Your message dated Sun, 08 Nov 2020 21:40:08 +0000
with message-id <e1kbspw-000h8m...@fasolo.debian.org>
and subject line Bug#972436: Removed package(s) from unstable
has caused the Debian Bug report #972436,
regarding RM: mapsembler2 [armel armhf i386 hurd-i386 kfreebsd-i386] -- ANAIS;
package broken on 32bits archs and non-maintained upstream
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
972436: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=972436
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: ftp.debian.org
Severity: normal
Greetings,
I spent some time on mapsembler2 to put it into adequate shape,
so that it might make it to Testing. This involved some
investigatons of autopkgtest regressions on 32 bits
architectures, at least armhf and i386, as reported by testing
excuses migrations[0].
[0] https://tracker.debian.org/pkg/mapsembler2
The initial segmentation fault encountered by the test allowed
me to locate a missing check of memory allocation, and change
some default program parameters to values more suitable for
32 bits architectures, when running on such arch[1].
[1]
https://salsa.debian.org/med-team/mapsembler2/-/commit/73d9dae0c0c876a415ba804e83602bb984a20ac0
I then had to track a second segmentation fault down to a highly
optimized hashing function, which looks compatible with all
combinations of 32, 64 bits, little and big endian. However one
of the steps of this hashing function is triggering the fault,
and I'm not comfortable enough with the program to identify
whether it is the value of the hash key which is at fault, or
the logic of the hashing function in itself. Looking at the
change log[2] of the program, I even think my change could have
undone a fix for that crash, or even for another crash:
> mapsembler2_2.2.4: fixes k-mer counting problems. Use by default 4GB memory
[2] https://colibread.inria.fr/software/mapsembler2/
There is always the possibility that a simple knob has changed
at some point, such as an architecture specific code path, but
if so, I failed to identify it. Bringing the issue to upstream
is not an option here unfortunately, as the program is not
maintained since 2014[2].
Due to the above reasons, I think mapsembler2 is probably
not suitable for 32 bits variants of Debian unfortunately.
Kind Regards,
--
Étienne Mollier <etienne.moll...@mailoo.org>
Old rsa/3072: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d
New rsa/4096: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/6, please excuse my verbosity.
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
We believe that the bug you reported is now fixed; the following
package(s) have been removed from unstable:
mapsembler2 | 2.2.4+dfsg1-1 | armel, armhf, i386
------------------- Reason -------------------
ANAIS; package broken on 32bits archs and non-maintained upstream
----------------------------------------------
Note that the package(s) have simply been removed from the tag
database and may (or may not) still be in the pool; this is not a bug.
The package(s) will be physically removed automatically when no suite
references them (and in the case of source, when no binary references
it). Please also remember that the changes have been done on the
master archive and will not propagate to any mirrors until the next
dinstall run at the earliest.
Packages are usually not removed from testing by hand. Testing tracks
unstable and will automatically remove packages which were removed
from unstable when removing them from testing causes no dependency
problems. The release team can force a removal from testing if it is
really needed, please contact them if this should be the case.
Bugs which have been reported against this package are not automatically
removed from the Bug Tracking System. Please check all open bugs and
close them or re-assign them to another package if the removed package
was superseded by another one.
The version of this package that was in Debian prior to this removal
can still be found using http://snapshot.debian.org/.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 972...@bugs.debian.org.
The full log for this bug can be viewed at https://bugs.debian.org/972436
This message was generated automatically; if you believe that there is
a problem with it please contact the archive administrators by mailing
ftpmas...@ftp-master.debian.org.
Debian distribution maintenance software
pp.
Joerg Jaspert (the ftpmaster behind the curtain)
--- End Message ---
