Hi Felix,
Interestingly the unit tests error on 64-bit Windows is gone today but
now the unit tests trigger a segfault on Linux:
https://bioconductor.org/checkResults/3.14/bioc-LATEST/mia/nebbiolo2-checksrc.html
The segfault seems to happen during a call to ape:::all.equal.phylo().
This kind of hard-to-reproduce segfault is usually caused by some
problematic native code. The usual suspects are uninitialized C
variables/arrays. Running the problematic test thru Valgrind might give
you some hints.
Best,
H.
On 26/10/2021 13:09, Felix Ernst wrote:
Thanks Herve!
-----Ursprüngliche Nachricht-----
Von: Hervé Pagès <hpages.on.git...@gmail.com>
Gesendet: Dienstag, 26. Oktober 2021 21:53
An: Felix Ernst <felix.gm.er...@outlook.com>; bioc-devel@r-project.org
Betreff: Re: [Bioc-devel] Windows specific error during CHECK
Hi Felix,
On 26/10/2021 12:10, Felix Ernst wrote:
Hi Bioc-Team,
I have got a problem with an error on Windows, which I am not able to debug.
http://bioconductor.org/checkResults/devel/bioc-LATEST/mia/riesling1-c
hecksrc.html
The testthat.out.fail output doesn't indicate any problems and the testthat.out
on other systems looks the same.
Can someone provide any hint on what might be going on? Thanks in advance!
Hmm.. even more puzzling is that if I go on riesling1, start R (in 64-bit
mode), and run the tests manually, I don't see any problem:
> test_check("mia")
|======================================================================|
100%
Time difference of 6.58 secs
Initializing error rates to maximum possible estimate.
selfConsist step 1 .
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 rounds.
Initializing error rates to maximum possible estimate.
selfConsist step 1 .
selfConsist step 2
selfConsist step 3
selfConsist step 4
Convergence after 4 rounds.
initial value 0.383462
iter 5 value 0.161655
iter 10 value 0.113278
final value 0.003270
converged
initial value 0.000000
final value 0.000000
converged
initial value 0.000000
final value 0.000000
converged
initial value 0.000000
final value 0.000000
converged
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 630 ]
So this only seems to happen in the context of 'R CMD check'. I wonder
if the fact that we run 'R CMD check' with the --force-multiarch option
(so the examples and tests are run for the 2 Windows archs) could be
somehow related to the issue.
Anyways, I won't be able to do more testing today because the builds on
riesling1 are going to start in a few minutes. I'll try to get back to
this tomorrow.
Cheers,
H.
Best regards,
Felix
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Bioconductor Core Team
hpages.on.git...@gmail.com
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