Date: Tue, 26 Sep 2000 15:09:37 -0700 (PDT) From: KATO@FreeBSD.ORG, Tsuguru@FreeBSD.ORG To: freebsd-gnats-submit@FreeBSD.org Subject: ports/21572: Update port: biology/clustalw Message-ID: <20000926220937.1F2C237B423@hub.freebsd.org>
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>Number: 21572 >Category: ports >Synopsis: Update port: biology/clustalw >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Sep 26 15:10:02 PDT 2000 >Closed-Date: >Last-Modified: >Originator: tkato@prontomail.ne.jp >Release: 4.1-RELEASE i386 >Organization: >Environment: >Description: - Support CC/CFLAGS/PREFIX properly - gets() -> fgets() - Add WWW: line into pkg/DESCR New file: patches/patch-ab patches/patch-ac patches/patch-ad Approved by maintainer. >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/clustalw/Makefile biology/clustalw/Makefile --- /usr/ports/biology/clustalw/Makefile Mon Jul 10 12:17:36 2000 +++ biology/clustalw/Makefile Tue Aug 8 02:29:02 2000 @@ -9,18 +9,18 @@ PORTVERSION= 1.81 CATEGORIES= biology MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ -DISTNAME= clustalw1.81.UNIX +DISTNAME= ${PORTNAME}${PORTVERSION}.UNIX MAINTAINER= dbader@eece.unm.edu WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} -do-build: - cd ${WRKSRC} ; ${MAKE} -f makefile +MAKEFILE= makefile +ALL_TARGET= # empty do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin - ${MKDIR} ${PREFIX}/share/${PORTNAME} - ${INSTALL_DATA} ${WRKSRC}/clustalw_help ${PREFIX}/share/${PORTNAME} + ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin + @${MKDIR} ${PREFIX}/share/${PORTNAME} + ${INSTALL_DATA} ${WRKSRC}/clustalw_help ${PREFIX}/share/${PORTNAME} .include <bsd.port.mk> diff -urN /usr/ports/biology/clustalw/patches/patch-aa biology/clustalw/patches/patch-aa --- /usr/ports/biology/clustalw/patches/patch-aa Mon Jul 10 12:17:40 2000 +++ biology/clustalw/patches/patch-aa Tue Aug 8 02:28:48 2000 @@ -5,7 +5,7 @@ char *help_file_name = "clustalw.hlp"; #else - char *help_file_name = "clustalw_help"; -+ char *help_file_name = "/usr/local/share/clustalw/clustalw_help"; ++ char *help_file_name = DATADIR "/clustalw_help"; #endif sint max_names; /* maximum length of names in current alignment file */ diff -urN /usr/ports/biology/clustalw/patches/patch-ab biology/clustalw/patches/patch-ab --- /usr/ports/biology/clustalw/patches/patch-ab Thu Jan 1 09:00:00 1970 +++ biology/clustalw/patches/patch-ab Tue Aug 8 02:31:02 2000 @@ -0,0 +1,15 @@ +--- makefile.orig Wed Jun 7 16:55:06 2000 ++++ makefile Tue Aug 8 02:30:53 2000 +@@ -10,9 +10,9 @@ + + HEADERS = general.h clustalw.h + +-CC = cc +-CFLAGS = -c -O +-LFLAGS = -O -lm ++CC ?= cc ++CFLAGS += -c -DDATADIR=\"${PREFIX}/share/clustalw\" ++LFLAGS = -lm + + clustalw : $(OBJECTS) amenu.o clustalw.o + $(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS) diff -urN /usr/ports/biology/clustalw/patches/patch-ac biology/clustalw/patches/patch-ac --- /usr/ports/biology/clustalw/patches/patch-ac Thu Jan 1 09:00:00 1970 +++ biology/clustalw/patches/patch-ac Tue Aug 8 03:11:41 2000 @@ -0,0 +1,74 @@ +--- interface.c.orig Wed Jun 7 16:50:07 2000 ++++ interface.c Tue Aug 8 03:11:33 2000 +@@ -1078,7 +1078,7 @@ + /* added for File System Standards - Francois */ + path1=(char *)ckalloc((strlen(path)+64)*sizeof(char)); + strcpy(path1,path); +- strcat(path1,"/usr/share/clustalx:/usr/local/share/clustalx"); ++ strcat(path1,DATADIR); + + lf=(sint)strlen(fname); + deb=path1; +@@ -2121,7 +2121,7 @@ + strcpy(local_prompt,"\n\nEnter new name to avoid overwriting "); + strcat(local_prompt," [%s]: "); + fprintf(stdout,local_prompt,file_name); +- gets(temp); ++ fgets(temp,sizeof(temp),stdin); + if(*temp != EOS) strcpy(file_name,temp); + } + } +@@ -2129,7 +2129,7 @@ + strcpy(local_prompt,prompt); + strcat(local_prompt," [%s]: "); + fprintf(stdout,local_prompt,file_name); +- gets(temp); ++ fgets(temp,sizeof(temp),stdin); + if(*temp != EOS) strcpy(file_name,temp); + } + +@@ -2335,7 +2335,7 @@ + if (usemenu) + fprintf(stdout,"\nUse the existing GUIDE TREE file, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,sizeof(temp),stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(phylip_name,tree_name); + use_tree = TRUE; +@@ -2567,7 +2567,7 @@ + + fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ", + phylip_name); +- gets(temp); ++ fgets(temp,sizeof(temp),stdin); + if(*temp != EOS) + strcpy(phylip_name,temp); + } +@@ -2676,7 +2676,7 @@ + #endif + fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,sizeof(temp),stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(p1_tree_name,tree_name); + use_tree1 = TRUE; +@@ -2702,7 +2702,7 @@ + #endif + fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,sizeof(temp),stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(p2_tree_name,tree_name); + use_tree2 = TRUE; +@@ -3730,7 +3730,7 @@ + if(usemenu) { + fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ", + parname); +- gets(temp); ++ fgets(temp,sizeof(temp),stdin); + if(*temp != EOS) + strcpy(parname,temp); + } diff -urN /usr/ports/biology/clustalw/patches/patch-ad biology/clustalw/patches/patch-ad --- /usr/ports/biology/clustalw/patches/patch-ad Thu Jan 1 09:00:00 1970 +++ biology/clustalw/patches/patch-ad Tue Aug 8 02:59:50 2000 @@ -0,0 +1,29 @@ +--- util.c.orig Wed Jun 7 16:50:08 2000 ++++ util.c Tue Aug 8 02:59:43 2000 +@@ -174,7 +174,7 @@ + void getstr(char *instr,char *outstr) + { + fprintf(stdout,"%s: ",instr); +- gets(outstr); ++ fgets(outstr,sizeof(outstr),stdin); + } + + double getreal(char *instr,double minx,double maxx,double def) +@@ -185,7 +185,7 @@ + + while(TRUE) { + fprintf(stdout,"%s (%.1f-%.1f) [%.1f]: ",instr,minx,maxx,def); +- gets(line); ++ fgets(line,sizeof(line),stdin); + status=sscanf(line,"%f",&ret); + if(status == EOF) return def; + if(ret>maxx) { +@@ -210,7 +210,7 @@ + while(TRUE) { + fprintf(stdout,"%s (%d..%d) [%d]: ", + instr,(pint)minx,(pint)maxx,(pint)def); +- gets(line); ++ fgets(line,sizeof(line),stdin); + status=sscanf(line,"%d",&ret); + if(status == EOF) return def; + if(ret>maxx) { diff -urN /usr/ports/biology/clustalw/pkg/DESCR biology/clustalw/pkg/DESCR --- /usr/ports/biology/clustalw/pkg/DESCR Mon Jul 10 12:17:40 2000 +++ biology/clustalw/pkg/DESCR Tue Aug 8 02:25:53 2000 @@ -21,4 +21,4 @@ CLUSTAL for multiple sequence alignments. Methods in Enzymology 266: 383-402. - See URL: www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html +WWW: http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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