[Debian-med-packaging] Bug#962974: t-coffee: fills RAM after reporting PID too high

[Étienne Mollier]

Package: t-coffee
Version: 13.41.0.28bdc39+dfsg-3
Severity: normal

Dear Maintainer,

When launching the t_coffee command with a high PID, probably
above the threshold of 260000, the program remains stuck in a
loop involving a memory leak.

To reproduce the issue, you need a system with a pid_max way
higher than 260000.  For instance I have the new default from
Linux:

	$ cat /proc/sys/kernel/pid_max
	4194304

and launching the command with the -version flag is sufficient
to trigger the bug (assuming the PID affected was higher than
260000):

	$ t_coffee -version
	PROGRAM: T-COFFEE Version_13.41.0.28bdc39 (2019-11-30 10:21:53 - Revision 5d5a1c1 - Build 465)
	
	--ERROR: MAX_N_PID exceded -- Recompile changing the value of MAX_N_PID (current: 260000 Requested: 374228)
	^C****** Forced interuption of main parent process 374228
	User defined signal 1

(SIGINT is trapped, so sending SIGUSR1 is necessary to stop it.)

Apparently pushing MAX_N_PID to 4194304, if possible, might help
in solving this is issue.

Kind Regards,
Étienne.


-- System Information:
Debian Release: bullseye/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.6.0-2-amd64 (SMP w/6 CPU cores)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages t-coffee depends on:
ii  libc6       2.30-8
ii  libgcc-s1   10.1.0-3
ii  libstdc++6  10.1.0-3

Versions of packages t-coffee recommends:
ii  amap-align          2.2+git20080214.600fc29+dfsg-1
ii  clustalo            1.2.4-6
ii  clustalw            2.1+lgpl-6
ii  dialign-tx          1.0.2-12
ii  fsa                 1.15.9+dfsg-4
ii  kalign              1:3.2.3-3
ii  libsoap-lite-perl   1.27-1
ii  libxml-simple-perl  2.25-1
ii  mafft               7.467-1
ii  muscle              1:3.8.1551-2
ii  mustang             3.2.3-3
ii  ncbi-blast+         2.10.0-1
ii  poa                 2.0+20060928-8
ii  prank               0.0.170427+dfsg-2
ii  probcons            1.12-12
ii  proda               1.0-12
ii  tm-align            20190822+dfsg-2

Versions of packages t-coffee suggests:
pn  boxshade           <none>
pn  seaview            <none>
pn  t-coffee-examples  <none>

-- no debconf information

-- 
Étienne Mollier <etienne.mollier at mailoo.org>
Fingerprint:  5ab1 4edf 63bb ccff 8b54  2fa9 59da 56fe fff3 882d
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