Author: smoe-guest Date: 2008-08-24 00:36:07 +0000 (Sun, 24 Aug 2008) New Revision: 2423
Added: trunk/packages/boxshade/trunk/debian/patches/kickOutGets.patch Modified: trunk/packages/boxshade/trunk/debian/README.Debian trunk/packages/boxshade/trunk/debian/changelog trunk/packages/boxshade/trunk/debian/patches/10_makefile.unx.patch trunk/packages/boxshade/trunk/debian/patches/series trunk/packages/boxshade/trunk/debian/rules Log: * give error message if running non-interactively for wrong filesname * removed gets Modified: trunk/packages/boxshade/trunk/debian/README.Debian =================================================================== --- trunk/packages/boxshade/trunk/debian/README.Debian 2008-08-23 05:28:01 UTC (rev 2422) +++ trunk/packages/boxshade/trunk/debian/README.Debian 2008-08-24 00:36:07 UTC (rev 2423) @@ -1,6 +1,9 @@ boxshade for Debian ------------------- +This program is not perfect. If it runs smoothly, though, then it produces +nice results. + The web interface for boxshade is available for download on ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/www/box_www.tar.Z Modified: trunk/packages/boxshade/trunk/debian/changelog =================================================================== --- trunk/packages/boxshade/trunk/debian/changelog 2008-08-23 05:28:01 UTC (rev 2422) +++ trunk/packages/boxshade/trunk/debian/changelog 2008-08-24 00:36:07 UTC (rev 2423) @@ -1,9 +1,17 @@ -boxshade (3.3.1-4) UNRELEASED; urgency=low +boxshade (3.3.1-4) unstable; urgency=low + [ Charles Plessy ] + * Updated my email address. - -- Charles Plessy <[EMAIL PROTECTED]> Sun, 27 Apr 2008 16:56:02 +0900 + [ Steffen Moeller ] + * Eliminated use of gets from source + * boxshade bails out with an error if there is an error and does not + expect sudden user input ... it is scriptable now. + + -- Steffen Moeller <[EMAIL PROTECTED]> Sun, 27 Apr 2008 16:56:02 +0900 + boxshade (3.3.1-3) unstable; urgency=low [ David Paleino ] Modified: trunk/packages/boxshade/trunk/debian/patches/10_makefile.unx.patch =================================================================== --- trunk/packages/boxshade/trunk/debian/patches/10_makefile.unx.patch 2008-08-23 05:28:01 UTC (rev 2422) +++ trunk/packages/boxshade/trunk/debian/patches/10_makefile.unx.patch 2008-08-24 00:36:07 UTC (rev 2423) @@ -1,7 +1,5 @@ -Index: trunk/makefile.unx -=================================================================== ---- trunk.orig/makefile.unx -+++ trunk/makefile.unx +--- boxshade-3.3.1.orig/makefile.unx ++++ boxshade-3.3.1/makefile.unx @@ -1,7 +1,7 @@ # BOXSHADE makefile for unix (tested under Linux && Solaris) CC = gcc @@ -11,12 +9,3 @@ LIBS = -lm OBJ =.o EXE = -@@ -40,3 +40,8 @@ - dv_ps$(OBJ): dv_ps.c bx_types.h bx_read.h dv_all.h version.h - dv_regis$(OBJ): dv_regis.c bx_types.h bx_read.h dv_all.h - dv_rtf$(OBJ): dv_rtf.c bx_types.h bx_read.h dv_all.h -+ -+.PHONY: clean -+ -+clean: -+ rm -f $(OBJS) boxshade$(EXE) Added: trunk/packages/boxshade/trunk/debian/patches/kickOutGets.patch =================================================================== --- trunk/packages/boxshade/trunk/debian/patches/kickOutGets.patch (rev 0) +++ trunk/packages/boxshade/trunk/debian/patches/kickOutGets.patch 2008-08-24 00:36:07 UTC (rev 2423) @@ -0,0 +1,256 @@ +--- boxshade-3.3.1.orig/box.c ++++ boxshade-3.3.1/box.c +@@ -136,6 +136,7 @@ + + ----------------------------------------------------------------------- */ + ++#include<errno.h> + + #define BX_TYPES_G + #include "bx_types.h" +@@ -193,7 +194,7 @@ + if (cl != NULL) { + printf("actual command line: %s\n", cl); + printf("add to command line: "); +- Gets(ncl); ++ Gets(ncl,sizeof(ncl)-1); + } else + *ncl = '\0'; + return ncl; +@@ -389,7 +390,7 @@ + if (explain == NULL) return FALSE; + for (;;) { + printf("%s %s does not exist, enter filename: ", explain, neu); +- Gets(fn); ++ Gets(fn,sizeof(fn)-1); + if (fexist(fn)) return TRUE; + strcpy(neu, fn); + printf("\007file does not exist \n"); +@@ -413,7 +414,7 @@ + do { + printf("Default-parameter file %s does not exist, enter filename: ", + parname); +- Gets(parname); ++ Gets(parname,sizeof(parname)-1); + ok = fexist(parname); + if (!ok) + printf("\007file does not exist \n"); +@@ -523,13 +524,15 @@ + do { + if (!clinflag) { + printf("name of aligned input-file : "); +- Gets(inname); ++ Gets(inname,sizeof(inname)-1); + printf("\n"); + } + ok = fexist(inname); + if (!ok) { +- printf("\007aligned input file does not exist \n"); +- clinflag = FALSE; ++ fprintf(stderr,"\007aligned input file '%s' could not be read: %s, maxsize of name is %d.\n",inname,strerror(errno),sizeof(inname)); ++ if (clinflag) { ++ exit(-1); ++ } + } + } while (!ok); + /**** ask for infile type ****/ +@@ -778,7 +781,7 @@ + ok = FALSE; + do { + printf("Similarity-file %s does not exist, enter filename: ", simname); +- Gets(simname); ++ Gets(simname,sizeof(simname)-1); + ok = fexist(simname); + if (!ok) + printf("\007file does not exist \n"); +@@ -792,7 +795,7 @@ + ok = FALSE; + do { + printf("Group-file %s does not exist, enter filename: ", grpname); +- Gets(grpname); ++ Gets(grpname,sizeof(grpname)-1); + ok = fexist(grpname); + if (!ok) + printf("\007file does not exist \n"); +@@ -851,7 +854,7 @@ + /**** ask for matrix file ****/ + *instring = '\0'; + printf("name of matrix output-file : "); +- Gets(identname); ++ Gets(identname,sizeof(identname)-1); + printf("\n"); + } + +--- boxshade-3.3.1.orig/bx_read.c ++++ boxshade-3.3.1/bx_read.c +@@ -2,9 +2,9 @@ + + FILE *infile = NULL; + +-char *Gets(char *s) { ++char *Gets(char *s, size_t length) { + fflush(stdout); +- return gets(s); ++ return fgets(s,length,stdin); + } + + /* +@@ -23,7 +23,7 @@ + BOOL cr, eoln = FALSE; + + if (f == stdin) +- return Gets(l); ++ return Gets(l,sze-1); + + if (feof(f)) return NULL; + +--- boxshade-3.3.1.orig/bx_read.h ++++ boxshade-3.3.1/bx_read.h +@@ -4,7 +4,7 @@ + + #include "bx_types.h" + +-extern char *Gets(char *s); ++extern char *Gets(char *s, size_t length); + extern char *Fgets(char *l, size_t sze, FILE *f); + + extern void read_file_clustal(void); +--- boxshade-3.3.1.orig/dv_ansi.c ++++ boxshade-3.3.1/dv_ansi.c +@@ -79,7 +79,7 @@ + lc[4] = FALSE; + if (!cloutflag) { + printf("filename for %s-output (return for terminal) : ", term); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/dv_ascii.c ++++ boxshade-3.3.1/dv_ascii.c +@@ -71,7 +71,7 @@ + lc[4] = FALSE; + if (!cloutflag) { + printf("filename for ASCII-output (return for terminal) : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/dv_fig.c ++++ boxshade-3.3.1/dv_fig.c +@@ -154,7 +154,7 @@ + } + if (!cloutflag) { + printf("name of fig-file : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/dv_hpgl.c ++++ boxshade-3.3.1/dv_hpgl.c +@@ -268,7 +268,7 @@ + } + if (!cloutflag) { + printf("filename for HPGL-output : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/dv_html.c ++++ boxshade-3.3.1/dv_html.c +@@ -158,7 +158,7 @@ + if (!cloutflag) + do { + printf("filename for HTML-output : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } while (*outname == '\0'); + } + +--- boxshade-3.3.1.orig/dv_lj250.c ++++ boxshade-3.3.1/dv_lj250.c +@@ -81,7 +81,7 @@ + lc[4] = FALSE; + if (!cloutflag) { + printf("name of print-file : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/dv_pict.c ++++ boxshade-3.3.1/dv_pict.c +@@ -201,7 +201,7 @@ + } + if (!cloutflag) { + printf("filename for PICT file output : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/dv_ps.c ++++ boxshade-3.3.1/dv_ps.c +@@ -199,7 +199,7 @@ + if (!cloutflag) + do { + printf("filename for POSTSCRIPT-output : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } while (*outname == '\0'); + } + +--- boxshade-3.3.1.orig/dv_regis.c ++++ boxshade-3.3.1/dv_regis.c +@@ -126,7 +126,7 @@ + lc[4] = FALSE; + if (!cloutflag) { + printf("filename for REGIS-output : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/dv_rtf.c ++++ boxshade-3.3.1/dv_rtf.c +@@ -127,7 +127,7 @@ + } + if (!cloutflag) { + printf("filename for RTF-output : "); +- gets(outname); ++ Gets(outname,sizeof(outname)-1); + } + } + +--- boxshade-3.3.1.orig/bx_misc.c ++++ boxshade-3.3.1/bx_misc.c +@@ -60,14 +60,22 @@ + + BOOL fexist(char *fname) + { +- BOOL Result; + FILE *f; + ++ if (NULL == fname) { ++ fprintf(stderr,"fexist: serious programming error, the filename is NULL.\n"); ++ exit(-1); ++ } ++ + f = fopen(fname, TXT_RD); +- Result = (f != NULL); +- if (f != NULL) ++ if (f) { + fclose(f); +- return Result; ++ return TRUE; ++ } ++ else { ++ // leaving it to calling function to interpret errno. ++ return FALSE; ++ } + } + + int indx(char *mainstring, char *substring) Modified: trunk/packages/boxshade/trunk/debian/patches/series =================================================================== --- trunk/packages/boxshade/trunk/debian/patches/series 2008-08-23 05:28:01 UTC (rev 2422) +++ trunk/packages/boxshade/trunk/debian/patches/series 2008-08-24 00:36:07 UTC (rev 2423) @@ -1 +1,2 @@ 10_makefile.unx.patch +kickOutGets.patch Modified: trunk/packages/boxshade/trunk/debian/rules =================================================================== --- trunk/packages/boxshade/trunk/debian/rules 2008-08-23 05:28:01 UTC (rev 2422) +++ trunk/packages/boxshade/trunk/debian/rules 2008-08-24 00:36:07 UTC (rev 2423) @@ -31,7 +31,7 @@ dh_testdir dh_testroot rm -f build-stamp - $(MAKE) -f makefile.unx clean + rm -f boxshade *.o dh_clean boxshade.1 install: build _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
