From owner-freebsd-ports@FreeBSD.ORG Sun Aug 24 09:27:01 2003 Return-Path: Delivered-To: freebsd-ports@freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 40DDD16A4BF for ; Sun, 24 Aug 2003 09:27:01 -0700 (PDT) Received: from cyber.cs.ntou.edu.tw (cyber.cs.ntou.edu.tw [140.121.196.97]) by mx1.FreeBSD.org (Postfix) with ESMTP id 3013343F75 for ; Sun, 24 Aug 2003 09:27:00 -0700 (PDT) (envelope-from tcs@kitty.2y.net) Received: from kitty.2y.net (root@cyber.cs.ntou.edu.tw [140.121.196.97]) by cyber.cs.ntou.edu.tw (8.12.1/8.12.1) with ESMTP id h7OGPVdB032438; Mon, 25 Aug 2003 00:25:35 +0800 (CST) Received: from 140.121.196.36 (140.121.196.36) by ASSP-nospam ; 24 Aug 03 16:25:31 -0000 Received: from PENGUIN (penguin.cs.nthu.edu.tw [140.114.88.175]) (authenticated bits=0) by kitty.2y.net (8.12.9/8.12.8) with ESMTP id h7OGPRUj078776; Mon, 25 Aug 2003 00:25:29 +0800 (CST) (envelope-from tcs@kitty.2y.net) Message-ID: <000001c36a5c$f88cd320$af58728c@PENGUIN> From: "=?big5?B?Q2h1bi1UaWVuIENoYW5nIFwosWmnZ6TRXCk=?=" To: Date: Mon, 25 Aug 2003 00:28:15 +0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0003_01C36A9F.C615D610" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Assp-Spam-Prob: 0.50000 X-Mailman-Approved-At: Sun, 24 Aug 2003 09:41:49 -0700 X-Content-Filtered-By: Mailman/MimeDel 2.1.1 cc: ports@FreeBSD.org Subject: FreeBSD Port: clustalw-1.83 X-BeenThere: freebsd-ports@freebsd.org X-Mailman-Version: 2.1.1 Precedence: list List-Id: Porting software to FreeBSD List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 24 Aug 2003 16:27:01 -0000 This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C36A9F.C615D610 Content-Type: text/plain; charset="big5" Content-Transfer-Encoding: quoted-printable Hi. The fgets keep the "\n" at end of line. Maybe we need to remove it. The attachment is my patch-ac It will make user to input a correct output filename. thx. ------=_NextPart_000_0003_01C36A9F.C615D610 Content-Type: application/octet-stream; name="clustalw.patch-ac.my" Content-Transfer-Encoding: quoted-printable Content-Disposition: attachment; filename="clustalw.patch-ac.my" --- interface.c.orig Thu Feb 13 15:17:33 2003=0A= +++ interface.c Thu Feb 13 15:26:28 2003=0A= @@ -1132,7 +1132,7 @@=0A= /* added for File System Standards - Francois */=0A= path1=3D(char *)ckalloc((strlen(path)+64)*sizeof(char));=0A= strcpy(path1,path);=0A= - strcat(path1,"/usr/share/clustalx:/usr/local/share/clustalx"); =0A= + strcat(path1,DATADIR); =0A= =0A= lf=3D(sint)strlen(fname);=0A= deb=3Dpath1;=0A= @@ -1224,7 +1224,7 @@=0A= if(strstr(temp, help_marker)){=0A= if(usemenu) {=0A= fprintf(stdout,"\n");=0A= - getstr("Press [RETURN] to continue",lin2);=0A= + getstr("Press [RETURN] to continue",lin2,MAXLINE);=0A= }=0A= fclose(help_file);=0A= return;=0A= @@ -1236,7 +1236,7 @@=0A= if(usemenu) {=0A= if(nlines >=3D PAGE_LEN) {=0A= fprintf(stdout,"\n");=0A= - getstr("Press [RETURN] to continue or X to stop",lin2);=0A= + getstr("Press [RETURN] to continue or X to = stop",lin2,MAXLINE);=0A= if(toupper(*lin2) =3D=3D 'X') {=0A= fclose(help_file);=0A= return;=0A= @@ -1248,7 +1248,7 @@=0A= }=0A= if(usemenu) {=0A= fprintf(stdout,"\n");=0A= - getstr("Press [RETURN] to continue",lin2);=0A= + getstr("Press [RETURN] to continue",lin2,MAXLINE);=0A= }=0A= fclose(help_file);=0A= }=0A= @@ -1287,7 +1287,7 @@=0A= ++nlines;=0A= if(nlines >=3D PAGE_LEN) {=0A= fprintf(stdout,"\n");=0A= - getstr("Press [RETURN] to continue or X to = stop",lin2);=0A= + getstr("Press [RETURN] to continue or X to = stop",lin2,MAXLINE);=0A= if(toupper(*lin2) =3D=3D 'X') {=0A= fclose(file);=0A= return;=0A= @@ -1298,7 +1298,7 @@=0A= }=0A= fclose(file);=0A= fprintf(stdout,"\n");=0A= - getstr("Press [RETURN] to continue",lin2);=0A= + getstr("Press [RETURN] to continue",lin2,MAXLINE);=0A= }=0A= =0A= =0A= @@ -1747,7 +1747,7 @@=0A= FILE *infile;=0A= =0A= if(usemenu)=0A= - getstr("Enter name of the matrix file",lin2);=0A= + getstr("Enter name of the matrix file",lin2,MAXLINE);=0A= else=0A= strcpy(lin2,str);=0A= =0A= @@ -1773,7 +1773,7 @@=0A= FILE *infile;=0A= =0A= if(usemenu)=0A= - getstr("Enter name of the matrix file",lin2);=0A= + getstr("Enter name of the matrix file",lin2,MAXLINE);=0A= else=0A= strcpy(lin2,str);=0A= =0A= @@ -2176,7 +2176,7 @@=0A= strcpy(local_prompt,"\n\nEnter new name to avoid overwriting ");=0A= strcat(local_prompt," [%s]: "); =0A= fprintf(stdout,local_prompt,file_name);=0A= - gets(temp);=0A= + fgets(temp,FILENAMELEN+1,stdin); if(*temp !=3D EOS) = temp[strlen(temp)-1]=3DEOS;=0A= if(*temp !=3D EOS) strcpy(file_name,temp);=0A= }=0A= }=0A= @@ -2184,7 +2184,7 @@=0A= strcpy(local_prompt,prompt);=0A= strcat(local_prompt," [%s]: "); =0A= fprintf(stdout,local_prompt,file_name);=0A= - gets(temp);=0A= + fgets(temp,FILENAMELEN+1,stdin); if(*temp !=3D EOS) = temp[strlen(temp)-1]=3DEOS;=0A= if(*temp !=3D EOS) strcpy(file_name,temp);=0A= }=0A= =0A= @@ -2385,7 +2385,7 @@=0A= if (usemenu)=0A= fprintf(stdout,"\nUse the existing GUIDE TREE file, %s = (y/n) ? [y]: ",=0A= tree_name);=0A= - gets(temp);=0A= + fgets(temp,MAXLINE,stdin); if(*temp !=3D EOS) = temp[strlen(temp)-1]=3DEOS;=0A= if(*temp !=3D 'n' && *temp !=3D 'N') {=0A= strcpy(phylip_name,tree_name);=0A= use_tree =3D TRUE;=0A= @@ -2617,7 +2617,7 @@=0A= =0A= fprintf(stdout,"\nEnter a name for the guide tree file = [%s]: ",=0A= phylip_name);=0A= - gets(temp);=0A= + fgets(temp,MAXLINE,stdin); if(*temp !=3D EOS) = temp[strlen(temp)-1]=3DEOS;=0A= if(*temp !=3D EOS)=0A= strcpy(phylip_name,temp);=0A= }=0A= @@ -2719,7 +2719,7 @@=0A= #endif=0A= fprintf(stdout,"\nUse the existing GUIDE TREE file for = Profile 1, %s (y/n) ? [y]: ",=0A= tree_name);=0A= - gets(temp);=0A= + fgets(temp,MAXLINE,stdin); if(*temp !=3D EOS) = temp[strlen(temp)-1]=3DEOS;=0A= if(*temp !=3D 'n' && *temp !=3D 'N') {=0A= strcpy(p1_tree_name,tree_name);=0A= use_tree1 =3D TRUE;=0A= @@ -2745,7 +2745,7 @@=0A= #endif=0A= fprintf(stdout,"\nUse the existing GUIDE TREE file for = Profile 2, %s (y/n) ? [y]: ",=0A= tree_name);=0A= - gets(temp);=0A= + fgets(temp,MAXLINE,stdin); if(*temp !=3D EOS) = temp[strlen(temp)-1]=3DEOS;=0A= if(*temp !=3D 'n' && *temp !=3D 'N') {=0A= strcpy(p2_tree_name,tree_name);=0A= use_tree2 =3D TRUE;=0A= @@ -4203,7 +4203,7 @@=0A= if(usemenu) {=0A= fprintf(stdout,"\nEnter a name for the parameter output file [%s]: = ",=0A= parname);=0A= - gets(temp);=0A= + fgets(temp,FILENAMELEN+1,stdin); if(*temp !=3D EOS) = temp[strlen(temp)-1]=3DEOS;=0A= if(*temp !=3D EOS)=0A= strcpy(parname,temp);=0A= }=0A= ------=_NextPart_000_0003_01C36A9F.C615D610--