t_coffee_source/data_headers/programmes_define.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 debian-specific adjustment.
 The program "probconsRNA" is called "probcons-RNA" in Debian.

example/tc_generic_method.pl | 28 11 + 17 - 0 !
1 file changed, 11 insertions(+), 17 deletions(-)

 see origin

t_coffee_source/makefile | 7 2 + 5 - 0 !
1 file changed, 2 insertions(+), 5 deletions(-)

 there is no need to build tmalign since the debian packaged
 version is used anyway

t_coffee_source/makefile | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 propagate hardening options

t_coffee_source/util_lib/util.c | 13 9 + 4 - 0 !
1 file changed, 9 insertions(+), 4 deletions(-)

 when creating subdirectories in $home do not
 make these world writable but keep users umask

t_coffee_source/util_lib/util.c | 7 6 + 1 - 0 !
1 file changed, 6 insertions(+), 1 deletion(-)

 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.

t_coffee_source/makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 provide stable file order for linking
 This makes the package reproducible.

install | 21 6 + 15 - 0 !
t_coffee_source/data_headers/programmes_define.h | 2 1 + 1 - 0 !
t_coffee_source/programmes_define.h | 2 1 + 1 - 0 !
t_coffee_source/util_lib/util_constraints_list.c | 10 5 + 5 - 0 !
tclinkdb.txt | 20 5 + 15 - 0 !
5 files changed, 18 insertions(+), 37 deletions(-)

 executable in clustalw 2.x package is named clustalw
 When using bioperl-run test suite it is uncovered that t-coffee is
 wrongly seeking for a clustalw2 executable.  A patch is applied to
 rather seek for clustalw.

t_coffee_source/makefile | 6 4 + 2 - 0 !
1 file changed, 4 insertions(+), 2 deletions(-)

 don't hide the build flags

t_coffee_source/coffee_defines.h | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 increase max_n_pid to linux 64 bits theoretical maximum
 Since Debian Bullseye, the system now has a default pid_max of 4194304 instead
 of the historical 32768.  This renders t-coffee much more likely to crash on
 compute nodes always powered on in computer centers.  This patch addresses
 that issue with a value set to the theoretical upper limit of Linux on 64 bits
 systems.