Attachment 62216 Details for Bug 93052 – fasta3.diff

[patch] fasta3.diff

fasta3.diff (text/plain; charset=us-ascii), 13.56 KB, created by Fernan Aguero on 2006-02-09 16:25:01 UTC

(hide)

Description:

Filename:

MIME Type:

Creator: Fernan Aguero

Created: 2006-02-09 16:25:01 UTC

Size: 13.56 KB

patch

obsolete

>diff -ruN /usr/ports/biology/fasta3/Makefile fasta3/Makefile
>--- /usr/ports/biology/fasta3/Makefile	Thu Jul  1 00:02:23 2004
>+++ fasta3/Makefile	Thu Feb  9 12:03:30 2006
>@@ -1,3 +1,4 @@
>+# ex:ts=8
> # New ports collection makefile for:	fasta3
> # Date created:		29 January 2001
> # Whom:	      		Johann Visagie <johann@egenetics.com>
>@@ -6,21 +7,25 @@
> #
> 
> PORTNAME=	fasta3
>-PORTVERSION=	33.t08.d4
>+PORTVERSION=	34.t25.d4
> CATEGORIES=	biology
> MASTER_SITES=	ftp://ftp.virginia.edu/pub/fasta/
> DISTNAME=	fasta${PORTVERSION:S/.//g}
> EXTRACT_SUFX=	.shar.Z
> 
> MAINTAINER=	fernan@iib.unsam.edu.ar
>-COMMENT=	A collection of programs for searching DNA and protein databases, v3
>+COMMENT=	A collection of programs for searching DNA and protein databases
> 
>-NO_CDROM=	May not be sold or incorporated into a commercial product
>-WRKSRC=		${WRKDIR}/fasta3
>-PKGMESSAGE=	${WRKDIR}/pkg-message
>-FASTA3_DOCDIR=	${PREFIX}/share/doc/fasta3
>-FASTA3_DOCS=	00README.1st README COPYRIGHT fasta3x.me fasta3x.doc \
>-		readme.*
>+NO_CDROM=	"May not be sold or incorporated into a commercial product"
>+WRKSRC=		${WRKDIR}/${PORTNAME}
>+SUB_FILES=	pkg-message
>+
>+MAKE_ENV+=	THR_LIBS=${PTHREAD_LIBS}
>+
>+FASTA3_DOCS=	README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \
>+		fasta20.doc fasta_func.doc readme.* fasta.defaults
>+DATA=		*.mat
>+EXAMPLES=	*.aa *.lc *.seq
> 
> MAN1=		fasta3.1 fastf3.1 fasts3.1 map_db.1 prss3.1
> MLINKS=		fasta3.1 tfasta3.1 fasta3.1 fastx3.1  fasta3.1 tfastx3.1  \
>@@ -35,19 +40,24 @@
> 	done
> 
> post-install:
>-	@ ${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
>+	${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
>+	@ ${MKDIR} ${DATADIR}
>+.for data in ${DATA}
>+	${INSTALL_DATA} ${WRKSRC}/${data} ${DATADIR}
>+.endfor
>+	@ ${MKDIR} ${EXAMPLESDIR}
>+.for ex in ${EXAMPLES}
>+	${INSTALL_DATA} ${WRKSRC}/${ex} ${EXAMPLESDIR}
>+.endfor
> .for manpage in ${MAN1}
> 	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
> .endfor
> .if !defined(NOPORTDOCS)
>-	@ ${MKDIR} ${FASTA3_DOCDIR}
>+	@ ${MKDIR} ${DOCSDIR}
> .for docfile in ${FASTA3_DOCS}
>-	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${FASTA3_DOCDIR}
>+	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
> .endfor
> .endif
>-.if !defined(BATCH)
>-	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#' ${.CURDIR}/pkg-message > ${PKGMESSAGE}
> 	@ ${CAT} ${PKGMESSAGE}
>-.endif
> 
> .include <bsd.port.mk>
>diff -ruN /usr/ports/biology/fasta3/distinfo fasta3/distinfo
>--- /usr/ports/biology/fasta3/distinfo	Wed Jan 25 11:31:47 2006
>+++ fasta3/distinfo	Sat Feb  4 18:24:02 2006
>@@ -1,3 +1,3 @@
>-MD5 (fasta33t08d4.shar.Z) = e6217268e122b2ca7c51b443425e40e3
>-SHA256 (fasta33t08d4.shar.Z) = f2eb329393cd330c6848cff2a147fcc2c2f74dff6033cf7ba70177ab4bcca231
>-SIZE (fasta33t08d4.shar.Z) = 685912
>+MD5 (fasta34t25d4.shar.Z) = 554190cb7bf2488150a96e309651e9c7
>+SHA256 (fasta34t25d4.shar.Z) = 4d901bc738074c6c72d568b3852cf7e8a91a71ca25a1b2d74b8b1ae997d956fe
>+SIZE (fasta34t25d4.shar.Z) = 799416
>diff -ruN /usr/ports/biology/fasta3/files/patch-Makefile fasta3/files/patch-Makefile
>--- /usr/ports/biology/fasta3/files/patch-Makefile	Mon May  7 09:16:33 2001
>+++ fasta3/files/patch-Makefile	Thu Feb  9 12:07:23 2006
>@@ -1,49 +1,33 @@
>---- Makefile.orig	Mon May  7 11:36:23 2001
>-+++ Makefile	Mon May  7 11:40:36 2001
>-@@ -12,13 +12,13 @@
>- 
>- # use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files
>- 
>--CC= cc -O -std1
>-+#CC= cc -O -std1
>- #CC= insure -g -DDEBUG
>- #CC= cc -g -DDEBUG -std1
>- #CC= gcc -g -Wall
>+--- Makefile.orig	Thu Feb  9 12:03:37 2006
>++++ Makefile	Thu Feb  9 12:07:21 2006
>+@@ -7,7 +7,7 @@
>+ # in dropnfa.c  (wrp 3/19/1998)
>  #
>- # standard line for normal searching
>--CFLAGS= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
>-+CFLAGS+= -DM10_CONS -DUNIX -DTIMES -DHZ=60 -DBIGMEM -DMAX_WORKERS=4 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"fasta.bioch.virginia.edu/fasta/cgi"' -DIS_LITTLE_ENDIAN -DUSE_MMAP
>- # -I/usr/local/include/mysql -DMYSQL_DB 
>- #(for mySQL databases)  (also requires change to Makefile33.common)
>  
>-@@ -32,11 +32,15 @@
>- HFLAGS= -o
>- NFLAGS= -o
>+-CC= gcc -g -O3
>++#CC= gcc -g -O3
>+ #CC=gcc -Wall -pedantic -ansi -g -O
>+ #CC = gcc -g -DDEBUG
>+ #CC= /opt/parasoft/bin.linux2/insure -g -pg -DDEBUG
>+@@ -21,7 +21,7 @@
>+ #CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="'|'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DSUPERFAMNUM -DUSE_MMAP -D_REENTRANT -DBIG_LIB64 -D_LARGE_FILE_SOURCE -DUSE_FSEEKO -D_FILE_OFFSET_BITS=64 -DHAS_INTTYPES -DSAMP_STATS
>+ 
>+ # standard options
>+-CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
>++CFLAGS+= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
>+ # -I/usr/local/include/mysql -DMYSQL_DB 
>+ #
>+ #(for mySQL databases)  (also requires change to Makefile34.common)
>+@@ -35,10 +35,10 @@
>  
>--#for DEC Unix V4.0 
>- THR_SUBS = pthr_subs
>--THR_LIBS = -threads
>-+THR_LIBS = -pthread
>+ # for Linux
>+ THR_SUBS = pthr_subs2
>+-THR_LIBS = -lpthread
>++#THR_LIBS = -lpthread
>  THR_CC =
>  
>-+#for DEC Unix V4.0 
>-+#THR_SUBS = pthr_subs
>-+#THR_LIBS = -threads
>-+#THR_CC =
>-+#
>- #for Sun
>- #THR_SUBS = uthr_subs
>- #THR_LIBS = -lthread
>-@@ -53,9 +57,9 @@
>- #THR_LIBS = -lpthreads
>- #THR_CC =
>- 
>--XDIR = /seqprg/slib/bin
>+-XDIR = /seqprg/bin
> +XDIR = ${PREFIX}/bin
>  
>- # renamed (fasta33)  programs
>--include Makefile33.common
>-+#include Makefile33.common
>- # conventional (fasta3) names
>--#include Makefile.common
>-+include Makefile.common
>+ DROPNFA_O = drop_nfa.o
>+ DROPGSW_O = dropgsw.o
>diff -ruN /usr/ports/biology/fasta3/files/patch-Makefile.common fasta3/files/patch-Makefile.common
>--- /usr/ports/biology/fasta3/files/patch-Makefile.common	Sun Feb 11 13:28:59 2001
>+++ fasta3/files/patch-Makefile.common	Wed Dec 31 21:00:00 1969
>@@ -1,20 +0,0 @@
>---- Makefile.common.orig	Mon Jan 29 12:42:32 2001
>-+++ Makefile.common	Mon Jan 29 13:44:06 2001
>-@@ -46,7 +46,7 @@
>- XTPROGS = fastx33_t tfastx33_t fasty33_t tfasty33_t
>- XPROGS = fastx33 tfastx33  fasty33 tfasty33
>- 
>--PROGS = $(SPROGS) $(TPROGS)
>-+PROGS = $(SPROGS) $(TPROGS) $(APROGS) $(XTPROGS) $(XPROGS)
>- 
>- all : $(PROGS)
>- 
>-@@ -60,7 +60,7 @@
>- 	rm -f *.o $(PROGS)
>- 
>- install:
>--	cp $(PROGS) $(XDIR)
>-+	$(BSD_INSTALL_PROGRAM) $(PROGS) $(XDIR)
>- 
>- sinstall:
>- 	cp $(SPROGS) $(XDIR)
>diff -ruN /usr/ports/biology/fasta3/files/patch-comp_thr.c fasta3/files/patch-comp_thr.c
>--- /usr/ports/biology/fasta3/files/patch-comp_thr.c	Fri Aug 23 00:36:33 2002
>+++ fasta3/files/patch-comp_thr.c	Wed Dec 31 21:00:00 1969
>@@ -1,11 +0,0 @@
>---- comp_thr.c.orig	Thu Aug 22 20:32:10 2002
>-+++ comp_thr.c	Thu Aug 22 20:32:25 2002
>-@@ -16,7 +16,7 @@
>- #include <time.h>
>- 
>- #ifdef UNIX
>--#if !defined(__NetBSD__) && !defined(MacOSX)
>-+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
>- #include <values.h>
>- #else
>- #include <limits.h>
>diff -ruN /usr/ports/biology/fasta3/files/patch-compacc.c fasta3/files/patch-compacc.c
>--- /usr/ports/biology/fasta3/files/patch-compacc.c	Fri Aug 23 00:36:33 2002
>+++ fasta3/files/patch-compacc.c	Wed Dec 31 21:00:00 1969
>@@ -1,11 +0,0 @@
>---- compacc.c.orig	Thu Aug 22 20:30:30 2002
>-+++ compacc.c	Thu Aug 22 20:30:43 2002
>-@@ -11,7 +11,7 @@
>- #if defined(UNIX) || defined(MSDOS)
>- #include <sys/types.h>
>- #endif
>--#if !defined(__MWERKS__) && !defined(MacOSX)
>-+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
>- #include <values.h>
>- #else
>- #include <limits.h>
>diff -ruN /usr/ports/biology/fasta3/files/patch-complib.c fasta3/files/patch-complib.c
>--- /usr/ports/biology/fasta3/files/patch-complib.c	Fri Aug 23 00:36:33 2002
>+++ fasta3/files/patch-complib.c	Wed Dec 31 21:00:00 1969
>@@ -1,11 +0,0 @@
>---- complib.c.orig	Thu Aug 22 20:33:57 2002
>-+++ complib.c	Thu Aug 22 20:34:07 2002
>-@@ -29,7 +29,7 @@
>- #include <ctype.h>
>- #include <time.h>
>- #ifdef UNIX
>--#if !defined(__NetBSD__) && !defined(MacOSX)
>-+#if !defined(__FreeBSD__) && !defined(__NetBSD__) && !defined(MacOSX)
>- #include <values.h>
>- #else
>- #include <limits.h>
>diff -ruN /usr/ports/biology/fasta3/files/patch-scaleswn.c fasta3/files/patch-scaleswn.c
>--- /usr/ports/biology/fasta3/files/patch-scaleswn.c	Fri Aug 23 00:36:33 2002
>+++ fasta3/files/patch-scaleswn.c	Wed Dec 31 21:00:00 1969
>@@ -1,11 +0,0 @@
>---- scaleswn.c.orig	Thu Aug 22 20:30:55 2002
>-+++ scaleswn.c	Thu Aug 22 20:31:06 2002
>-@@ -26,7 +26,7 @@
>- #include <math.h>
>- #include <string.h>
>- 
>--#if !defined(__MWERKS__) && !defined(MacOSX)
>-+#if !defined(__FreeBSD__) && !defined(__MWERKS__) && !defined(MacOSX)
>- #include <values.h>
>- #else
>- #include <limits.h>	/* needed for LONG_MAX */
>diff -ruN /usr/ports/biology/fasta3/files/pkg-message.in fasta3/files/pkg-message.in
>--- /usr/ports/biology/fasta3/files/pkg-message.in	Wed Dec 31 21:00:00 1969
>+++ fasta3/files/pkg-message.in	Sun Feb  5 00:27:29 2006
>@@ -0,0 +1,16 @@
>+=============================================================================
>+
>+ The FASTA3 package has been successfully installed.
>+
>+ A sample configuration file has been installed to 
>+ %%PREFIX%%/etc 
>+ as "fastlibs.sample". This may be renamed to "fastlibs" and edited
>+ to suit the requirements of a particular site.
>+
>+ In order to use the FASTA3 programs, a user must set the environment
>+ variable FASTLIBS to contain the full path of the FASTA3 configuration
>+ file, e.g.:
>+
>+ set FASTLIBS to: "%%PREFIX%%/etc/fastlibs"
>+
>+==============================================================================
>diff -ruN /usr/ports/biology/fasta3/pkg-message fasta3/pkg-message
>--- /usr/ports/biology/fasta3/pkg-message	Sun Feb 11 13:28:59 2001
>+++ fasta3/pkg-message	Wed Dec 31 21:00:00 1969
>@@ -1,15 +0,0 @@
>---------------------------------------------------------------------------
>-
>-The FASTA3 package has been successfully installed.
>-
>-NB:  A sample configuration file has been installed to %%PREFIX%%/etc as
>-"fastlibs.sample".  This may be renamed to "fastlibs" and edited
>-to suit the requirements of a particular site.
>-
>-In order to use the FASTA3 programs, a user must set the environment
>-variable FASTLIBS to contain the full path of the FASTA3 configuration
>-file, e.g.:
>-
>-- set FASTLIBS to:  "%%PREFIX%%/etc/fastlibs"
>-
>---------------------------------------------------------------------------
>diff -ruN /usr/ports/biology/fasta3/pkg-plist fasta3/pkg-plist
>--- /usr/ports/biology/fasta3/pkg-plist	Wed Oct 22 06:29:51 2003
>+++ fasta3/pkg-plist	Thu Feb  9 12:12:48 2006
>@@ -1,11 +1,41 @@
>-%%PORTDOCS%%%%DOCSDIR%%/00README.1st
>-%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
>+bin/fasta34
>+bin/prss34_t
>+bin/tfastf34_t
>+bin/fastf34_t
>+bin/fastm34_t
>+bin/tfasts34_t
>+bin/tfasty34_t
>+bin/fasty34_t
>+bin/tfastx34_t
>+bin/fastx34_t
>+bin/tfasta34_t
>+bin/fasts34_t
>+bin/fasta34_t
>+bin/ssearch34_t
>+bin/tfastf34
>+bin/fastf34
>+bin/prfx34
>+bin/prss34
>+bin/tfastm34
>+bin/fastm34
>+bin/tfasts34
>+bin/tfasty34
>+bin/fasty34
>+bin/tfastx34
>+bin/fastx34
>+bin/fasts34
>+bin/tfasta34
>+bin/ssearch34
>+bin/prfx34_t
>+etc/fastlibs.sample
> %%PORTDOCS%%%%DOCSDIR%%/README
>-%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
>+%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
>+%%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST
> %%PORTDOCS%%%%DOCSDIR%%/fasta3x.me
>+%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
>+%%PORTDOCS%%%%DOCSDIR%%/fasta20.doc
>+%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
> %%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3
>-%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_2.0
>-%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.0
> %%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2
> %%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3
> %%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4
>@@ -16,30 +46,57 @@
> %%PORTDOCS%%%%DOCSDIR%%/readme.v31t1
> %%PORTDOCS%%%%DOCSDIR%%/readme.v32t0
> %%PORTDOCS%%%%DOCSDIR%%/readme.v33t0
>+%%PORTDOCS%%%%DOCSDIR%%/readme.v34t0
> %%PORTDOCS%%%%DOCSDIR%%/readme.w32
>-bin/fasta3
>-bin/fasta3_t
>-bin/fastf3
>-bin/fastf3_t
>-bin/fasts3
>-bin/fasts3_t
>-bin/fastx3
>-bin/fastx3_t
>-bin/fasty3
>-bin/fasty3_t
>-bin/map_db
>-bin/prss3
>-bin/ssearch3
>-bin/ssearch3_t
>-bin/tfasta3
>-bin/tfasta3_t
>-bin/tfastf3
>-bin/tfastf3_t
>-bin/tfasts3
>-bin/tfasts3_t
>-bin/tfastx3
>-bin/tfastx3_t
>-bin/tfasty3
>-bin/tfasty3_t
>-etc/fastlibs.sample
>+%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
>+%%EXAMPLESDIR%%/egmsmg.aa
>+%%EXAMPLESDIR%%/gtm1_human.aa
>+%%EXAMPLESDIR%%/gtt1_drome.aa
>+%%EXAMPLESDIR%%/h10_human.aa
>+%%EXAMPLESDIR%%/hahu.aa
>+%%EXAMPLESDIR%%/lcbo.aa
>+%%EXAMPLESDIR%%/m1r.aa
>+%%EXAMPLESDIR%%/m2.aa
>+%%EXAMPLESDIR%%/mchu.aa
>+%%EXAMPLESDIR%%/mgstm1.aa
>+%%EXAMPLESDIR%%/ms1.aa
>+%%EXAMPLESDIR%%/musplfm.aa
>+%%EXAMPLESDIR%%/mwkw.aa
>+%%EXAMPLESDIR%%/mwrtc1.aa
>+%%EXAMPLESDIR%%/n0.aa
>+%%EXAMPLESDIR%%/n1.aa
>+%%EXAMPLESDIR%%/n2.aa
>+%%EXAMPLESDIR%%/n2s.aa
>+%%EXAMPLESDIR%%/n2t.aa
>+%%EXAMPLESDIR%%/ngt.aa
>+%%EXAMPLESDIR%%/ngts.aa
>+%%EXAMPLESDIR%%/oohu.aa
>+%%EXAMPLESDIR%%/prio_atepa.aa
>+%%EXAMPLESDIR%%/qrhuld.aa
>+%%EXAMPLESDIR%%/xurt8c.aa
>+%%EXAMPLESDIR%%/xurtg.aa
>+%%EXAMPLESDIR%%/mgstm1.lc
>+%%EXAMPLESDIR%%/xurt8c.lc
>+%%EXAMPLESDIR%%/bovgh.seq
>+%%EXAMPLESDIR%%/bovprl.seq
>+%%EXAMPLESDIR%%/gst.seq
>+%%EXAMPLESDIR%%/hsgstm1b.seq
>+%%EXAMPLESDIR%%/humgstd.seq
>+%%EXAMPLESDIR%%/mgstm1.seq
>+%%EXAMPLESDIR%%/mgtt2_x.seq
>+%%DATADIR%%/blosum45.mat
>+%%DATADIR%%/blosum50.mat
>+%%DATADIR%%/blosum62.mat
>+%%DATADIR%%/blosum80.mat
>+%%DATADIR%%/dna.mat
>+%%DATADIR%%/idn_aa.mat
>+%%DATADIR%%/md_10.mat
>+%%DATADIR%%/md_20.mat
>+%%DATADIR%%/md_40.mat
>+%%DATADIR%%/pam120.mat
>+%%DATADIR%%/pam250.mat
>+%%DATADIR%%/rna.mat
>+%%DATADIR%%/vtml160.mat
> %%PORTDOCS%%@dirrm %%DOCSDIR%%
>+@dirrm %%EXAMPLESDIR%%
>+@dirrm %%DATADIR%%

Actions: View | Diff

Attachments on bug 93052: 62215 | 62216