[med-svn] [Git][med-team/t-coffee][master] 2 commits: A patch to fix autopkgtest COREDUMP

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / t-coffee


Commits:
c95d597d by Liubov Chuprikova at 2019-02-04T09:48:44Z
A patch to fix autopkgtest COREDUMP

- - - - -
8282ba9a by Liubov Chuprikova at 2019-02-04T09:50:17Z
Standards-Version: 4.3.0

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/fix_tempfile_name_sharing.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+t-coffee (12.00.7fb08c2-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Fix "t-coffee breaks libbio-tools-run-alignment-tcoffee-perl
+    autopkgtest: COREDUMP" fix_tempfile_name_sharing.patch
+    (Closes: #917143)
+  * Standards-Version: 4.3.0
+
+ -- Liubov Chuprikova <chuprikovalv at gmail.com>  Mon, 04 Feb 2019 10:37:01 +0100
+
 t-coffee (12.00.7fb08c2-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/t-coffee
 Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git
 Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html


=====================================
debian/patches/fix_tempfile_name_sharing.patch
=====================================
@@ -0,0 +1,29 @@
+Author: Liubov Chuprikova <chuprikovalv at gmail.com> 
+Bug-Debian: https://bugs.debian.org/917143
+Last-Update: Sun, 03 Feb 2019 23:42:41 +0100
+Description: Delete static for tempfile names so that 
+different processes do not use the same file.
+
+
+--- a/t_coffee_source/util_lib/reformat.c
++++ b/t_coffee_source/util_lib/reformat.c
+@@ -1524,8 +1524,8 @@
+ 	 }
+        else if      (format && (strm(format, "saga_aln" ) ||strm(format, "clustal_aln")||strm(format, "t_coffee_aln" ) || strm (format, "msf_aln")))
+ 	 {
+-	   static char*tmp_name1=vtmpnam (NULL);
+-	   static char*tmp_name2=vtmpnam (NULL);
++	   char*tmp_name1=vtmpnam (NULL);
++	   char*tmp_name2=vtmpnam (NULL);
+ 	   
+ 	   printf_system ( "seq2name_seq.pl %s > %s",name, tmp_name1);
+ 	   printf_system ( "nameseq2fasta.pl %s > %s",tmp_name1, tmp_name2);
+@@ -1534,6 +1534,8 @@
+ 	   A=seq2aln (S, A, 0);
+ 	   //read_aln ( name, A);
+ 
++	   vfree(tmp_name1);
++	   vfree(tmp_name2);
+ 	 }
+        
+        else if (format && strm (format, "conc_aln"))A=input_conc_aln (name,NULL);


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ set_proper_dir_permissions.patch
 mayhem.patch
 stable-linking-inputs.patch
 clustalw2.patch
+fix_tempfile_name_sharing.patch



View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773

-- 
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773
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