Date: Fri, 4 Apr 2008 19:01:01 GMT From: Tassilo Philipp <tphilipp@potion-studios.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/122452: New port: biology/mapm3 Message-ID: <200804041901.m34J11jH023780@www.freebsd.org> Resent-Message-ID: <200804041910.m34JA3sC074886@freefall.freebsd.org>
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>Number: 122452 >Category: ports >Synopsis: New port: biology/mapm3 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Fri Apr 04 19:10:02 UTC 2008 >Closed-Date: >Last-Modified: >Originator: Tassilo Philipp >Release: 6.3 >Organization: Potion Studios >Environment: FreeBSD 6.3-RELEASE FreeBSD 6.3-RELEASE #0: Wed Jan 16 01:43:02 UTC 2008 root@palmer.cse.buffalo.edu:/usr/obj/usr/src/sys/SMP amd64 >Description: >How-To-Repeat: >Fix: Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # mapm3 # mapm3/Makefile # mapm3/pkg-descr # mapm3/files # mapm3/files/patch-Makefile # mapm3/files/patch-lib-iolib.c # mapm3/files/patch-lib-iolib.h # mapm3/files/patch-lib-makehelp.c # mapm3/files/patch-lib-shell.c # mapm3/files/patch-lib-syscode.c # mapm3/files/patch-lib-system.h # mapm3/files/patch-mapm-chroms.c # mapm3/files/patch-mapm-database.c # mapm3/files/patch-mapm-info.c # mapm3/files/patch-mapm-map_info.h # mapm3/files/patch-mapm-mapm.h # mapm3/files/patch-mapm-maps.c # mapm3/files/patch-mapm-npt_cmds.c # mapm3/files/patch-mapm-print.c # mapm3/files/patch-mapm-reader.c # mapm3/files/patch-mapm-state.c # mapm3/files/patch-mapm-sys_cmds.c # mapm3/files/patch-mapm-two_cmds.c # mapm3/files/patch-quant-qcmds.c # mapm3/files/patch-quant-qraw.c # mapm3/files/patch-sun-xqtl # mapm3/files/patch-sun-xmapmaker # mapm3/pkg-plist # mapm3/distinfo # echo c - mapm3 mkdir -p mapm3 > /dev/null 2>&1 echo x - mapm3/Makefile sed 's/^X//' >mapm3/Makefile << 'END-of-mapm3/Makefile' X# New ports collection makefile for: mapm3 X# Date created: 26 March 2008 X# Whom: Tassilo Philipp <tphilipp@potion-studios.com> X# X# $FreeBSD$ X# X XPORTNAME= mapm3 XPORTVERSION= 3.0 XCATEGORIES= biology XMASTER_SITES= http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ \ X ftp://ftp.ibiblio.org/pub/academic/biology/molbio/mapmaker/ \ X http://iubio.bio.indiana.edu/soft/molbio/qtl/mapmaker/ \ X http://www.mirrorservice.org/sites/iubio.bio.indiana.edu/molbio/qtl/mapmaker/ XDISTNAME= mapm3-source XEXTRACT_SUFX= .tar.Z X XMAINTAINER= tphilipp@potion-studios.com XCOMMENT= Constructs linkage maps of markers segregating in experimental crosses X XNO_WRKSUBDIR= yes X Xpost-patch: X ${CP} ${WRKSRC}/sun/* ${WRKSRC} X X.include <bsd.port.mk> END-of-mapm3/Makefile echo x - mapm3/pkg-descr sed 's/^X//' >mapm3/pkg-descr << 'END-of-mapm3/pkg-descr' XMAPMAKER/EXP is a linkage analysis package designed to help construct primary Xlinkage maps of markers segregating in experimental crosses. MAPMAKER/EXP Xperforms full multipoint linkage analysis (simultaneous estimation of all Xrecombination fractions from the primary data) for dominant, recessive, and co- Xdominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only Xsuccessor to the original MAPMAKER program. X XMAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map Xgenes controlling polygenic quantitative traits in F2 intercrosses and BC1 Xbackcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL Xcan be found in the technical report (included with MAPMAKER/QTL). X XWWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ END-of-mapm3/pkg-descr echo c - mapm3/files mkdir -p mapm3/files > /dev/null 2>&1 echo x - mapm3/files/patch-Makefile sed 's/^X//' >mapm3/files/patch-Makefile << 'END-of-mapm3/files/patch-Makefile' X--- Makefile.orig 2008-04-04 20:05:29.000000000 +0000 X+++ Makefile 2008-04-04 19:51:04.000000000 +0000 X@@ -16,6 +16,7 @@ X #### X #### For Macs with A/UX, use: SYS= -D_SYS_AUX X #### For DECStations, use: SYS= -D_SYS_ULTRIX X+#### For modern BSD systems (added for FreeBSD 6.3 port) use: SYS= -D_SYS_BSD X #### For PC's with WATCOM C/386 use the special Makefile instead, X #### No other ports are built in yet. Please do them, and tell us how! X #### Refer to lib/system.h and lib/syscode.c for ideas. X@@ -24,7 +25,7 @@ X #### datasets (roughly 5000 loci vs 1000 loci). For even bigger datasets, X #### modify mapm/mapm.h. X X-SYS= -D_SYS_SUNOS X+SYS= -D_SYS_BSD -D_BIG_DATASETS X X #### Next define the system libraries to link with Mapmaker. On SunOS, Ultrix X #### and other vanilla-ish BSD systems, the correct setting is: X@@ -46,7 +47,7 @@ X #### Be sure that you have write permission to this directory (e.g. you may X #### need to be logged in as "root" to install MAPMAKER in some directories). X X-DIR= /usr/local/bin X+DIR= ${PREFIX}/bin X X #### RDLN below refers to the GNU Readline library, which can (optionally) be X #### used by MAPMAKER to provide interactive command line editing. See the X@@ -70,9 +71,11 @@ X #### (see the end of readline/readline.c). Readline will not compile on X #### A/UX without using GCC instead of A/UX's cc (because it needs alloca). X X-OUR_LIB= gnu.o X-GNU_OPT= -D_GNU_READLINE -I. X-GNU_LIBS= -L$(RDLN) -lreadline X+#OUR_LIB= gnu.o X+#GNU_OPT= -D_GNU_READLINE -I. X+OUR_LIB= lib.o X+GNU_OPT= X+#GNU_LIBS= -L$(RDLN) -lreadline X X #### Now we specify the commands used to compile MAPMAKER. The stuff X #### below works on Sun SPARCStations running SunOS 4.1.x (aka Solaris 1.x) X@@ -82,8 +85,8 @@ X #### person at your site should be able to figure out what to do almost X #### trivially. See the file INSTALL.ME for details. X X-COMPILE= cc X-LINKALL= cc X+COMPILE= gcc X+LINKALL= gcc X LINKLIB= ld -r X DELETE= rm -f X INSTALL= cp END-of-mapm3/files/patch-Makefile echo x - mapm3/files/patch-lib-iolib.c sed 's/^X//' >mapm3/files/patch-lib-iolib.c << 'END-of-mapm3/files/patch-lib-iolib.c' X--- lib/iolib.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ lib/iolib.c 2008-03-23 15:39:56.000000000 +0000 X@@ -299,7 +299,7 @@ X } X X X-void fgetln(fp) /* ln is side-effected. */ X+void fgetln_(fp) /* ln is side-effected. */ X FILE *fp; X { X if (fp==stdin) { getln("? "); return; } END-of-mapm3/files/patch-lib-iolib.c echo x - mapm3/files/patch-lib-iolib.h sed 's/^X//' >mapm3/files/patch-lib-iolib.h << 'END-of-mapm3/files/patch-lib-iolib.h' X--- lib/iolib.h.orig 2008-04-04 20:05:29.000000000 +0000 X+++ lib/iolib.h 2008-04-03 20:00:49.000000000 +0000 X@@ -53,9 +53,9 @@ X conditions. Assume its really only one (or maybe 2-3) lines. ps_ is similar, X but for internal use only by the functions in this library. X X-Ln is a global input string side-effected by getln() and fgetln(). X+Ln is a global input string side-effected by getln() and fgetln_(). X The pointer ln itself may be side-effected, (eg: by the token parsing X-routines) as it is reset during each call to getln() or fgetln(). X+routines) as it is reset during each call to getln() or fgetln_(). X However, the string space used to hold the input line is reused, and X any pointers into the ln string which you saved may point to trash X after one of these calls. Ln is alloced for 2K chars, leaving lots of X@@ -66,7 +66,7 @@ X word breaks, converting tabs to spaces (every 8 chars), buffering X output (perhaps multiple lines!) and more. The do_fwrite() function does X not do this. Similarly, the getln() function despace()es, X-lowercase()es, and filter()s its input, while fgetln(), input(), and X+lowercase()es, and filter()s its input, while fgetln_(), input(), and X finput() functions do not [yes, it's a somewhat odd inconsistancy, but X it's handy]. X X@@ -254,6 +254,14 @@ X files! (The obvious exception is logging and input redirection, for which X you should use the rather carefuly crafted routines described above!) */ X X+/* Mimics 'writable string' behaviour which wasn't problematic in some old X+ pre '89 code. GCC supported it for a long time via the -fwritable-strings X+ option. However, as of version 3.4, it was declared deprecated, and removed X+ in later versions. A lot of the code depends on this questionable behaviour, X+ so the following macro is used throughout this *BSD port. */ X+#define WRS(s) (char[]){(s)} X+ X+ X bool make_filename(); /* args: char *name; int mode; char *extension; X This turns name into a perfectly valid file name, and returns TRUE if this X was possible. The name may include a directory specification - otherwise it X@@ -277,7 +285,7 @@ X #define APPEND "a" X void close_file(); /* args: FILE *fp; */ X X-bool end_of_file(); /* args: FILE *fp; returns TRUE if finput() or fgetln() X+bool end_of_file(); /* args: FILE *fp; returns TRUE if finput() or fgetln_() X will be able to grab a new line from the file. */ X bool end_of_text(); /* args: FILE *fp; Like an end-of-file test, except it also X returns TRUE if rest of the file is white. As a side-effect, it will step X@@ -289,17 +297,17 @@ X X #define fpr(fp) fprint(fp,ps) X #define fwp(fp) fwrite(fp,ps) X-#define fnl(fp) fwrite(fp,"\n") X+#define fnl(fp) fwrite(fp,WRS("\n")) X X void finput(); /* args: FILE *fp; char *str; int max_input_chars; */ X-void fgetln(); /* args: FILE *fp; side-effects global char *ln; X- Finput() and fgetln() both return a filter()ed line, and on end-of-file, the X+void fgetln_(); /* args: FILE *fp; side-effects global char *ln; X+ Finput() and fgetln_() both return a filter()ed line, and on end-of-file, the X ENDOFILE message is sent. Str must have room for max_input_chars+1 chars, X and only max_input_chars-1 chars can usually be read, as a '\n' may be read X in at the end and then deleted from the string. */ X X void fgetdataln(); /* args: FILE *fp; int *count; side-effects global ln; X- Like fgetln(), although this skips null (white) and comment lines (those X+ Like fgetln_(), although this skips null (white) and comment lines (those X beginning with a '#' in the leftmost position. Also, each time any line is X read from the file (data, null, or comment), *count is incremented. */ X X@@ -329,7 +337,7 @@ X X extern char *ps_, *ln_; /* input and output strings for the library only */ X extern char *linebuf; /* tty output buffer */ X-extern char *gotln, *lnptr; /* input line for getln(), fgetln() */ X+extern char *gotln, *lnptr; /* input line for getln(), fgetln_() */ X X extern FILE **in_fp; /* the "stack" of input files for redirecting input */ X extern int redirs; END-of-mapm3/files/patch-lib-iolib.h echo x - mapm3/files/patch-lib-makehelp.c sed 's/^X//' >mapm3/files/patch-lib-makehelp.c << 'END-of-mapm3/files/patch-lib-makehelp.c' X--- lib/makehelp.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ lib/makehelp.c 2008-03-27 21:52:37.000000000 +0000 X@@ -131,7 +131,7 @@ X { X close_file(file); X X- fwrite(hlp,"@end\n"); X+ fwrite(hlp,WRS("@end\n")); X close_file(hlp); X X write_topics_and_end(); X@@ -172,9 +172,9 @@ X strcpy(man_name, argv[4]); X X strcpy(code_failed,code_name); X- make_filename(code_failed,FORCE_EXTENSION,"failed"); X+ make_filename(code_failed,FORCE_EXTENSION,WRS("failed")); X strcpy(final_hlp_name,hlp_name); X- make_filename_in_dir(final_hlp_name,FORCE_EXTENSION,"help", X+ make_filename_in_dir(final_hlp_name,FORCE_EXTENSION,WRS("help"), X FORCE_DIR,argv[5]); X X file= open_file(file_name,READ); X@@ -187,16 +187,16 @@ X matrix(entry,MAX_COMMANDS,MAXLINE+1,char); X X /* start help file 12345678901234567890123456789012345 */ X- fwrite(hlp, "#MAPMAKER help file - do not edit!\n"); X+ fwrite(hlp,WRS("#MAPMAKER help file - do not edit!\n")); X pos= 34l + LINE_BREAK_LEN; X X /* code file */ X- fwrite(code,"/* MAPMAKER help code file - do not edit! */ \n\n"); X- fwrite(code,"#define INC_LIB \n#define INC_SHELL \n"); X- fwrite(code,"#include \"system.h\" \n\n"); X+ fwrite(code,WRS("/* MAPMAKER help code file - do not edit! */ \n\n")); X+ fwrite(code,WRS("#define INC_LIB \n#define INC_SHELL \n")); X+ fwrite(code,WRS("#include \"system.h\" \n\n")); X /* sf(ps,"char help_filename[]= \"%s\";\n\n",final_hlp_name); X fwrite(code,ps); */ X- fwrite(code,"void make_help_entries()\n{\n"); X+ fwrite(code,WRS("void make_help_entries()\n{\n")); X X /* man file */ X man_write_title(); X@@ -242,7 +242,7 @@ X strcpy(name,str+i); despace(name); X nextstr(); X sf(ps,"\t%s... ",name); pr(); flush(); X- X+ X if (streq(type,"cmd")) parse_entry(CMD,name,abbreviation); X else if (streq(type,"opt")) parse_entry(OPT,name,abbreviation); X else if (streq(type,"param")) parse_entry(PAR,name,abbreviation); X@@ -419,7 +419,7 @@ X sf(ps," mktopic(%d,\"%s\",TOP,%ldl);\n",s,temp,position[s]); X fpr(code); s++; X } X- fprint(code,"}\n"); X+ fprint(code,WRS("}\n")); X } X X X@@ -681,7 +681,7 @@ X case TOP: X man_write_line(""); X strcpy(upcase,section[s]); uppercase(upcase); X- sf(temp," %s\(%d\) %s ",(s>=10 ? "":" "),s,upcase); s++; break; X+ sf(temp," %s(%d) %s ",(s>=10 ? "":" "),s,upcase); s++; break; X case CMD: X strcpy(upcase,entry[i]); uppercase(upcase); X sf(temp," %s Command ",upcase); break; X@@ -718,7 +718,7 @@ X if (entry_type[i]==TOP) { X man_write_line(""); X strcpy(upcase,section[s]); uppercase(upcase); X- sf(temp,"%s\(%d\) %s ",(s>=10 ? "":""),s,upcase); s++; X+ sf(temp,"%s(%d) %s ",(s>=10 ? "":""),s,upcase); s++; X man_write_line(temp); X } else { X sf(temp,"%s%s",entry[i],(entry_type[i]==HLP ? "*":"")); END-of-mapm3/files/patch-lib-makehelp.c echo x - mapm3/files/patch-lib-shell.c sed 's/^X//' >mapm3/files/patch-lib-shell.c << 'END-of-mapm3/files/patch-lib-shell.c' X--- lib/shell.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ lib/shell.c 2008-03-27 21:24:20.000000000 +0000 X@@ -129,7 +129,7 @@ X X run { X strcpy(name,version_filename); X- if (!make_filename_in_dir(name,FORCE_EXTENSION,".v", X+ if (!make_filename_in_dir(name,FORCE_EXTENSION,WRS(".v"), X FORCE_DIR,CODE_DIR)) send(CANTOPEN); X fp=open_file(name,READ); X finput(fp,ln_,MAXLINE); p=ln_; /* don't hack &ln_ */ X@@ -226,7 +226,7 @@ X help_uses_wimp_help= FALSE; X X help_file=NULL; X- if (make_filename_in_dir(help_filename,FORCE_EXTENSION,HELP_EXT, X+ if (make_filename_in_dir(help_filename,FORCE_EXTENSION,WRS(HELP_EXT), X DEFAULT_DIR,CODE_DIR)) { X run help_file=open_file(help_filename,READ); X except_when(CANTOPEN) {} X@@ -950,7 +950,7 @@ X use_uncrunched_args(); X get_one_arg(stoken,sREQUIRED,file_name); X X- if (!make_filename(file_name,DEFAULT_EXTENSION,"in")) X+ if (!make_filename(file_name,DEFAULT_EXTENSION,WRS("in"))) X error("bad input file name"); X else redirect_input(file_name,TRUE); /* verbose -> messages */ X } X@@ -972,7 +972,7 @@ X usage_error(1); X X } else if (!nullstr(file_name)) { X- if (!make_filename(file_name,DEFAULT_EXTENSION,"out")) X+ if (!make_filename(file_name,DEFAULT_EXTENSION,WRS("out"))) X sf(ps,"error: Bad photo file name"); X if (!photo_to_file(file_name,"a")) X sf(ps,"error: Unable to open photo file '%s'\n",file_name); X@@ -1080,12 +1080,12 @@ X else if (topic_help_key[i]==HELPLESS) print(NO_HELP_KEY); X else { X fgoto_line(help_file,topic_help_key[i]); X- fgetln(help_file); X+ fgetln_(help_file); X got_any=FALSE; X while (ln[0]!='@') { X got_any=TRUE; X print(ln); nl(); X- fgetln(help_file); X+ fgetln_(help_file); X } X if (!got_any) print(NO_HELP_KEY); X } X@@ -1131,12 +1131,12 @@ X else if (cmd[i]->help_key==HELPLESS) print(NO_HELP_KEY); X else { X fgoto_line(help_file,cmd[i]->help_key); X- fgetln(help_file); X+ fgetln_(help_file); X got_any=FALSE; X while (ln[0]!='@') { X got_any=TRUE; X print(ln); nl(); X- fgetln(help_file); X+ fgetln_(help_file); X } X if (!got_any) print(NO_HELP_KEY); X } X@@ -1164,10 +1164,10 @@ X { print(NO_HELP_KEY); nl(); print(SURROGATE_ABOUT); } X else { X fgoto_line(help_file,n); X- fgetln(help_file); X+ fgetln_(help_file); X while (ln[0]!='@') { X print(ln); nl(); X- fgetln(help_file); X+ fgetln_(help_file); X } X } X nl(); print(MOREHELP0); print(MOREHELP1); print(MOREHELP2); END-of-mapm3/files/patch-lib-shell.c echo x - mapm3/files/patch-lib-syscode.c sed 's/^X//' >mapm3/files/patch-lib-syscode.c << 'END-of-mapm3/files/patch-lib-syscode.c' X--- lib/syscode.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ lib/syscode.c 2008-03-27 21:03:12.000000000 +0000 X@@ -198,7 +198,7 @@ X long fseekvalue= 0L; X frewind(fp); X run while (fseekvalue < index-1) { X- fgetln(help_file); X+ fgetln_(help_file); X fseekvalue+=len(ln)+1; X } except_when(ENDOFILE) return(FALSE); X return(TRUE); X@@ -742,26 +742,26 @@ X X } else if (matches(argv[i]+1,"load")) { X check_file_arg(*argc_ptr-i,argv[i+1],file_arg[LOAD_FILE_ARG], X- "load","data",argv[0],READ); X+ WRS("load"),WRS("data"),argv[0],READ); X prep_it=FALSE; X argv[i++][0]='\0'; argv[i][0]='\0'; X } else if (matches(argv[i]+1,"prep")) { X check_file_arg(*argc_ptr-i,argv[i+1],file_arg[LOAD_FILE_ARG], X- "prep","raw",argv[0],READ); X+ WRS("prep"),WRS("raw"),argv[0],READ); X prep_it=TRUE; X argv[i++][0]='\0'; argv[i][0]='\0'; X } else if (matches(argv[i]+1,"run")) { X check_file_arg(*argc_ptr-i,argv[i+1],file_arg[RUN_FILE_ARG], X- "run","in",argv[0],READ); X+ WRS("run"),WRS("in"),argv[0],READ); X argv[i++][0]='\0'; argv[i][0]='\0'; X } else if (matches(argv[i]+1,"photo")) { X check_file_arg(*argc_ptr-i,argv[i+1],file_arg[PHOTO_FILE_ARG], X- "photo","out",argv[0],APPEND); X+ WRS("photo"),WRS("out"),argv[0],APPEND); X append_it=TRUE; X argv[i++][0]='\0'; argv[i][0]='\0'; X } else if (matches(argv[i]+1,"out")) { X check_file_arg(*argc_ptr-i,argv[i+1],file_arg[PHOTO_FILE_ARG], X- "photo","out",argv[0],WRITE); X+ WRS("photo"),WRS("out"),argv[0],WRITE); X append_it=FALSE; X argv[i++][0]='\0'; argv[i][0]='\0'; X } else if (matches(argv[i]+1,"help")) { END-of-mapm3/files/patch-lib-syscode.c echo x - mapm3/files/patch-lib-system.h sed 's/^X//' >mapm3/files/patch-lib-system.h << 'END-of-mapm3/files/patch-lib-system.h' X--- lib/system.h.orig 2008-04-04 20:05:29.000000000 +0000 X+++ lib/system.h 2008-03-27 20:49:34.000000000 +0000 X@@ -43,6 +43,7 @@ X _SYS_OSF Specifics for OSF/1 for DEC Alpha (like, if it ever ships) X _SYS_AIX Specifics for the inferior but marketable AIX (RISC or other?) X _SYS_HPUX Specifics for HP-UX (8.x?) for HP 9000/700 series. X+ _SYS_BSD Specifics for modern BSD systems (tested on FreeBSD 6.3) X _SYS_UNIX Basic Unix semantics, defined if any one of the above is X X _SYS_WATCOM Specifics for WATCOM C/386 9.0 with apropriate libraries X@@ -86,6 +87,11 @@ X #else X #ifdef _SYS_AUX X #define _SYS_UNIX /* Note: NOT _SYS_MAC */ X+#else X+#ifdef _SYS_BSD X+#define _SYS_UNIX X+#else X+#endif X #endif X #endif X #endif X@@ -191,6 +197,9 @@ X #ifdef _SYS_ULTRIX X #define SIGHANDLE void X #endif X+#ifdef _SYS_BSD X+#define SIGHANDLE void X+#endif X X X X@@ -210,10 +219,14 @@ X #ifdef _SYS_ULTRIX X #define USE_RANDOM X #else X+#ifdef _SYS_BSD X+#define USE_DRAND48 /* bsd has 'random' */ X+#else X #define USE_SRAND X #endif X #endif X #endif X+#endif X X X /***************************** C-Library ************************************** X@@ -282,6 +295,14 @@ X #define QSORT_LENGTH int /* actually width is an int, not a unsigned */ X #endif X X+#ifdef _SYS_BSD /* modern BSD systems (tested on FreeBSD 6.3) */ X+#define CALLOC_PTR_TO char X+#define CALLOC_NUM_TYPE size_t /* unsigned in man page is wrong? */ X+#define SIZEOF_TYPE size_t X+#define QSORT_DATA_PTR_TO char X+#define QSORT_LENGTH int /* actually width is an int, not a unsigned */ X+#endif X+ X #ifdef _SYS_AUX /* just like ULTRIX? */ X #define CALLOC_PTR_TO char X #define CALLOC_NUM_TYPE size_t /* unsigned in man page is wrong? */ X@@ -583,7 +604,7 @@ X #include <signal.h> X #include <errno.h> X #include <time.h> /* for ctime() def - Who does not have this file? */ X-#include <malloc.h> X+#include <stdlib.h> X #include <sys/types.h> X X #ifdef TRY_WINSIZE END-of-mapm3/files/patch-lib-system.h echo x - mapm3/files/patch-mapm-chroms.c sed 's/^X//' >mapm3/files/patch-mapm-chroms.c << 'END-of-mapm3/files/patch-mapm-chroms.c' X--- mapm/chroms.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/chroms.c 2008-03-27 21:25:42.000000000 +0000 X@@ -909,7 +909,7 @@ X write_map(fp, chromosome->map_list[i]); X } X X- fprint(fp,"*Assignments and Placements:\n"); X+ fprint(fp,WRS("*Assignments and Placements:\n")); X for (locus=0; locus< raw.num_markers; locus++) { X sf(ps,"*%-8s %2d",raw.locus_name[locus],assignment[locus]->status); X fpr(fp); X@@ -943,7 +943,7 @@ X MAP *map; X X /* chromosomes */ X- fgetln(fp); X+ fgetln_(fp); X stoken(&ln,sREQUIRED,word); X if (!streq(word,"*Chromosomes:") || !itoken(&ln,iREQUIRED,&num_chroms)) { X baddata("error finding *Chromosomes:"); X@@ -957,7 +957,7 @@ X baddata("listed number of chromosomes and actual number do not agree"); X } X X- fgetln(fp); X+ fgetln_(fp); X if (!streq(ln,"*Assignments and Placements:")) X baddata("error finding *Assignments and Placements:"); X for (locus=0; locus < raw.num_markers; locus++) { END-of-mapm3/files/patch-mapm-chroms.c echo x - mapm3/files/patch-mapm-database.c sed 's/^X//' >mapm3/files/patch-mapm-database.c << 'END-of-mapm3/files/patch-mapm-database.c' X--- mapm/database.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/database.c 2008-03-27 21:26:48.000000000 +0000 X@@ -45,7 +45,7 @@ X get_one_arg(stoken, sREQUIRED, out_name); X X /* force file extension to be ".data" */ X- make_filename(out_name, FORCE_EXTENSION, ".data"); X+ make_filename(out_name, FORCE_EXTENSION, WRS(".data")); X X /* make a function call to a procedure which connects to the database */ X get_from_database(); END-of-mapm3/files/patch-mapm-database.c echo x - mapm3/files/patch-mapm-info.c sed 's/^X//' >mapm3/files/patch-mapm-info.c << 'END-of-mapm3/files/patch-mapm-info.c' X--- mapm/info.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/info.c 2008-03-27 21:26:18.000000000 +0000 X@@ -966,9 +966,9 @@ X class[locus]); X fpr(fp); X } X- fprint(fp,"*Classes:\n"); X+ fprint(fp,WRS("*Classes:\n")); X for (i=0; i<NUM_CLASSES; i++) X- { fprint(fp,"*"); fprint(fp,class_name[i]); fnl(fp); } X+ { fprint(fp,WRS("*")); fprint(fp,class_name[i]); fnl(fp); } X } X X X@@ -980,12 +980,12 @@ X real rate; X char temp_locus_name[NAME_LEN+2], word[TOKLEN+1]; X X- fgetln(fp); X+ fgetln_(fp); X if (sscanf(ln,"%s %d %d",word,&num_groups,&num_orders)!=3 || X !streq(word,"*OrderInfo:")) baddata("expected '*OrderInfo: # #'"); X X for (locus=0; locus < raw.num_markers; locus++) { X- fgetln(fp); X+ fgetln_(fp); X X if (!nstoken(&ln,sREQUIRED,temp_locus_name,NAME_LEN+1) || X temp_locus_name[0]!='*' || len(temp_locus_name)<2) X@@ -1007,9 +1007,9 @@ X order_next[locus]= ord_next; X class[locus]= class_num; X } X- fgetln(fp); if (!streq(ln,"*Classes:")) baddata("bad classes"); X+ fgetln_(fp); if (!streq(ln,"*Classes:")) baddata("bad classes"); X for (i=0; i<NUM_CLASSES; i++) X- { fgetln(fp); strcpy(class_name[i],ln+1); } X+ { fgetln_(fp); strcpy(class_name[i],ln+1); } X } X X END-of-mapm3/files/patch-mapm-info.c echo x - mapm3/files/patch-mapm-map_info.h sed 's/^X//' >mapm3/files/patch-mapm-map_info.h << 'END-of-mapm3/files/patch-mapm-map_info.h' X--- mapm/map_info.h.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/map_info.h 2008-03-31 00:14:48.000000000 +0000 X@@ -215,7 +215,7 @@ X /***** Chromosome framework, assignment, and placement stuff - chroms.c *****/ X X extern SAVED_LIST *chromosome; /* malloced by allocate_mapping_structs() */ X-#define chrom2str(x) ((x)>=0 ? chromosome->map_list[x]->map_name : "none") X+#define chrom2str(x) ((x)>=0 ? chromosome->map_list[x]->map_name : WRS("none")) X bool isa_chrom(); /* args: char *name; int *chrom; side-effected if TRUE */ X #define num_chromosomes (chromosome->num_maps) X extern int current_chrom; /* set by the sequence command or reset_state() */ END-of-mapm3/files/patch-mapm-map_info.h echo x - mapm3/files/patch-mapm-mapm.h sed 's/^X//' >mapm3/files/patch-mapm-mapm.h << 'END-of-mapm3/files/patch-mapm-mapm.h' X--- mapm/mapm.h.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/mapm.h 2008-03-16 13:53:32.000000000 +0000 X@@ -19,7 +19,7 @@ X #define command void /* needed if INC_SHELL was not defined */ X #endif X X-#include "system.h" X+#include "../lib/system.h" X X X /***************** MAPM Constants *****************/ END-of-mapm3/files/patch-mapm-mapm.h echo x - mapm3/files/patch-mapm-maps.c sed 's/^X//' >mapm3/files/patch-mapm-maps.c << 'END-of-mapm3/files/patch-mapm-maps.c' X--- mapm/maps.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/maps.c 2008-03-23 15:39:56.000000000 +0000 X@@ -592,7 +592,7 @@ X X clean_map(map); X X- fgetln(fp); X+ fgetln_(fp); X if (!nstoken(&ln,sREQUIRED,name,NAME_LEN+1) || name[0]!='*' || X sscanf(ln,"%d %d %d %d %lf",&num_loci,&unlink,&sex,&errors,&like)!=5) X baddata("expected *chrom-name # # # #"); X@@ -603,31 +603,31 @@ X strcpy(map->map_name,name+1); map->allow_errors= errors; X map->num_loci=num_loci; map->log_like=like; X X- fgetln(fp); X+ fgetln_(fp); X for (i=0; i<num_loci; i++) { X- if (nullstr(ln)) fgetln(fp); X+ if (nullstr(ln)) fgetln_(fp); X if (!itoken(&ln,iREQUIRED,&num)) send(CRASH); X map->locus[i]=num; X } X- fgetln(fp); X+ fgetln_(fp); X for (i=0; i<num_loci-1; i++) { X- if (nullstr(ln)) fgetln(fp); X+ if (nullstr(ln)) fgetln_(fp); X if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH); X map->rec_frac[i][MALE]=rnum; X } X X if (raw.data_type==CEPH && sex) { X- fgetln(fp); X+ fgetln_(fp); X for(i=0; i<num_loci-1; i++) { X- if (nullstr(ln)) fgetln(fp); X+ if (nullstr(ln)) fgetln_(fp); X if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH); X map->rec_frac[i][FEMALE]=rnum; X } X } else for (i=0; i<num_loci-1; i++) map->rec_frac[i][FEMALE]=0.0; X X- fgetln(fp); X+ fgetln_(fp); X for(i=0; i<num_loci-1; i++) { X- if (nullstr(ln)) fgetln(fp); X+ if (nullstr(ln)) fgetln_(fp); X if (!itoken(&ln,iREQUIRED,&num)) send(CRASH); X map->fix_interval[i]=num; X } X@@ -637,7 +637,7 @@ X matrix(map->error_lod,map->max_loci,raw.data.f2.num_indivs,real); X } X for (i=0; i<map->num_loci; i++) { X- fgetln(fp); X+ fgetln_(fp); X if (!stoken(&ln,sREQUIRED,str) || !streq(str,"errors")) X send(CRASH); X if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH); X@@ -646,9 +646,9 @@ X for(j=0; j<raw.data.f2.num_indivs; j++) X map->error_lod[i][j]= 0.0; X } else { X- fgetln(fp); X+ fgetln_(fp); X for (j=0; j<raw.data.f2.num_indivs; j++) { X- if (nullstr(ln)) fgetln(fp); X+ if (nullstr(ln)) fgetln_(fp); X if (!rtoken(&ln,rREQUIRED,&rnum)) send(CRASH); X map->error_lod[i][j]=rnum; X } END-of-mapm3/files/patch-mapm-maps.c echo x - mapm3/files/patch-mapm-npt_cmds.c sed 's/^X//' >mapm3/files/patch-mapm-npt_cmds.c << 'END-of-mapm3/files/patch-mapm-npt_cmds.c' X--- mapm/npt_cmds.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/npt_cmds.c 2008-03-27 21:27:12.000000000 +0000 X@@ -78,7 +78,7 @@ X nomore_args(num_args); X X run { X- if (!make_filename(name,FORCE_EXTENSION,PS_EXT)) X+ if (!make_filename(name,FORCE_EXTENSION,WRS(PS_EXT))) X { sf(ps,"illegal filename '%s'",name); error(ps); } X fp= open_file(name,WRITE); X sf(ps,"Drawing map in PostScript file '%s'... \n",name); pr(); END-of-mapm3/files/patch-mapm-npt_cmds.c echo x - mapm3/files/patch-mapm-print.c sed 's/^X//' >mapm3/files/patch-mapm-print.c << 'END-of-mapm3/files/patch-mapm-print.c' X--- mapm/print.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/print.c 2008-03-27 21:34:40.000000000 +0000 X@@ -540,7 +540,7 @@ X } X } X X-#define MAPPING_HEAD1\ X+#define MAPPING_HEAD1 \ X " 2nd Left " X #define MAPPING_HEAD2 \ X " Num Name Assignment Chrom LOD Mapping Like Locus Errors" END-of-mapm3/files/patch-mapm-print.c echo x - mapm3/files/patch-mapm-reader.c sed 's/^X//' >mapm3/files/patch-mapm-reader.c << 'END-of-mapm3/files/patch-mapm-reader.c' X--- mapm/reader.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/reader.c 2008-03-27 21:10:18.000000000 +0000 X@@ -81,7 +81,7 @@ X X void getdataln(fp) /* get next nonblank,noncomment data file line */ X FILE *fp; X-{ do { fgetln(fp); data_line++; } while (nullstr(ln)||ln[0]=='#'); } X+{ do { fgetln_(fp); data_line++; } while (nullstr(ln)||ln[0]=='#'); } X X X void baddata(reason) /* send data reading error message */ X@@ -135,7 +135,7 @@ X char tmpname[PATH_LENGTH+1]; X X make_filename(name,FORCE_EXTENSION,ext); X- strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,TEMP_EXT); X+ strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,WRS(TEMP_EXT)); X X fp=NULL; *exists=FALSE; X run { X@@ -162,7 +162,7 @@ X bool exists; X { X char tmpname[PATH_LENGTH+1], oldname[PATH_LENGTH+1]; X- strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,TEMP_EXT); X+ strcpy(tmpname,name); make_filename(tmpname,FORCE_EXTENSION,WRS(TEMP_EXT)); X strcpy(oldname,name); make_filename(oldname,FORCE_EXTENSION,oldext); X X if (exists) { rename_file(name,oldname); } X@@ -214,7 +214,7 @@ X raw.data.f2.cross_type); X print(" ok\n"); X X- make_filename(name,FORCE_EXTENSION,MAPS_EXT); strcpy(type,"map"); X+ make_filename(name,FORCE_EXTENSION,WRS(MAPS_EXT)); strcpy(type,"map"); X run { X fp2=NULL; X fp2=open_file(name,READ); X@@ -228,7 +228,7 @@ X close_file(fp2); X } except_when(CANTOPEN) { } /* need a better handler */ X X- make_filename(name,FORCE_EXTENSION,TWO_EXT); strcpy(type,"two-point"); X+ make_filename(name,FORCE_EXTENSION,WRS(TWO_EXT)); strcpy(type,"two-point"); X run { X fp2=NULL; X fp2=open_file(name,READ); X@@ -240,7 +240,7 @@ X close_file(fp2); X } except_when(CANTOPEN) { } /* need a better handler */ X X- make_filename(name,FORCE_EXTENSION,THREE_EXT); strcpy(type,"three-point"); X+ make_filename(name,FORCE_EXTENSION,WRS(THREE_EXT)); strcpy(type,"three-point"); X run { X fp2=NULL; X fp2=open_file(name,READ); X@@ -285,39 +285,39 @@ X run { X strcpy(name,base_name); X if (save_genos_too) { X- fp= start_save_to_file(name,DATA_EXT,"genotype",&exists); X+ fp= start_save_to_file(name,WRS(DATA_EXT),"genotype",&exists); X write_f2_data(fp); /* deals with header and magic number */ X close_file(fp); fp=NULL; X- finish_save_to_file(name,DATA_OLD,exists); X+ finish_save_to_file(name,WRS(DATA_OLD),exists); X } X- fp= start_save_to_file(name,MAPS_EXT,"map",&exists); X+ fp= start_save_to_file(name,WRS(MAPS_EXT),"map",&exists); X write_magic_number(fp,"map"); X write_order_data(fp); X write_mapping_data(fp); X write_status(fp); X close_file(fp); fp=NULL; X- finish_save_to_file(name,MAPS_OLD,exists); X+ finish_save_to_file(name,WRS(MAPS_OLD),exists); X X if (two_pt_touched) { X- fp= start_save_to_file(name,TWO_EXT,"two-point",&exists); X+ fp= start_save_to_file(name,WRS(TWO_EXT),"two-point",&exists); X write_magic_number(fp,"two-point"); X write_two_pt(fp); X close_file(fp); fp=NULL; X- finish_save_to_file(name,TWO_OLD,exists); X+ finish_save_to_file(name,WRS(TWO_OLD),exists); X } X if (three_pt_touched) { X- fp= start_save_to_file(name,THREE_EXT,"three-point",&exists); X+ fp= start_save_to_file(name,WRS(THREE_EXT),"three-point",&exists); X write_magic_number(fp,"three-point"); X write_three_pt(fp); X close_file(fp); fp=NULL; X- finish_save_to_file(name,THREE_OLD,exists); X+ finish_save_to_file(name,WRS(THREE_OLD),exists); X } X if (num_traits>0) { X- fp= start_save_to_file(name,TRAIT_EXT,"traits",&exists); X+ fp= start_save_to_file(name,WRS(TRAIT_EXT),"traits",&exists); X write_magic_number(fp,"trait"); X write_traits(fp); X close_file(fp); fp=NULL; X- finish_save_to_file(name,TRAIT_OLD,exists); X+ finish_save_to_file(name,WRS(TRAIT_OLD),exists); X free_traits(); X } X two_pt_touched= FALSE; X@@ -576,15 +576,15 @@ X char header[MAXLINE+1]; X X if (raw.data.f2.cross_type==F2_INTERCROSS) X- fprint(fp,"prepared data f2 intercross\n"); X+ fprint(fp,WRS("prepared data f2 intercross\n")); X else if (raw.data.f2.cross_type==F2_BACKCROSS) X- fprint(fp,"prepared data f2 backcross\n"); X+ fprint(fp,WRS("prepared data f2 backcross\n")); X else if (raw.data.f2.cross_type==RI_SIB) X- fprint(fp,"prepared data f2 ri-sib\n"); X+ fprint(fp,WRS("prepared data f2 ri-sib\n")); X else if (raw.data.f2.cross_type==RI_SELF) X- fprint(fp,"prepared data f2 ri-self\n"); X+ fprint(fp,WRS("prepared data f2 ri-self\n")); X else if (raw.data.f2.cross_type==F3_SELF) X- fprint(fp,"prepared data f3\n"); X+ fprint(fp,WRS("prepared data f3\n")); X X sf(header,"%d %d %d\n",raw.filenumber,raw.data.f2.num_indivs, X raw.num_markers); fprint(fp,header); X@@ -593,7 +593,7 @@ X sf(ps,"*%-10s ", raw.locus_name[i]); X fpr(fp); X for (j=0; j<raw.data.f2.num_indivs; j++) { X- if (j%50==0 && j!=0) fprint(fp,"\n "); X+ if (j%50==0 && j!=0) fprint(fp,WRS("\n ")); X sf(ps,"%c",raw.data.f2.allele[i][j]); X fpr(fp); X } X@@ -828,9 +828,7 @@ X char *symb; X { X /* CHANGED FOR THIS VERION - NOW READS "-AHBCD" */ X- X- if (chr==symb[0]) return(MISSING_DATA); X- else if (chr==symb[1]) return(PARENTAL_TYPE_A); X+if (chr==symb[0]) return(MISSING_DATA); else if (chr==symb[1]) return(PARENTAL_TYPE_A); X else if (chr==symb[2]) return(HYBRID_TYPE_H); X else if (chr==symb[3]) return(PARENTAL_TYPE_B); X else if (chr==symb[4]) return(TYPE_NOT_A); X@@ -856,26 +854,26 @@ X fnl(fp); X } X fnl(fp); X- fprint(fp,"#QTL only variables:\n"); X- fprint(fp,"*Print mapm loci: 1\n"); X- fprint(fp,"*Like tolerance: 0.001\n"); X- fprint(fp,"*Brute force: 1\n"); X- fprint(fp,"*Max intervals: -7\n"); X- fprint(fp,"*Max continuous vars: -3\n"); X- fprint(fp,"*Max wiggles: 0\n"); X- fprint(fp,"*Max compares: 0\n"); X- fprint(fp,"*Default units: 1\n"); X- fprint(fp,"*Chromosomes: 0\n"); X- fprint(fp,"*Number of contexts: 1\n"); X- fprint(fp,"*Active context: 0\n"); X+ fprint(fp,WRS("#QTL only variables:\n")); X+ fprint(fp,WRS("*Print mapm loci: 1\n")); X+ fprint(fp,WRS("*Like tolerance: 0.001\n")); X+ fprint(fp,WRS("*Brute force: 1\n")); X+ fprint(fp,WRS("*Max intervals: -7\n")); X+ fprint(fp,WRS("*Max continuous vars: -3\n")); X+ fprint(fp,WRS("*Max wiggles: 0\n")); X+ fprint(fp,WRS("*Max compares: 0\n")); X+ fprint(fp,WRS("*Default units: 1\n")); X+ fprint(fp,WRS("*Chromosomes: 0\n")); X+ fprint(fp,WRS("*Number of contexts: 1\n")); X+ fprint(fp,WRS("*Active context: 0\n")); X fnl(fp); X- fprint(fp,"*Context 1\n"); X+ fprint(fp,WRS("*Context 1\n")); X if(num_traits == 1) X- fprint(fp,"*Trait: 0\n"); X+ fprint(fp,WRS("*Trait: 0\n")); X else X- fprint(fp,"*Trait: -1\n"); X- fprint(fp,"*Named sequences: 0\n"); X- fprint(fp,"*Sequence history: 0\n"); X+ fprint(fp,WRS("*Trait: -1\n")); X+ fprint(fp,WRS("*Named sequences: 0\n")); X+ fprint(fp,WRS("*Sequence history: 0\n")); X } X X END-of-mapm3/files/patch-mapm-reader.c echo x - mapm3/files/patch-mapm-state.c sed 's/^X//' >mapm3/files/patch-mapm-state.c << 'END-of-mapm3/files/patch-mapm-state.c' X--- mapm/state.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/state.c 2008-04-03 19:37:40.000000000 +0000 X@@ -734,7 +734,7 @@ X { X int i, usenum; X X- fprint(fp,"*MapmakerStatusInfo:\n"); X+ fprint(fp,WRS("*MapmakerStatusInfo:\n")); X X sf(ps,"*PrintNames: %d\n",print_names); fpr(fp); X sf(ps,"*Tolerance: %lf\n",tolerance); fpr(fp); X@@ -852,5 +852,5 @@ X load_table(context[i]->sequence_history,fp,INDEX_BY_NUMBER,num); X } X X- if (the_seq_history_num>0) set_current_seq("none",FALSE); X+ if (the_seq_history_num>0) set_current_seq(WRS("none"),FALSE); X } END-of-mapm3/files/patch-mapm-state.c echo x - mapm3/files/patch-mapm-sys_cmds.c sed 's/^X//' >mapm3/files/patch-mapm-sys_cmds.c << 'END-of-mapm3/files/patch-mapm-sys_cmds.c' X--- mapm/sys_cmds.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/sys_cmds.c 2008-03-27 21:28:05.000000000 +0000 X@@ -98,7 +98,7 @@ X close_file(fp); X if (raw) { X strcpy(run_file,name); X- make_filename(run_file,FORCE_EXTENSION,PREP_EXT); X+ make_filename(run_file,FORCE_EXTENSION,WRS(PREP_EXT)); X if (!redirect_input(run_file,FALSE)) { X sf(ps,"unable to run file '%s'... skipping initialization\n", X run_file); pr(); X@@ -145,7 +145,7 @@ X if (!prev_data) print("no data are loaded\n"); X else { sf(ps,DATA_LOADED,raw.filename,data_info(TRUE)); pr(); } X } else { X- fp=try_to_open(name,FORCE_EXTENSION,DATA_EXT,prev_data); X+ fp=try_to_open(name,FORCE_EXTENSION,WRS(DATA_EXT),prev_data); X if (prev_data) try_to_unload(fp,TRUE,auto_save,TRUE,just_prepared); X try_to_load(fp,name,prev_data,FALSE); X just_prepared=FALSE; X@@ -169,7 +169,7 @@ X if (streq(&name[end-4],DATA_EXT) || streq(&name[end-4],DATA_OLD) ||... X error(RAW_EXTENSION); */ X X- fp= try_to_open(name,DEFAULT_EXTENSION,RAW_EXT,prev_data); X+ fp= try_to_open(name,DEFAULT_EXTENSION,WRS(RAW_EXT),prev_data); X if (prev_data) try_to_unload(fp,TRUE,auto_save,TRUE,just_prepared); X try_to_load(fp,name,prev_data,TRUE); X just_prepared=TRUE; X@@ -186,7 +186,7 @@ X get_one_arg(stoken,"",name); new_name= !nullstr(name); X /* want to change this so it sets raw.filename only AFTER it writes OK */ X X- if (new_name && !make_filename(name,FORCE_EXTENSION,DATA_EXT)) X+ if (new_name && !make_filename(name,FORCE_EXTENSION,WRS(DATA_EXT))) X { sf(ps,BAD_FILENAME,name); error(ps); } X X run { X@@ -621,7 +621,7 @@ X for (j=num_seq_tokens-1; j>i; j--) X strcpy(seq_tokens[j+1],seq_tokens[j]); X /* this is severly broken, if len(appendage) > TOKLEN */ X- strcpy(seq_tokens[i+i],appendage); X+ strcpy(seq_tokens[i+1],appendage); X num_seq_tokens++; X X untokenize_seq(new_seq,seq_tokens,num_seq_tokens); END-of-mapm3/files/patch-mapm-sys_cmds.c echo x - mapm3/files/patch-mapm-two_cmds.c sed 's/^X//' >mapm3/files/patch-mapm-two_cmds.c << 'END-of-mapm3/files/patch-mapm-two_cmds.c' X--- mapm/two_cmds.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ mapm/two_cmds.c 2008-04-03 19:58:42.000000000 +0000 X@@ -698,11 +698,11 @@ X X if (!print_names) { X print("\n log-likelihood differences\n"); X-print( " count markers a-b-c b-a-c a-c-b\n"); X+print(" count markers a-b-c b-a-c a-c-b\n"); X /* 12345: 1234 1234 1234 */ X } else { X print("\n log-likelihood differences\n"); X-print( " count markers a-b-c b-a-c a-c-b\n"); X+print(" count markers a-b-c b-a-c a-c-b\n"); X /* 12345: 123456789 123456789 123456789 */ X } X END-of-mapm3/files/patch-mapm-two_cmds.c echo x - mapm3/files/patch-quant-qcmds.c sed 's/^X//' >mapm3/files/patch-quant-qcmds.c << 'END-of-mapm3/files/patch-quant-qcmds.c' X--- quant/qcmds.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ quant/qcmds.c 2008-03-27 21:30:08.000000000 +0000 X@@ -1348,7 +1348,7 @@ X if (nullstr(args)) { X if (!data_loaded()) print(NO_LOADED_DATA); else { X strcpy(tfile,raw.file); X- make_filename(tfile,FORCE_EXTENSION,TRAIT_EXT); X+ make_filename(tfile,FORCE_EXTENSION,WRS(TRAIT_EXT)); X sf(ps,LOADED_DATA,raw.file,tfile,"",raw.n_indivs, X (raw.data_type==BACKCROSS ? "backcross":"intercross"), X raw.n_loci,raw.n_traits,maybe_s(raw.n_traits)); pr(); X@@ -1363,9 +1363,9 @@ X nstoken(&args,sREQUIRED,dfile,PATH_LENGTH); tfile[0]='\0'; X nomore_args(num_args); X run { X- if (!make_filename(dfile,FORCE_EXTENSION,DATA_EXT)) send(CANTOPEN); X+ if (!make_filename(dfile,FORCE_EXTENSION,WRS(DATA_EXT))) send(CANTOPEN); X fpa= open_file(dfile,READ); X- fgetln(fpa); X+ fgetln_(fpa); X X if (streq(ln,"prepared data f2 backcross")) { X strcpy(geno_chars,default_backcross_chars); X@@ -1384,11 +1384,11 @@ X } X X strcpy(tfile,dfile); X- if (!make_filename(tfile,FORCE_EXTENSION,TRAIT_EXT)) X+ if (!make_filename(tfile,FORCE_EXTENSION,WRS(TRAIT_EXT))) X send(CANTOPEN); X fpb = open_file(tfile,READ); X strcpy(mfile,dfile); X- if (!make_filename(mfile,FORCE_EXTENSION,MAPS_EXT)) X+ if (!make_filename(mfile,FORCE_EXTENSION,WRS(MAPS_EXT))) X send(CANTOPEN); X fpc = open_file(mfile,READ); X X@@ -1449,7 +1449,7 @@ X X out_name = get_temp_string(); X strcpy(out_name,in_name); X- make_filename(out_name,FORCE_EXTENSION,DATA_EXT); X+ make_filename(out_name,FORCE_EXTENSION,WRS(DATA_EXT)); X X fp = open_file(in_name,READ); X getdataln(fp); crunch(ln); X@@ -1488,7 +1488,7 @@ X name = mkstrcpy(raw.file); X name3 = mkstrcpy(raw.file); X name2 = "dummy.qtls"; X- make_filename(name, FORCE_EXTENSION, QTL_EXT); X+ make_filename(name, FORCE_EXTENSION, WRS(QTL_EXT)); X X /* The following accounts for the case where there is no file 'name' X (i.e. it makes one) */ X@@ -1500,7 +1500,7 @@ X close_file(fp); X } X X- make_filename(name3, FORCE_EXTENSION, QTL_OLD); X+ make_filename(name3, FORCE_EXTENSION, WRS(QTL_OLD)); X run { X fp = open_file(name2, WRITE); X sf(ps,"Now saving %s...\n",name); pr(); X@@ -1520,8 +1520,8 @@ X } X X name2="dummy.traits"; X- make_filename(name, FORCE_EXTENSION, TRAIT_EXT); X- make_filename(name3, FORCE_EXTENSION, TRAIT_OLD); X+ make_filename(name, FORCE_EXTENSION, WRS(TRAIT_EXT)); X+ make_filename(name3, FORCE_EXTENSION, WRS(TRAIT_OLD)); X run { X fp = open_file(name2, WRITE); X sf(ps,"Now saving %s...\n",name); pr(); X@@ -1560,7 +1560,7 @@ X save_wiggle(fp,i); X } X X- fprint(fp,"#Compares\n"); X+ fprint(fp,WRS("#Compares\n")); X X fprintf(fp,"%d %d\n",num_compares,first_compare); X for(i = 0; i < num_compares; i++) { X@@ -1587,7 +1587,7 @@ X X run { X strcpy(name,raw.file); X- make_filename(name,FORCE_EXTENSION,QTL_EXT); X+ make_filename(name,FORCE_EXTENSION,WRS(QTL_EXT)); X fp= open_file(name,READ); X X if(fscanf(fp,"%d\n",&filenum) != 1) send(IOERROR); /* KLUDGE */ END-of-mapm3/files/patch-quant-qcmds.c echo x - mapm3/files/patch-quant-qraw.c sed 's/^X//' >mapm3/files/patch-quant-qraw.c << 'END-of-mapm3/files/patch-quant-qraw.c' X--- quant/qraw.c.orig 2008-04-04 20:05:29.000000000 +0000 X+++ quant/qraw.c 2008-03-27 21:30:39.000000000 +0000 X@@ -124,7 +124,7 @@ X X void getdataln(fp) /* get next nonblank/noncomment data file line */ X FILE *fp; X-{ do { fgetln(fp); BADDATA_line_num++; } while(nullstr(ln) || ln[0]=='#'); X+{ do { fgetln_(fp); BADDATA_line_num++; } while(nullstr(ln) || ln[0]=='#'); X BADDATA_ln= ln; } X real read_map_distance(); X void read_map_locus(); X@@ -426,13 +426,13 @@ X X for(j=0;j<raw.n_indivs;j++) { X if(j % 5 == 0 && j != 0) X- fprint(fp,"\n "); X+ fprint(fp,WRS("\n ")); X sf(ps,"%12.3lf ", raw.trait[j][i]);fpr(fp); X } X fnl(fp); X } X X- fprint(fp,"#QTL only variables:\n"); X+ fprint(fp,WRS("#QTL only variables:\n")); X sf(ps,"*Print mapm loci: %d\n", print_mapm_loci);fpr(fp); X sf(ps,"*Like tolerance: %lf\n",like_tolerance);fpr(fp); X sf(ps,"*Brute force: %d\n",brute_force);fpr(fp); X@@ -452,21 +452,21 @@ X sf(ps, "chr%d %d\n", i+1, raw.chrom_n_loci[i]); fpr(fp); X for(j=0;j<raw.chrom_n_loci[i];j++) { X if(j % 18 == 0 && j != 0) X- fprint(fp,"\n"); X+ fprint(fp,WRS("\n")); X sf(ps, "%d ",order[loci_tot]);fpr(fp); X loci_tot++; X } X fnl(fp); X for(j=0;j<raw.chrom_n_loci[i]-1;j++) { X if(j % 12 == 0 && j != 0) X- fprint(fp,"\n"); X+ fprint(fp,WRS("\n")); X sf(ps, "%.4lf ",map_space[map_tot]);fpr(fp); X map_tot++; X } X fnl(fp); X map_tot++; X- fprint(fp,"0\n"); X- fprint(fp,"0\n"); X+ fprint(fp,WRS("0\n")); X+ fprint(fp,WRS("0\n")); X } X sf(ps,"*Number of contexts: %d\n",num_contexts); X fpr(fp); END-of-mapm3/files/patch-quant-qraw.c echo x - mapm3/files/patch-sun-xqtl sed 's/^X//' >mapm3/files/patch-sun-xqtl << 'END-of-mapm3/files/patch-sun-xqtl' X--- sun/xqtl.orig 2008-04-04 20:05:29.000000000 +0000 X+++ sun/xqtl 2008-04-04 19:59:41.000000000 +0000 X@@ -10,5 +10,5 @@ X else if (-e /usr/openwin/demo/xterm) then X exec /usr/openwin/demo/xterm $xoptions $fontsize -e $program $* X else X- exec xterm $options $fontsize -e $program X+ exec xterm $xoptions $fontsize -e $program X endif END-of-mapm3/files/patch-sun-xqtl echo x - mapm3/files/patch-sun-xmapmaker sed 's/^X//' >mapm3/files/patch-sun-xmapmaker << 'END-of-mapm3/files/patch-sun-xmapmaker' X--- sun/xmapmaker.orig 2008-04-04 20:05:29.000000000 +0000 X+++ sun/xmapmaker 2008-04-04 19:59:32.000000000 +0000 X@@ -10,5 +10,5 @@ X else if (-e /usr/openwin/demo/xterm) then X exec /usr/openwin/demo/xterm $xoptions $fontsize -e $program $* X else X- exec xterm $options $fontsize -e $program X+ exec xterm $xoptions $fontsize -e $program X endif END-of-mapm3/files/patch-sun-xmapmaker echo x - mapm3/pkg-plist sed 's/^X//' >mapm3/pkg-plist << 'END-of-mapm3/pkg-plist' Xbin/mapmaker Xbin/mapmaker.help Xbin/qtl Xbin/qtl.help Xbin/xmapmaker Xbin/xqtl END-of-mapm3/pkg-plist echo x - mapm3/distinfo sed 's/^X//' >mapm3/distinfo << 'END-of-mapm3/distinfo' XMD5 (mapm3-source.tar.Z) = 8aa7a061d32a49c8704c1a5c4b31aa2d XSHA256 (mapm3-source.tar.Z) = 107c8d0e7e89e2fe43fe17233d38c22161def851c8094435f3440a39c0cdca4c XSIZE (mapm3-source.tar.Z) = 1321227 END-of-mapm3/distinfo exit >Release-Note: >Audit-Trail: >Unformatted:
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