diff options
Diffstat (limited to 'sci-biology/t-coffee/files')
3 files changed, 81 insertions, 0 deletions
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch new file mode 100644 index 000000000000..cbfeeabc181b --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch @@ -0,0 +1,25 @@ +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. + . + Unfortunately this does not solve the issue completely since inside the + Exit call a "Segmentation fault" happens - so some broken pointer handling + seems to happen somewhere before. + +--- a/t_coffee_source/util_lib/util.c ++++ b/t_coffee_source/util_lib/util.c +@@ -4642,7 +4642,8 @@ 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); ++ exit(EXIT_FAILURE); + } + + diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch new file mode 100644 index 000000000000..a3f47cd9fce2 --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch @@ -0,0 +1,35 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Mon, 21 Dec 2015 21:30:36 +0100 +Bug-Debian: https://bugs.debian.org/751579 +Description: When creating subdirectories in $HOME do not + make these world writable but keep users umask + +--- a/t_coffee_source/util_lib/util.c ++++ b/t_coffee_source/util_lib/util.c +@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in) + int a, buf; + char *dir; + ++ static char *home = getenv ("HOME"); ++ static mode_t oldmask = umask(0); ++ int change_umask = 0; ++ if (strncmp (dir_in, home, strlen(home))==0) change_umask = 1; + + dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char)); + sprintf ( dir, "%s", dir_in); +@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in) + + if (access(dir, F_OK)==-1) + { +- mode_t oldmask = umask(0); +- mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO); +- umask(oldmask); +- ++ if ( change_umask == 1 ) mkdir (dir, 0777-oldmask); ++ else { ++ mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO); ++ umask(oldmask); ++ } + if ( access (dir, F_OK)==-1) + { + myexit(fprintf_error ( stderr, "\nERROR: Could Not Create Directory %s [FATAL:%s]", dir, PROGRAM)); } diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch new file mode 100644 index 000000000000..5b15108b3bfa --- /dev/null +++ b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch @@ -0,0 +1,21 @@ + t_coffee_source/makefile | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile +index 9e01ba0..026b714 100644 +--- a/t_coffee_source/makefile ++++ b/t_coffee_source/makefile +@@ -1,6 +1,6 @@ + + t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o +- $(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm ++ $(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm + + all: t_coffee TMalign + +@@ -8,4 +8,4 @@ clean: + rm *.o + + TMalign: +- $(FCC) TMalign.f -o TMalign ++ $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign |