[med-svn] [Git][med-team/theseus][master] 6 commits: Removing the linefix function, which tries to return a resource after releasing it

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / theseus


Commits:
be3df59c by Pierre Gruet at 2022-08-16T22:04:40+02:00
Removing the linefix function, which tries to return a resource after releasing it

- - - - -
c93fbadc by Pierre Gruet at 2022-08-16T22:12:43+02:00
Wrote an error in the last patch

- - - - -
75befd89 by Pierre Gruet at 2022-08-16T22:19:31+02:00
Removing now useless debian/dirs file

- - - - -
1e64b2a3 by Pierre Gruet at 2022-08-16T22:20:05+02:00
Raising Standards version to 4.6.1

- - - - -
5be27874 by Pierre Gruet at 2022-08-16T22:25:02+02:00
Updating d/watch URI, which is now secure

- - - - -
b4be0d39 by Pierre Gruet at 2022-08-16T22:25:25+02:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- − debian/dirs
- + debian/patches/remove_linefix.patch
- debian/patches/series
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+theseus (3.3.0-12) unstable; urgency=medium
+
+  * Team upload
+  * Removing unused linefix function, which returns a resource just after
+    releasing it (Closes: #1017325)
+  * Raising Standards version to 4.6.1 (no change)
+  * Removing now useless debian/dirs file
+  * Updating d/watch URI, which is now secure
+
+ -- Pierre Gruet <pgt at debian.org>  Tue, 16 Aug 2022 22:25:07 +0200
+
 theseus (3.3.0-11) unstable; urgency=medium
 
   * Adapt theseus_align to muscle version 5


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                libgsl-dev
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/theseus
 Vcs-Git: https://salsa.debian.org/med-team/theseus.git
 Homepage: http://www.theseus3d.org


=====================================
debian/dirs deleted
=====================================
@@ -1 +0,0 @@
-usr/bin


=====================================
debian/patches/remove_linefix.patch
=====================================
@@ -0,0 +1,120 @@
+Description: removing unused linefix function, which releases a resource just
+ before returning it!
+Author: Pierre Gruet <pgt at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1017325
+Forwarded: no
+Last-Update: 2022-08-16
+
+--- a/DLTutils.h
++++ b/DLTutils.h
+@@ -91,9 +91,6 @@
+ int
+ isendline(int ch);
+ 
+-FILE
+-*linefix(char *infile_name);
+-
+ char
+ skipspace(FILE *afp);
+ 
+--- a/libDLTutils/DLTutils.c
++++ b/libDLTutils/DLTutils.c
+@@ -360,74 +360,6 @@
+ }
+ 
+ 
+-/* this takes DOS and Mac files as input and outputs unix files
+-   fixing all endlines */
+-FILE
+-*linefix(char *infile_name)
+-{
+-    FILE           *infile = NULL;
+-    FILE           *outfile = NULL;
+-    int             ch = '\0';
+-
+-    infile = fopen(infile_name, "r");
+-    if (infile == NULL)
+-    {
+-        perror("\n ERROR");
+-        fprintf(stderr, "\n ERROR56: file \"%s\" not found \n", infile_name);
+-        exit(EXIT_FAILURE);
+-    }
+-
+-    outfile = tmpfile();
+-    if (outfile == NULL)
+-    {
+-        perror("\n ERROR");
+-        fprintf(stderr, "\n ERROR56: temp file could not be opened \n");
+-        exit(EXIT_FAILURE);
+-    }
+-
+-    do
+-    {
+-        ch = getc(infile);
+-        if (ch == EOF)
+-            break;
+-        if (ch == 13)    /* replace returns with nothing */
+-        {
+-            ch = getchar();
+-            if (ch == 10)
+-            {
+-                putchar(ch);
+-            }
+-            else if (ch == 13)
+-            {
+-                putchar(10);
+-                putchar(10);
+-            }
+-            else if (ch == EOF)
+-            {
+-                break;
+-            }
+-            else
+-            {
+-                putchar(10);
+-                putchar(ch);
+-            }
+-        }
+-        else
+-        {
+-            fputc(ch, outfile);
+-        }
+-    }
+-    while(1);
+-
+-    cpfile_fp(outfile, infile);
+-
+-    fclose(infile);
+-    fclose(outfile);
+-
+-    return(outfile);
+-}
+-
+-
+ char
+ skipspace(FILE *afp)
+ {
+--- a/libDLTutils/DLTutils.h
++++ b/libDLTutils/DLTutils.h
+@@ -91,9 +91,6 @@
+ int
+ isendline(int ch);
+ 
+-FILE
+-*linefix(char *infile_name);
+-
+ char
+ skipspace(FILE *afp);
+ 
+--- a/libmsa/DLTutils.h
++++ b/libmsa/DLTutils.h
+@@ -91,9 +91,6 @@
+ int
+ isendline(int ch);
+ 
+-FILE
+-*linefix(char *infile_name);
+-
+ char
+ skipspace(FILE *afp);
+ 


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ gcc-7.patch
 0004-create-lib-dir.patch
 0005_stringbuffer.patch
 adapt_to_muscle5.patch
+remove_linefix.patch


=====================================
debian/watch
=====================================
@@ -1,2 +1,2 @@
 version=4
-http://www.theseus3d.org/index.html .*/src/theseus_(.*).tar.gz
+https://theobald.brandeis.edu/theseus/ .*/src/theseus_(.*).tar.gz



View it on GitLab: https://salsa.debian.org/med-team/theseus/-/compare/db477b8da277380d1840d3bf844ff48dae9d251c...b4be0d3959454da6d3ae48379a412051b110dc9d

-- 
View it on GitLab: https://salsa.debian.org/med-team/theseus/-/compare/db477b8da277380d1840d3bf844ff48dae9d251c...b4be0d3959454da6d3ae48379a412051b110dc9d
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