diff options
Diffstat (limited to 'biology/ncbi-toolkit/files')
| -rw-r--r-- | biology/ncbi-toolkit/files/freebsd.ncbi.mk | 31 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-aa | 8 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-ab | 19 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-ac | 11 | ||||
| -rw-r--r-- | biology/ncbi-toolkit/files/patch-ncbilcl.fbd | 18 |
5 files changed, 22 insertions, 65 deletions
diff --git a/biology/ncbi-toolkit/files/freebsd.ncbi.mk b/biology/ncbi-toolkit/files/freebsd.ncbi.mk deleted file mode 100644 index ccbb2bf8f60f..000000000000 --- a/biology/ncbi-toolkit/files/freebsd.ncbi.mk +++ /dev/null @@ -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 --git a/biology/ncbi-toolkit/files/patch-aa b/biology/ncbi-toolkit/files/patch-aa index e2e8abb9e5a7..8bb479ec9b0b 100644 --- a/biology/ncbi-toolkit/files/patch-aa +++ b/biology/ncbi-toolkit/files/patch-aa @@ -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 --git a/biology/ncbi-toolkit/files/patch-ab b/biology/ncbi-toolkit/files/patch-ab deleted file mode 100644 index 886047ae18c8..000000000000 --- a/biology/ncbi-toolkit/files/patch-ab +++ /dev/null @@ -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 <stdio.h> - #include <ctype.h> - #include <string.h> --#include <malloc.h> - #include <memory.h> - #include <stdlib.h> - #include <math.h> -@@ -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 --git a/biology/ncbi-toolkit/files/patch-ac b/biology/ncbi-toolkit/files/patch-ac deleted file mode 100644 index 3099d88124c9..000000000000 --- a/biology/ncbi-toolkit/files/patch-ac +++ /dev/null @@ -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 <pwd.h> -+#include <sys/param.h> -+#define LOGNAME_MAX MAXLOGNAME - #endif /* OS_UNIX */ - #ifdef OS_MAC - #include <Gestalt.h> diff --git a/biology/ncbi-toolkit/files/patch-ncbilcl.fbd b/biology/ncbi-toolkit/files/patch-ncbilcl.fbd new file mode 100644 index 000000000000..75dae534e758 --- /dev/null +++ b/biology/ncbi-toolkit/files/patch-ncbilcl.fbd @@ -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 <errno.h> + #include <float.h> + #include <unistd.h> ++#include <sys/select.h> /* req. for 5.0. fd_set def. moved from types.h */ + + /* Check if there are POSIX threads available */ + #ifdef _POSIX_THREADS |