[med-svn] [Git][med-team/t-coffee][master] 5 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Mon Sep 24 07:48:52 BST 2018
Andreas Tille pushed to branch master at Debian Med / t-coffee
Commits:
25ecc1a1 by Andreas Tille at 2018-09-24T06:35:27Z
debhelper 11
- - - - -
418596a6 by Andreas Tille at 2018-09-24T06:36:30Z
Point Vcs fields to salsa.debian.org
- - - - -
f4b2d5c3 by Andreas Tille at 2018-09-24T06:36:30Z
Standards-Version: 4.2.1
- - - - -
29904a59 by Andreas Tille at 2018-09-24T06:40:21Z
Remove unused patch
- - - - -
cd9296d8 by Andreas Tille at 2018-09-24T06:43:06Z
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/compat
- debian/control
- − debian/patches/mayhem_debug.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+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 at 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
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -4,10 +4,10 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at 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 deleted
=====================================
@@ -1,176 +0,0 @@
-Author: Andreas Tille <tille at 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);
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/53cff21446eee93bcb187107ab902f6c6e96c35c...cd9296d825f7d8e5ec7c5ebca216ab2c7966e7bf
--
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/53cff21446eee93bcb187107ab902f6c6e96c35c...cd9296d825f7d8e5ec7c5ebca216ab2c7966e7bf
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