debian/changelog

+t-coffee (11.00.8cbe486-7) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Mon, 24 Sep 2018 08:41:01 +0200
+
 t-coffee (11.00.8cbe486-6) unstable; urgency=medium
 
   * Standards-Version: 4.1.0 (no changes needed)

debian/compat

-10
+11

debian/control

@@ -4,10 +4,10 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10)
-Standards-Version: 4.1.0
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/t-coffee.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/t-coffee.git
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.2.1
+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
 
 Package: t-coffee

debian/patches/mayhem_debug.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
-Bug-Debian: https://bugs.debian.org/716373
-Description: Fix Mayhem issue
- The idea behind this patch is that if there is a problem to set the HOME
- directories no additional processes can exist and so we should *really*
- exit.  Somehow the printf_exit() function does some logic which ends up
- in an endless loop and thus forcing the exit will help here.
- .
- Since the exit call triggers some "Segmentation fault" I'll leave some
- debug printf lines for further debugging.
-
---- a/t_coffee_source/util_lib/util.c
-+++ b/t_coffee_source/util_lib/util.c
-@@ -4618,9 +4618,9 @@ char *get_home_4_tcoffee ()
-   static char *home_4_tcoffee;
-   static char home[1000];
- 
--
-   if ( !home_4_tcoffee)
-     home_4_tcoffee=(char*)vcalloc ( 1000, sizeof (char));
-+printf("%s (%d): home_4_tcoffee = %s\n", __FILE__, __LINE__, home_4_tcoffee); fflush(stdout);
- 
-   if ( home_4_tcoffee[0])return home_4_tcoffee;
-   else if ( check_dir_getenv ("HOME_4_TCOFFEE"))
-@@ -4642,7 +4642,9 @@ char *get_home_4_tcoffee ()
-     }
-   else
-     {
--      printf_exit (EXIT_FAILURE, stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
-+      fprintf(stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
-+printf("%s (%d): PROGRAM = %s\n", __FILE__, __LINE__, PROGRAM); fflush(stdout);
-+      exit(EXIT_FAILURE);
-     }
- 
- 
-@@ -4880,7 +4882,7 @@ int cputenv (char *string, ...)
- 
- 
- 
--
-+printf("%s (%d): string = %s\n", __FILE__, __LINE__, string); fflush(stdout);
- 
-   char *s;
-   char *s2;
-@@ -6524,7 +6526,7 @@ int get_cl_param (int argc, char **argv,
- 	int    n_pv_r;
- 	char   value[STRING];
- 
--
-+printf("%s(%d) argc=%d, argv[1] = %s, para_name_in =%s\n", __FILE__, __LINE__, argc, argv[1], para_name_in);
- /*CHECK THAT ALL THE PARAM IN ARG EXIST*/
- 	if ( para_name_in==NULL)
- 	   {
-@@ -8818,7 +8820,6 @@ char ** standard_initialisation  (char *
- /*Standard exit*/
-   global_exit_signal=EXIT_SUCCESS;
-   atexit (clean_exit);
--
-   signal (SIGTERM,signal_exit);
-   signal (SIGINT, signal_exit);
-   signal (SIGKILL, signal_exit);
-@@ -8826,7 +8827,6 @@ char ** standard_initialisation  (char *
-   signal (SIGFPE, error_exit);
-   signal (SIGILL, error_exit);
-   signal (SIGSEGV, error_exit);
--
-   program_name=(char*)vcalloc ( strlen (in_argv[0])+strlen (PROGRAM)+1, sizeof (char));
-   if (in_argv)
-     {
-@@ -8836,7 +8836,6 @@ char ** standard_initialisation  (char *
-       set_command_line (s);
-     }
-   else sprintf ( program_name, "%s",PROGRAM);
--
-   if ( name_is_in_list ( "-no_error_report", out_argv, in_argc[0], 100)!=-1)no_error_report=1;
- 
-   //Plugins
-@@ -8845,6 +8844,7 @@ char ** standard_initialisation  (char *
- //  get_nproc();
- 
- 
-+printf("%s (%d): in_argc = %d, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, *in_argc, in_argv[1], in_argv[2]);
- 
-   if (!getenv ("UPDATED_ENV_4_TCOFFEE"))
-     {
-@@ -8856,13 +8856,17 @@ char ** standard_initialisation  (char *
-       if (getenv ("ENV_4_TCOFFEE"))file_putenv (getenv ("ENV_4_TCOFFEE"));
-     }
- 
-+printf("%s (%d): in_argc = %d, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, *in_argc, in_argv[1], in_argv[2]); fflush(stdout);
-   string_putenv (s); //let Command line update go through
--
-+printf("%s (%d): in_argc = %d, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, *in_argc, in_argv[1], in_argv[2]); fflush(stdout);
-+printf("%s (%d): in_argc = %d, in_argv[1][1] = %d, in_argv[2][1] = %d\n", __FILE__, __LINE__, *in_argc, in_argv[1][1], in_argv[2][1]); fflush(stdout);
- 
-   cputenv ("HOME_4_TCOFFEE=%s",get_home_4_tcoffee());
-+printf("%s (%d): in_argc = %d, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, *in_argc, in_argv[1], in_argv[2]); fflush(stdout);
-   cputenv ("DIR_4_TCOFFEE=%s",get_dir_4_tcoffee());
-   cputenv ("TMP_4_TCOFFEE=%s",get_tmp_4_tcoffee());
-   cputenv ("CACHE_4_TCOFFEE=%s",get_cache_4_tcoffee());
-+printf("%s (%d): in_argc = %d, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, *in_argc, in_argv[1], in_argv[2]); fflush(stdout);
-   cputenv ("MCOFFEE_4_TCOFFEE=%s",get_mcoffee_4_tcoffee());
-   cputenv ("METHODS_4_TCOFFEE=%s",get_methods_4_tcoffee());
-   cputenv ("PLUGINS_4_TCOFFEE=%s",get_plugins_4_tcoffee());
-@@ -8871,6 +8875,7 @@ char ** standard_initialisation  (char *
- 
- 
- 
-+printf("%s (%d): in_argc = %d, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, *in_argc, in_argv[1], in_argv[2]);
- 
- 
-   string_putenv (s); //let Command line update go through //Twice in case an executable dir not created
-@@ -8893,6 +8898,7 @@ char ** standard_initialisation  (char *
-   lock(getpid(),LLOCK, LRESET, "%d\n",getppid());//set the main lock
-   if (is_shellpid(getppid()))lock(getppid(),LLOCK, LSET, "%d\n",getpid());//update parent lock when parent is shell
- 
-+printf("%s (%d): in_argc = %d, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, *in_argc, in_argv[1], in_argv[2]);
- 
-   //set special Variables
-   if (getenv ("MAFFT_BINARIES") || isdir4path ("/usr/local/lib/mafft"));
-@@ -8905,6 +8911,8 @@ char ** standard_initialisation  (char *
-   //pipe_in
-   for (a=1, stdi=0; a<in_argc[0]; a++)
- 	{
-+printf("%s (%d): a = %s, in_argv[1] = %s, in_argv[2] = %s\n", __FILE__, __LINE__, a, in_argv[1], in_argv[2]);
-+
- 	  if ( (strm ( out_argv[a], "stdin") || strm (out_argv[a], "STDIN")) && stdi==0)
- 	    {
- 	      char *file;
---- a/t_coffee_source/t_coffee_lib/t_coffee.c
-+++ b/t_coffee_source/t_coffee_lib/t_coffee.c
-@@ -156,8 +156,10 @@ int main (int argc, char *argv[])
- // printf("RUNNING DEBUG\n");
-   int r, a;
- 
-+printf("%s (%d): argc = %d, argv[1] = %s, argv[2] = %s\n", __FILE__, __LINE__, argc, argv[1], argv[2]);
-   if (argc>=2 && strcmp (argv[1], "-batch")==0)
-     {
-+printf("%s (%d): argc = %d, argv[1] = %s\n", __FILE__, __LINE__, argc, argv[1]);
-       char **list;
-       list=file2lines (argv[2]);
-       for (a=1; a<atoi (list[0]); a++)
-@@ -170,8 +172,10 @@ int main (int argc, char *argv[])
-     }
-   else
-     {
-+printf("%s (%d): argc = %d, argv[1] = %s, argv[2] = %s\n", __FILE__, __LINE__, argc, argv[1], argv[2]);
-       r=batch_main (argc, argv);
-     }
-+printf("%s (%d): argc = %d, argv[1] = %s\n", __FILE__, __LINE__, argc, argv[1]);
-   myexit (r);
- }
- 
-@@ -512,7 +516,7 @@ int batch_main ( int argc, char **argv)
- 	
- 	int sand_box=0;
- 
--
-+printf("%s (%d): argc = %d, argv[1] = %s, argv[2] = %s\n", __FILE__, __LINE__, argc, argv[1], argv[2]);
- 
- 	if (sand_box==1)
- 	  {
-@@ -525,9 +529,12 @@ int batch_main ( int argc, char **argv)
- 	 *        If so, redirect to ::run_other_pg.
- 	 *        (In case of kmcoffee, load the kmcoffee arguments from ::km_coffee)
- 	 */
-+printf("%s (%d): argc = %d, argv[1] = %s, argv[2] = %s\n", __FILE__, __LINE__, argc, argv[1], argv[2]);
- 	argv=standard_initialisation (argv, &argc);
- 	set_string_variable ("t_coffee", argv[0]);
- 
-+printf("%s (%d): argc = %d, argv[1] = %s\n", __FILE__, __LINE__, argc, argv[1]);
-+
- 	if (argc>=3 && strm (argv[1], "-other_pg"))
- 	  {
- 	    //standard_initialisation (NULL,NULL);