 megablast.1 \
>+		blast.1 seedtop.1 blast.1 rpsblast.1 
>+
>+.include <bsd.port.options.mk>
> 
> post-patch:
>-	@${REINPLACE_CMD} -e 's,/usr/X11R6,${LOCALBASE},g' \
>-		${WRKSRC}/make/makedis.csh \
>-		${WRKSRC}/platform/freebsd.ncbi.mk
>+	@${REINPLACE_CMD} -e \
>+		's|/usr/X11R6|${LOCALBASE}|g' ${WRKSRC}/make/makedis.csh
>+	@${REINPLACE_CMD} -e \
>+		'/^NCBI_CC/s|=.*|= ${CC}| ; \
>+		 /^NCBI_LDFLGS1/s|=.*|= ${LDFLAGS}| ; \
>+		 /^NCBI_OPTFLAG/s|= .*|= ${CFLAGS}| ; \
>+		 s|-I/usr/X11R6/include||g ; \
>+		 s|-L/usr/X11R6/lib||g ; \
>+		 s|/usr/local|${LOCALBASE}|g ; \
>+		 s|-Wl,-Bstatic|| ; \
>+		 s|-Wl,-Bdynamic||' ${WRKSRC}/platform/freebsd.ncbi.mk
> 
> # the ncbi-toolkit provides a shell script to drive the build
> # and we use it
>@@ -68,36 +80,33 @@
> .for blastexe in ${BLAST_EXE}
> 	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${blastexe} ${PREFIX}/bin)
> .endfor
>-
> .for toolkitexe in ${TOOLKIT_EXE}
> 	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${toolkitexe} ${PREFIX}/bin)
> .endfor
>-
> .for x11exe in ${X11_EXE}
> 	(cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} ${x11exe} ${PREFIX}/bin)
> .endfor
>-
> 	@${MKDIR} ${PREFIX}/lib/${DISTNAME}
> 	(cd ${WRKSRC}/lib && ${INSTALL_DATA} *.a ${PREFIX}/lib/${DISTNAME})
>+	@${MKDIR} ${PREFIX}/include/${DISTNAME}
>+	(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h \
>+		${PREFIX}/include/${DISTNAME})
> 	@${MKDIR} ${PREFIX}/include/${DISTNAME}/connect
>-	(cd ${WRKSRC}/include && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME})
>-	(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h ${PREFIX}/include/${DISTNAME}/connect)
>-
>+	(cd ${WRKSRC}/include/connect && ${INSTALL_DATA} *.h \
>+		${PREFIX}/include/${DISTNAME}/connect)
> .for man in ${MAN1}
>-	(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${PREFIX}/man/man1)
>+	(cd ${WRKSRC}/doc/man && ${INSTALL_MAN} ${man} ${MANPREFIX}/man/man1)
> .endfor
>-
>-post-install:
> 	@${MKDIR} ${DATADIR}
>-	(cd ${WRKSRC}/data/ && ${INSTALL_DATA} * ${DATADIR})
>-
>-.if !defined(NOPORTDOCS)
>+	(cd ${WRKSRC}/data && ${INSTALL_DATA} * ${DATADIR})
>+.if ${PORT_OPTIONS:MDOCS}
> 	@${MKDIR} ${DOCSDIR}
>-	(cd ${WRKSRC}/doc && ${FIND} * | ${CPIO} ${CPIO_ARGS} ${SHAREOWN}:${SHAREGRP} ${DOCSDIR})
>-.endif
>-
>-.if !defined(BATCH)
>-	@ ${CAT} ${PKGMESSAGE}
>+	@(cd ${WRKSRC}/doc && ${TAR} --exclude man -cf - .) | \
>+		(cd ${DOCSDIR} && ${TAR} --unlink -xf -)
>+	@${FIND} ${DOCSDIR} | ${XARGS} ${CHOWN} ${SHAREOWN}:${SHAREGRP}
>+	@${FIND} ${DOCSDIR} -type d | ${XARGS} ${CHMOD} a+rx
>+	@${FIND} ${DOCSDIR} -type f | ${XARGS} ${CHMOD} ${SHAREMODE}
> .endif
>+	@${CAT} ${PKGMESSAGE}
> 
> .include <bsd.port.mk>
>diff -urN /usr/ports/biology/ncbi-toolkit/distinfo biology/ncbi-toolkit/distinfo
>--- /usr/ports/biology/ncbi-toolkit/distinfo	2012-11-08 06:53:08.000000000 +0900
>+++ biology/ncbi-toolkit/distinfo	2013-02-19 15:57:12.000000000 +0900
>@@ -1,2 +1,2 @@
>-SHA256 (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df
>-SIZE (ncbi-toolkit-2009.03.01/ncbi.tar.gz) = 64548732
>+SHA256 (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 603c9a4ade2a6f2f8e412558b732924d78fae403d225706e2ac38d553b08073c
>+SIZE (ncbi-toolkit-2012.06.20/ncbi.tar.gz) = 68428744
>diff -urN /usr/ports/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c
>--- /usr/ports/biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c	1970-01-01 09:00:00.000000000 +0900
>+++ biology/ncbi-toolkit/files/patch-corelib__ncbimisc.c	2013-03-02 13:46:40.000000000 +0900
>@@ -0,0 +1,11 @@
>+--- corelib/ncbimisc.c.orig
>++++ corelib/ncbimisc.c
>+@@ -1266,7 +1266,7 @@
>+   if (len < 1) return NULL;
>+ 
>+   rsult = (Nlm_CharPtr) MemNew (len + 3);
>+-  if (rsult == NULL) return;
>++  if (rsult == NULL) return NULL;
>+   tmp = rsult;
>+ 
>+   for (i = 0; /* local [i] != NULL */ i < numitems; i++) {
>diff -urN /usr/ports/biology/ncbi-toolkit/files/patch-make-makenet.unx biology/ncbi-toolkit/files/patch-make-makenet.unx
>--- /usr/ports/biology/ncbi-toolkit/files/patch-make-makenet.unx	2012-11-08 06:53:08.000000000 +0900
>+++ biology/ncbi-toolkit/files/patch-make-makenet.unx	2013-02-22 03:49:09.000000000 +0900
>@@ -8,7 +8,7 @@
>  SEQUIN_OPTS =
>  LIBCOPY = cp -p
>  SRCCOPY = ./ln-if-absent
>-@@ -923,17 +924,17 @@
>+@@ -934,17 +935,17 @@
>  	$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
>  	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
>  	$(LIBCOMPADJ) $(LIB2) $(LIB1) \
>@@ -17,19 +17,19 @@
>  
>  udv    : $(OBJUDV)
>  	$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
>-     $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
>+ 	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
>  	$(LIB23) $(LIBCOMPADJ) $(LIB2) \
> -	$(LIB1) $(VIBLIBS) $(OTHERLIBS)
> +	$(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
>  
>  Nentrez : entrez.c $(ULIB31)
>  	$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
>--    $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
>-+    $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
>+-	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
>++	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
>  
>  # left this in (Tentrez) for script backwards compatibility
>  Tentrez : entrez.c $(ULIB31)
>-@@ -1114,7 +1115,7 @@
>+@@ -1140,7 +1141,7 @@
>  entrez2 :	entrez2.c
>  	$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
>  		$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
>@@ -38,7 +38,7 @@
>  	$(VIB_POST_LINK) entrez2
>  
>  # demo program (spidey)
>-@@ -1383,7 +1384,7 @@
>+@@ -1421,7 +1422,7 @@
>  	$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \
>  	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
>  	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
>@@ -47,7 +47,7 @@
>  	$(VIB_POST_LINK) Psequin
>  
>  # 'sbtedit' Submission Template Editor
>-@@ -1395,7 +1396,7 @@
>+@@ -1433,7 +1434,7 @@
>  	$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \
>  	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
>  	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
>@@ -55,4 +55,4 @@
> +	$(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS) $(USERLIBS)
>  	$(VIB_POST_LINK) sbtedit
>  
>- salogif.o:	salogif.c
>+ # 'streamer' Sequinesque Stream Editor
>diff -urN /usr/ports/biology/ncbi-toolkit/pkg-descr biology/ncbi-toolkit/pkg-descr
>--- /usr/ports/biology/ncbi-toolkit/pkg-descr	2012-11-08 06:53:08.000000000 +0900
>+++ biology/ncbi-toolkit/pkg-descr	2013-02-23 08:06:49.000000000 +0900
>@@ -16,4 +16,4 @@
>   have found it a useful and stable basis for a number of tools and
>   applications.
> 
>-WWW: http://www.ncbi.nlm.nih.gov/blast/blast_whatsnew.shtml
>+WWW: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html
>diff -urN /usr/ports/biology/ncbi-toolkit/pkg-plist biology/ncbi-toolkit/pkg-plist
>--- /usr/ports/biology/ncbi-toolkit/pkg-plist	2012-11-08 06:53:09.000000000 +0900
>+++ biology/ncbi-toolkit/pkg-plist	2013-02-23 16:57:54.000000000 +0900
>@@ -1,87 +1,51 @@
>-bin/bl2seq
>-bin/blastall
>-bin/blastcl3
>-bin/blastclust
>-bin/blastpgp
>-bin/copymat
>-bin/fastacmd
>-bin/formatdb
>-bin/formatrpsdb
>-bin/impala
>-bin/makemat
>-bin/megablast
>-bin/rpsblast
>-bin/seedtop
>-bin/taxblast
>+bin/Nentrez
>+bin/Psequin
> bin/asn2ff
> bin/asn2gb
> bin/asn2idx
> bin/asn2xml
> bin/asndhuff
> bin/asntool
>+bin/bl2seq
>+bin/blastall
>+bin/blastcl3
>+bin/blastclust
>+bin/blastpgp
>+bin/cdscan
> bin/checksub
>+bin/copymat
>+bin/ddv
> bin/debruijn
>+bin/demo_regexp
>+bin/demo_regexp_grep
>+bin/dosimple
> bin/entrcmd
>+bin/entrez2
>+bin/errhdr
> bin/fa2htgs
>+bin/fastacmd
> bin/findspl
>+bin/formatdb
>+bin/formatrpsdb
>+bin/gene2xml
> bin/getmesh
> bin/getpub
>-bin/ddv
> bin/gil2bin
> bin/idfetch
>+bin/impala
> bin/indexpub
>+bin/makemat
> bin/makeset
>-bin/tbl2asn
>-bin/vecscreen
>-bin/demo_regexp
>-bin/demo_regexp_grep
>-bin/errhdr
>-bin/gene2xml
>+bin/megablast
> bin/ncbisort
>-bin/seqtest
>-bin/test_regexp
>-bin/Nentrez
>-bin/Psequin
>-bin/entrez2
>+bin/rpsblast
> bin/sbtedit
>+bin/seedtop
>+bin/seqtest
>+bin/taxblast
>+bin/tbl2asn
> bin/udv
>-include/ncbi/connect/connect_export.h
>-include/ncbi/connect/ncbi_ansi_ext.h
>-include/ncbi/connect/ncbi_assert.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_connssl.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_ftp_connector.h
>-include/ncbi/connect/ncbi_gnutls.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_lb.h
>-include/ncbi/connect/ncbi_lbsmd.h
>-include/ncbi/connect/ncbi_local.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
>-include/ncbi/connect/ncbi_server_infop.h
>-include/ncbi/connect/ncbi_service.h
>-include/ncbi/connect/ncbi_service_connector.h
>-include/ncbi/connect/ncbi_servicep.h
>-include/ncbi/connect/ncbi_socket.h
>-include/ncbi/connect/ncbi_socket_connector.h
>-include/ncbi/connect/ncbi_socket_unix.h
>-include/ncbi/connect/ncbi_socketp.h
>-include/ncbi/connect/ncbi_types.h
>-include/ncbi/connect/ncbi_util.h
>+bin/vecscreen
> include/ncbi/FSpCompat.h
> include/ncbi/FullPath.h
> include/ncbi/MoreCarbonAccessors.h
>@@ -155,6 +119,7 @@
> include/ncbi/asntax3.h
> include/ncbi/asntaxon.h
> include/ncbi/asntseq.h
>+include/ncbi/asnvalid.h
> include/ncbi/bandalgn.h
> include/ncbi/binary.h
> include/ncbi/biosrc.h
>@@ -185,7 +150,6 @@
> include/ncbi/cdromlib.h
> include/ncbi/cn3d.h
> include/ncbi/cn3dentr.h
>-include/ncbi/codon.h
> include/ncbi/cn3dmain.h
> include/ncbi/cn3dmesh.h
> include/ncbi/cn3dmodl.h
>@@ -196,10 +160,50 @@
> include/ncbi/cn3dshim.h
> include/ncbi/cn3dstyl.h
> include/ncbi/cn3dxprt.h
>+include/ncbi/codon.h
> include/ncbi/compo_heap.h
> include/ncbi/compo_mode_condition.h
> include/ncbi/composition_adjustment.h
> include/ncbi/composition_constants.h
>+include/ncbi/connect/connect_export.h
>+include/ncbi/connect/ncbi_ansi_ext.h
>+include/ncbi/connect/ncbi_assert.h
>+include/ncbi/connect/ncbi_base64.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_connssl.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_ftp_connector.h
>+include/ncbi/connect/ncbi_gnutls.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_lb.h
>+include/ncbi/connect/ncbi_lbsmd.h
>+include/ncbi/connect/ncbi_local.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
>+include/ncbi/connect/ncbi_server_infop.h
>+include/ncbi/connect/ncbi_service.h
>+include/ncbi/connect/ncbi_service_connector.h
>+include/ncbi/connect/ncbi_servicep.h
>+include/ncbi/connect/ncbi_socket.h
>+include/ncbi/connect/ncbi_socket_connector.h
>+include/ncbi/connect/ncbi_socket_unix.h
>+include/ncbi/connect/ncbi_socketp.h
>+include/ncbi/connect/ncbi_types.h
>+include/ncbi/connect/ncbi_util.h
>+include/ncbi/connect/ncbi_version.h
> include/ncbi/corematx.h
> include/ncbi/db_list.h
> include/ncbi/ddvclick.h
>@@ -240,12 +244,12 @@
> include/ncbi/gbfeat.h
> include/ncbi/gbftdef.h
> include/ncbi/gbparlex.h
>-include/ncbi/id1.h
> include/ncbi/gifgen.h
> include/ncbi/glbpic.h
> include/ncbi/gphdraw.h
> include/ncbi/gtrdraw.h
> include/ncbi/gxydraw.h
>+include/ncbi/id1.h
> include/ncbi/id1arch.h
> include/ncbi/id1gen.h
> include/ncbi/id1map.h
>@@ -289,9 +293,9 @@
> include/ncbi/medview.h
> include/ncbi/mimapi.h
> include/ncbi/mkbioseq.h
>-include/ncbi/mmdb1.h
> include/ncbi/mla2api.h
> include/ncbi/mlkludge.h
>+include/ncbi/mmdb1.h
> include/ncbi/mmdb2.h
> include/ncbi/mmdb3.h
> include/ncbi/mmdbapi.h
>@@ -303,6 +307,7 @@
> include/ncbi/mmdblocl.h
> include/ncbi/motif.h
> include/ncbi/ncbi.h
>+include/ncbi/ncbi_skew_guard.h
> include/ncbi/ncbibs.h
> include/ncbi/ncbidraw.h
> include/ncbi/ncbienv.h
>@@ -338,11 +343,8 @@
> include/ncbi/netlib.h
> include/ncbi/netpriv.h
> include/ncbi/netscape.h
>-include/ncbi/ni_defin.h
> include/ncbi/ni_error.h
>-include/ncbi/ni_lib.h
> include/ncbi/ni_lib_.h
>-include/ncbi/ni_net.h
> include/ncbi/ni_types.h
> include/ncbi/nlm_linear_algebra.h
> include/ncbi/objacces.h
>@@ -392,6 +394,7 @@
> include/ncbi/objtax1.h
> include/ncbi/objtax3.h
> include/ncbi/objtseq.h
>+include/ncbi/objvalid.h
> include/ncbi/odlbox.h
> include/ncbi/optimize_target_freq.h
> include/ncbi/panels.h
>@@ -478,7 +481,6 @@
> include/ncbi/suggest.h
> include/ncbi/suggslp.h
> include/ncbi/sugmap.h
>-include/ncbi/terr.h
> include/ncbi/sugprefx.h
> include/ncbi/tax1map.h
> include/ncbi/tax3api.h
>@@ -488,6 +490,7 @@
> include/ncbi/taxon1.h
> include/ncbi/taxuerr.h
> include/ncbi/taxutil.h
>+include/ncbi/terr.h
> include/ncbi/tfuns.h
> include/ncbi/thrdatd.h
> include/ncbi/thrddecl.h
>@@ -523,6 +526,8 @@
> include/ncbi/urlquery.h
> include/ncbi/utilpars.h
> include/ncbi/utilpub.h
>+include/ncbi/valapi.h
>+include/ncbi/valdlg.h
> include/ncbi/valid.h
> include/ncbi/validatr.h
> include/ncbi/validerr.h
>@@ -531,7 +536,6 @@
> include/ncbi/vast2pdb.h
> include/ncbi/vastlocl.h
> include/ncbi/vastsrv.h
>-include/ncbi/vsm.h
> include/ncbi/vecscnapi.h
> include/ncbi/vecscrn.h
> include/ncbi/vibdefns.h
>@@ -551,6 +555,7 @@
> include/ncbi/viewer3d.h
> include/ncbi/viewerp.h
> include/ncbi/viewmgr.h
>+include/ncbi/vsm.h
> include/ncbi/vsmfile.h
> include/ncbi/vsmpriv.h
> include/ncbi/vsmutil.h
>@@ -586,10 +591,10 @@
> %%PORTDOCS%%%%DOCSDIR%%/access.txt
> %%PORTDOCS%%%%DOCSDIR%%/asn2gb.txt
> %%PORTDOCS%%%%DOCSDIR%%/asn2gph.txt
>-%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html
> %%PORTDOCS%%%%DOCSDIR%%/blast/bl2seq.html
> %%PORTDOCS%%%%DOCSDIR%%/blast/blast.html
> %%PORTDOCS%%%%DOCSDIR%%/blast/blastall.html
>+%%PORTDOCS%%%%DOCSDIR%%/blast/blastclust.html
> %%PORTDOCS%%%%DOCSDIR%%/blast/blastdb.html
> %%PORTDOCS%%%%DOCSDIR%%/blast/blastftp.html
> %%PORTDOCS%%%%DOCSDIR%%/blast/blastpgp.html
>@@ -613,7 +618,6 @@
> %%PORTDOCS%%%%DOCSDIR%%/firewall.html
> %%PORTDOCS%%%%DOCSDIR%%/fwd_check.sh
> %%PORTDOCS%%%%DOCSDIR%%/gene2xml.txt
>-%%PORTDOCS%%%%DOCSDIR%%/images/logo.png
> %%PORTDOCS%%%%DOCSDIR%%/images/affil.png
> %%PORTDOCS%%%%DOCSDIR%%/images/annot.png
> %%PORTDOCS%%%%DOCSDIR%%/images/authors.png
>@@ -624,6 +628,7 @@
> %%PORTDOCS%%%%DOCSDIR%%/images/genbank.png
> %%PORTDOCS%%%%DOCSDIR%%/images/graphic.png
> %%PORTDOCS%%%%DOCSDIR%%/images/loc_page.png
>+%%PORTDOCS%%%%DOCSDIR%%/images/logo.png
> %%PORTDOCS%%%%DOCSDIR%%/images/ncbi_sequin.css
> %%PORTDOCS%%%%DOCSDIR%%/images/net_cfg.png
> %%PORTDOCS%%%%DOCSDIR%%/images/nucaln.png
>@@ -639,67 +644,11 @@
> %%PORTDOCS%%%%DOCSDIR%%/images/update.png
> %%PORTDOCS%%%%DOCSDIR%%/images/validate.png
> %%PORTDOCS%%%%DOCSDIR%%/images/welcome.png
>-%%PORTDOCS%%%%DOCSDIR%%/man/Psequin.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asn2all.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asn2asn.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asn2ff.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asn2fsa.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asn2gb.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asn2idx.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asn2xml.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asndhuff.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asntool.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/asnval.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/bl2seq.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/blast.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/blastall.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/blastall_old.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/blastcl3.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/blastclust.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/blastpgp.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/cdscan.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/checksub.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/cleanasn.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/copymat.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/ddv.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/debruijn.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/entrez2.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/errhdr.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/vecscreen.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/fa2htgs.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/fastacmd.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/findspl.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/fmerge.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/formatdb.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/getpub.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/formatrpsdb.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/gbseqget.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/gene2xml.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/getmesh.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/gil2bin.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/idfetch.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/impala.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/indexpub.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/insdseqget.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/makemat.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/makeset.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/megablast.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/nps2gps.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/rpsblast.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/sbtedit.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/seedtop.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/sortbyquote.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/spidey.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/tbl2asn.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/trna2sap.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/trna2tbl.1
>-%%PORTDOCS%%%%DOCSDIR%%/man/udv.1
> %%PORTDOCS%%%%DOCSDIR%%/ncbixml.txt
> %%PORTDOCS%%%%DOCSDIR%%/sdk.doc
>-%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/Makefile
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/bg.gif
>-%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.css
>+%%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.css
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/ftp_example.xml
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/left.GIF
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/mac-ie.css
>@@ -709,12 +658,12 @@
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.css
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.html
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_download.xml
>+%%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.css
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.html
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_ftp_download.xml
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_install.html
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.css
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.html
>-%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_mac_download.xml
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.css
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_trouble.html
>@@ -726,6 +675,7 @@
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.html
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/seq_win_download.xml
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/sequin-icon-win.gif
>+%%PORTDOCS%%%%DOCSDIR%%/seq_install/sniff.js
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/spacer10.GIF
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/template.xml
> %%PORTDOCS%%%%DOCSDIR%%/seq_install/win-ie.css
>@@ -736,6 +686,12 @@
> %%DATADIR%%/16SCore.nhr
> %%DATADIR%%/16SCore.nin
> %%DATADIR%%/16SCore.nsq
>+%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nhr
>+%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nin
>+%%DATADIR%%/64-matK-FINAL-aligned-DNA.fas.nsq
>+%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nhr
>+%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nin
>+%%DATADIR%%/64-rbcL-FINAL-aligned-DNA.fas.nsq
> %%DATADIR%%/BLOSUM45
> %%DATADIR%%/BLOSUM50
> %%DATADIR%%/BLOSUM62
>@@ -752,7 +708,6 @@
> %%DATADIR%%/KSchoth.flt
> %%DATADIR%%/KSesigc.mat
> %%DATADIR%%/KSesigl.mat
>-%%DATADIR%%/PAM250
> %%DATADIR%%/KSgc.flt
> %%DATADIR%%/KShopp.flt
> %%DATADIR%%/KSkyte.flt
>@@ -768,6 +723,7 @@
> %%DATADIR%%/LSURef_93.fasta.nhr
> %%DATADIR%%/LSURef_93.fasta.nin
> %%DATADIR%%/LSURef_93.fasta.nsq
>+%%DATADIR%%/PAM250
> %%DATADIR%%/PAM30
> %%DATADIR%%/PAM70
> %%DATADIR%%/SSURef_93.fasta.nhr
>@@ -780,6 +736,7 @@
> %%DATADIR%%/UniVec_Core.nin
> %%DATADIR%%/UniVec_Core.nsq
> %%DATADIR%%/asn2ff.prt
>+%%DATADIR%%/autofix.prt
> %%DATADIR%%/blast.prt
> %%DATADIR%%/bstdt.prt
> %%DATADIR%%/bstdt.val
>@@ -794,6 +751,9 @@
> %%DATADIR%%/gc.val
> %%DATADIR%%/humrep.fsa
> %%DATADIR%%/institution_codes.txt
>+%%DATADIR%%/lat_lon_country.txt
>+%%DATADIR%%/lat_lon_island.txt
>+%%DATADIR%%/lat_lon_water.txt
> %%DATADIR%%/lineages.txt
> %%DATADIR%%/makerpt.prt
> %%DATADIR%%/ncbiendo.dat
>@@ -802,6 +762,8 @@
> %%DATADIR%%/ncbiren.dat
> %%DATADIR%%/ncbirnam.dat
> %%DATADIR%%/objprt.prt
>+%%DATADIR%%/organelle_products.prt
>+%%DATADIR%%/product_rules.prt
> %%DATADIR%%/pubkey.enc
> %%DATADIR%%/rRNA_blast.nal
> %%DATADIR%%/rRNAstrand.nal
>@@ -810,13 +772,13 @@
> %%DATADIR%%/sequin.hlp
> %%DATADIR%%/sgmlbb.ent
> %%DATADIR%%/taxlist.txt
>-@dirrm include/ncbi/connect
>-@dirrm include/ncbi
>-@dirrm lib/ncbi
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
>-%%PORTDOCS%%@dirrm %%DOCSDIR%%/man
>+%%DATADIR%%/validrules.prt
>+@dirrmtry %%DATADIR%%
> %%PORTDOCS%%@dirrm %%DOCSDIR%%/seq_install
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/fa2htgs
>+%%PORTDOCS%%@dirrm %%DOCSDIR%%/blast
> %%PORTDOCS%%@dirrm %%DOCSDIR%%
>-@dirrmtry %%DATADIR%%
>+@dirrm lib/ncbi
>+@dirrm include/ncbi/connect
>+@dirrm include/ncbi

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Attachments on bug 176544: 132279 | 132280