Update to 34.t25.d4.

PR:		ports/93052
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

7 files changed, 41 insertions, 105 deletions

diff --git a/biology/fasta3/files/patch-Makefile b/biology/fasta3/files/patch-Makefile
index 8930300dacd2..60b18c9b84a0 100644
--- a/biology/fasta3/files/patch-Makefile
+++ b/biology/fasta3/files/patch-Makefile
@@ -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 @@
+--- 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)
+ #
  
- # use -DBIG_LIB64 to generate 64-bit offsets in map_db .xin files
+-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
  
--CC= cc -O -std1
-+#CC= cc -O -std1
- #CC= insure -g -DDEBUG
- #CC= cc -g -DDEBUG -std1
- #CC= gcc -g -Wall
- #
- # 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
+ # 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 Makefile33.common)
- 
-@@ -32,11 +32,15 @@
- HFLAGS= -o
- NFLAGS= -o
+ #
+ #(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 --git a/biology/fasta3/files/patch-Makefile.common b/biology/fasta3/files/patch-Makefile.common
deleted file mode 100644
index 395da695e031..000000000000
--- a/biology/fasta3/files/patch-Makefile.common
+++ /dev/null
@@ -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 --git a/biology/fasta3/files/patch-comp_thr.c b/biology/fasta3/files/patch-comp_thr.c
deleted file mode 100644
index 24a0904c0d1c..000000000000
--- a/biology/fasta3/files/patch-comp_thr.c
+++ /dev/null
@@ -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 --git a/biology/fasta3/files/patch-compacc.c b/biology/fasta3/files/patch-compacc.c
deleted file mode 100644
index c6a493f81a31..000000000000
--- a/biology/fasta3/files/patch-compacc.c
+++ /dev/null
@@ -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 --git a/biology/fasta3/files/patch-complib.c b/biology/fasta3/files/patch-complib.c
deleted file mode 100644
index d5f27bd708d0..000000000000
--- a/biology/fasta3/files/patch-complib.c
+++ /dev/null
@@ -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 --git a/biology/fasta3/files/patch-scaleswn.c b/biology/fasta3/files/patch-scaleswn.c
deleted file mode 100644
index 3fd5f2023b63..000000000000
--- a/biology/fasta3/files/patch-scaleswn.c
+++ /dev/null
@@ -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 --git a/biology/fasta3/files/pkg-message.in b/biology/fasta3/files/pkg-message.in
new file mode 100644
index 000000000000..f43513546af4
--- /dev/null
+++ b/biology/fasta3/files/pkg-message.in
@@ -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"
+
+==============================================================================