On Fri, May 1, 2020 at 3:05 AM Jeffrey Walton wrote:
>
> On Fri, May 1, 2020 at 2:14 AM Andreas Tille wrote:
> >
> > ...
> > ==13209== Process terminating with default action of signal 10 (SIGBUS)
> > ==13209==at 0x12D5CC: PairDistances (pair_dist.c:346)
> > ==13209==by 0x119410:
On Fri, May 1, 2020 at 2:14 AM Andreas Tille wrote:
>
> ...
> ==13209== Process terminating with default action of signal 10 (SIGBUS)
> ==13209==at 0x12D5CC: PairDistances (pair_dist.c:346)
> ==13209==by 0x119410: AlignmentOrder (clustal-omega.c:835)
> ==13209==by 0x11A6C4: Align
Hi Matthew,
On Thu, Apr 30, 2020 at 05:53:29PM -0700, Matthew Fernandez wrote:
>
> Is the priority goal here to simply ship a non-crashing clustalo mipsel
> binary that BioPython can depend on? If so, maybe we can just disable
> compiler optimisation (-O0) and this may avoid provoking the bus
> One small issue... Valgrind recommends -O0 or -O1
TIL :) Thanks, Jeff!
> You can sometimes locate a bus error at build time with -Wcast-align.
> At runtime you can usually locate them with -fsanitize=undefined.
I had previously tried UBSan and, while it turned up a number of shifting and
Hi Jeffrey,
thanks a lot for this analysis. Any chance that somebody could
turn this into a patch I could try?
Kind regards
Andreas.
On Thu, Apr 30, 2020 at 03:40:12PM -0400, Jeffrey Walton wrote:
> On Fri, Apr 17, 2020 at 7:21 AM Andreas Tille wrote:
> > ...
> > So it seems the bus
On Fri, Apr 17, 2020 at 7:21 AM Andreas Tille wrote:
> ...
> So it seems the bus error occures somehow here:
>
>
> https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346
NewProgress is at
On Fri, Apr 17, 2020 at 7:21 AM Andreas Tille wrote:
>
> Control: tags -1 help
>
> as it can be seen on the recent build log of clustalo on mips[1] the
> build fails with
>
> # Run additional test from python-biopython package to verify that
> # this will work as well
> src/clustalo -i
On Thu, Apr 30, 2020 at 10:33 AM Matthew Fernandez
wrote:
>
> > On Apr 30, 2020, at 00:31, Andreas Tille wrote:
> >
> > On Wed, Apr 29, 2020 at 05:51:26PM -0700, Matthew Fernandez wrote:
> >
> >> The other option I suggested was Valgrind, but if you can’t run apt-file
> >> you probably can’t
On Thu, Apr 30, 2020 at 07:17:50AM -0700, Matthew Fernandez wrote:
>
> Valgrind, in its default mode, checks for a variety of memory issues
> (use-after-free, write out-of bounds, …). You don’t need any special
> configure/build options, but you probably want to enable debug symbols
> (`export
> On Apr 30, 2020, at 00:31, Andreas Tille wrote:
>
> On Wed, Apr 29, 2020 at 05:51:26PM -0700, Matthew Fernandez wrote:
>
>> The other option I suggested was Valgrind, but if you can’t run apt-file you
>> probably can’t install Valgrind either.
>
> Well, I guess apt-get is permitted for
Hi Matthew,
On Wed, Apr 29, 2020 at 05:51:26PM -0700, Matthew Fernandez wrote:
> > Any more help from debian-mipsel is really appreciated.
>
> Hm yes, “--disable-libsanitizer” is rather ominous. I guess the mipsel GCC
> package has been built without ASan support. Surprising that it fails so
>
> On Apr 29, 2020, at 09:04, Andreas Tille wrote:
>
> On Wed, Apr 29, 2020 at 07:14:30AM -0700, Matthew Fernandez wrote:
>
>> For those on this thread who have access to mipsel hardware or can shell in
>> to one of the mipsel build machines, I would suggest running an
>> ASan-instrumented
Hi Matthew,
On Wed, Apr 29, 2020 at 07:14:30AM -0700, Matthew Fernandez wrote:
>
> To add another data point to this discussion, one other (fruitless) thing I
> tried previously was cross-compiling Clustal Omega. From an amd64 host, it’s
> possible to target mipsel using the GCC
> On Apr 29, 2020, at 02:12, Andreas Tille wrote:
>
> Hi,
>
> On Wed, Apr 29, 2020 at 10:30:35AM +0800, 黄佳文 wrote:
>> I am a developer from Loongson company (R & D CPU/mip64el), I've been
>> looking at this recently.
>
> Very nice to see mips developers to care for biological software. :-)
>
Hi,
On Wed, Apr 29, 2020 at 10:30:35AM +0800, 黄佳文 wrote:
> I am a developer from Loongson company (R & D CPU/mip64el), I've been
> looking at this recently.
Very nice to see mips developers to care for biological software. :-)
> I did two experiments, and I found that when I used Python 3,7 to
Control: affects -1 src:python-biopython
On Tue, 14 Apr 2020 at 17:39, Andreas Tille wrote:
> Control: reassign -1 clustalo
> Control: retitle -1 "clustalo: Bus error on mipsel"
> Control: tags -1 upstream
> Control: forwarded -1 clust...@ucd.ie
Marking this bug as affecting
Processing control commands:
> affects -1 src:python-biopython
Bug #956324 [clustalo] "clustalo: Bus error on mipsel"
Added indication that 956324 affects src:python-biopython
--
956324: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956324
Debian Bug Tracking System
Contact
Hi Matthew,
many thanks again for your investigation.
On Sat, Apr 18, 2020 at 01:15:49PM -0700, Matthew Fernandez wrote:
> > Upstream is in the row of this investigation. Its quite interesting
> > that the issue could also observed on amd64. So probably this is a real
> > issue which is just
> On Apr 17, 2020, at 22:39, Andreas Tille wrote:
>
> Hi Matthew,
>
> thanks a lot for your detailed investigation.
>
> On Fri, Apr 17, 2020 at 04:28:23PM -0700, Matthew Fernandez wrote:
>>> Program received signal SIGBUS, Bus error.
>>> 0x5556a1b8 in PairDistances (distmat=0x7fff278c,
Hi Matthew,
thanks a lot for your detailed investigation.
On Fri, Apr 17, 2020 at 04:28:23PM -0700, Matthew Fernandez wrote:
> > Program received signal SIGBUS, Bus error.
> > 0x5556a1b8 in PairDistances (distmat=0x7fff278c, mseq=0x55692a30,
> > pairdist_type=, bPercID=, istart=0, iend=3,
> >
> On Apr 17, 2020, at 13:18, Andreas Tille wrote:
>
> Hi Matthew,
>
> On Fri, Apr 17, 2020 at 08:18:29AM -0700, Matthew Fernandez wrote:
>>> Thanks for the patch which I applied to packaging Git. I assume you
>>> want to express that while these fixes are definitely good coding
>>> practice
Hi Matthew,
On Fri, Apr 17, 2020 at 08:18:29AM -0700, Matthew Fernandez wrote:
> > Thanks for the patch which I applied to packaging Git. I assume you
> > want to express that while these fixes are definitely good coding
> > practice the bus error problem is not fixed by it, right?
>
> Thanks,
On Fri, 17 Apr 2020 at 08:09, Andreas Tille wrote:
> Hi Matthew,
>
> On Fri, Apr 17, 2020 at 07:40:54AM -0700, Matthew Fernandez wrote:
> >
> > As a jumping off point, the attached patch fixes some issues with
> logging calls in the upstream 1.2.4 source release.
>
> Thanks for the patch which I
Hi Matthew,
On Fri, Apr 17, 2020 at 07:40:54AM -0700, Matthew Fernandez wrote:
>
> As a jumping off point, the attached patch fixes some issues with logging
> calls in the upstream 1.2.4 source release.
Thanks for the patch which I applied to packaging Git. I assume you
want to express that
> On Apr 17, 2020, at 04:20, Andreas Tille wrote:
>
> Control: tags -1 help
>
> Hi,
>
> as it can be seen on the recent build log of clustalo on mips[1] the
> build fails with
>
>
> # Run additional test from python-biopython package to verify that
> # this will work as well
> src/clustalo
Processing control commands:
> tags -1 help
Bug #956324 [clustalo] "clustalo: Bus error on mipsel"
Added tag(s) help.
--
956324: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956324
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
Control: tags -1 help
Hi,
as it can be seen on the recent build log of clustalo on mips[1] the
build fails with
# Run additional test from python-biopython package to verify that
# this will work as well
src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out
temp_test.dnd -o
ons of bug #956324 to the same values
previously set
> retitle -1 "clustalo: Bus error on mipsel"
Bug #956324 [clustalo] python-biopython: FTBFS on mipsel
Changed Bug title to '"clustalo: Bus error on mipsel"' from 'python-biopython:
FTBFS on mipsel'.
> tags -1 upstream
Bug
Control: reassign -1 clustalo
Control: retitle -1 "clustalo: Bus error on mipsel"
Control: tags -1 upstream
Control: forwarded -1 clust...@ucd.ie
Hi,
I took over the test done by biopython into the clustalo build time and
autopkgtest. As Peter assumed this is an issue in clustalo as you can
see
I agree this is most likely a clustalo error. I think the first two
examples use
temporary input files created during the Biopython tests. However, the third
failing example ought to be useful in isolation:
clustalo -i Fasta/f002 --guidetree-out temp_test.dnd -o temp_test.aln
--outfmt clustal
Processing control commands:
> forwarded -1 Peter Cock
Bug #956324 [src:python-biopython] python-biopython: FTBFS on mipsel
Set Bug forwarded-to-address to 'Peter Cock '.
--
956324: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956324
Debian Bug Tracking System
Contact
Control: forwarded -1 Peter Cock
Hi Peter,
the log that is linked to below says in the end:
==
ERROR: test_input_filename_with_space
(test_ClustalOmega_tool.ClustalOmegaTestNormalConditions)
Test an input filename containing
Source: python-biopython
Version: 1.76+dfsg-1
Severity: serious
Tags: ftbfs sid bullseye
Justification: fails to build from source (but built successfully in the past)
python-biopython failed to build on mipsel:
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