I now believe this to be fixed in SVN. Hopefully it hasn't broken
anything either, although I don't have any valid tar files using that
particular prefix encoding to test on.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
though.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes
this required a *very* slow QEMU
emulation.)
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net
e package with a modern gcc and stress test it
locally. I can't support the old legacy bits, but at the very least
they should be able to compile.
Thanks for the bug report.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
S $editor
> James, if you are interested there are some more patches[2] in the
> packaging reporitory. Some of them might be of interest - at least
> the spelling.patch with some spelling fixes.
Thanks, I'll take a look.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora a
ler still typing in
sh -x `which pregap4`
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/stad
on is under user control and Y dimension under the program
control.
I don't know if this is sufficient as testing this requires checking
every window manager out there and see which options they honour, but
it cures the problem for me with xfwm4.
James
--
James Bonfield (j...@sanger.ac.uk) | Hor
e it to cope with modern window
managers.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projec
taden Package as a whole is pretty much on life support. The
only tool that gets any real updates is Gap5, and they have slowed up
a lot in the last couple years. Things like "eba" are long since dead
really, but basic things like fixing compilation errors is OK to
solve.
James
--
Ja
see bgzip.c doesn't have the standard boilerplate header setup of:
#ifdef HAVE_CONFIG_H
#include "io_lib_config.h"
#endif
Does adding that fix the fseeko call to start working again?
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
Now fixed and pushed. Thanks.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden
guess.
I'll correct it.
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ |
32-bit build systems any more though.
> > > Does adding that fix the fseeko call to start working again?
> >
> > Unfortunately not - see here the build logs:
> >
> > https://buildd.debian.org/status/package.php?p=staden-io-lib
James
--
James Bonfield (j...
/b0fa4620e7b7d9fc05dd5cd001f4dce9606d2776
I'm not sure quite what happened here. Was this fixed inside debian
using a manual patch, rather than pulling the fix from upstream?
Anyway, problem resolved.
Regards,
James
--
James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
run
multiple data generation steps in parallel, but it hasn't cured it.
A simple method is probably the best way to go.
James
--
James Bonfield (j...@sanger.ac.uk)
The Sanger Institute, Hinxton, Cambs, CB10 1SA
--
The Wellcome Sanger Institute is operated by Genome Research
Limite
rk to grant access to a remote
server. It's slow to execute, but I can live with that.
James
--
James Bonfield (j...@sanger.ac.uk)
The Sanger Institute, Hinxton, Cambs, CB10 1SA
--
The Wellcome Sanger Institute is operated by Genome Research
Limited, a charity registered in England with num
; FAIL scram.test (exit status: 1)
This however appears to be a genuine bug. I'll try and reproduce it.
I'm guessing I'll need the exact OS rather than the RedHat based AWS
image I launched last time to test non-intel platforms.
Do you have AWS-ified Debian ARM images for people t
and it's fixed upstream in commit
242cd6b.
The bug affected 32-bit systems, leading to uninitialised memory
accesses in the hash table code.
I'm hoping this covers all the recently detected io_lib bugs. (This
isn't a recent bug - it's been there for years!)
James
--
James Bonfield (j...@
an
ones revealed after the CRC issue was fixed).
The other bugs reported appear to be multi-threading related and will
be dealt with in separate commits.
James
--
James Bonfield (j...@sanger.ac.uk)
The Sanger Institute, Hinxton, Cambs, CB10 1SA
--
The Wellcome Sanger Institute is operated by G
test (exit status: 1)
Bug identified and fixed in upstream commit 37b33d3.
Thanks for the bug report.
It turned out to not be a multi-threading issue per-se, but rather my
use of a pooled memory allocator when working in a threaded
environment. I forgot to ensure all my pooled structures were word
ling for it I finally found it listed as an error in GNU malloc,
which possibly means there is a memory corruption. I will run through
the entire test harness using address sanitiser and if that doesn't
work with Valgrind.
James
--
James Bonfield (j...@sanger.ac.uk)
The Sanger Institute, Hinxton,
On Mon, Nov 26, 2018 at 11:37:19AM +0100, Andreas Tille wrote:
> On Mon, Nov 26, 2018 at 09:39:33AM +0000, James Bonfield wrote:
> > I looked at this and don't see test failures, only "build attempted".
> > Has it changed since this email?
>
> The "Build-Atte
On Mon, Nov 26, 2018 at 11:37:19AM +0100, Andreas Tille wrote:
> On Mon, Nov 26, 2018 at 09:39:33AM +0000, James Bonfield wrote:
> > I looked at this and don't see test failures, only "build attempted".
> > Has it changed since this email?
>
> The "Build-Atte
:19AM +0100, Andreas Tille wrote:
> Hi James,
>
> On Mon, Nov 26, 2018 at 09:39:33AM +0000, James Bonfield wrote:
> > I looked at this and don't see test failures, only "build attempted".
> > Has it changed since this email?
>
> The "Buil
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