Hi Martin,
Agreed that FMA [1] could be the cause. Anyhow, I had disabled that specific
unit-test. That is the quickest fix right now to meet the Bioconductor 3.18
release date. I will try to revisit the C code that you mentioned and see if I
can fix the problem.
Thanks so much for your help!
Hi Reina,
I tried to debug it but without success!
I think the problem is at
https://code.bioconductor.org/browse/CaDrA/blob/devel/src/score_fun.c#L613
because it fails only with method = "ks_score"
It does a lot of calculations with doubles and I am almost sure FMA [1] is
to blame.
You could try
Hi Martin,
Yes, I removed that specified test case that failed the check in order to meet
Bioconductor 3.18 release deadline.
Thanks again for looking into this!
Best,
Reina C.
On Oct 19, 2023, at 4:20 AM, Martin Grigorov wrote:
Hello Reina,
The checks pass now after your last commit:
Hello Reina,
The checks pass now after your last commit:
```
...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R
Hi Martin,
That would be very helpful. Thanks so much! Right now, it is failing in one of
the unit test cases. In particular, our core function, CaDrA::CaDrA, which is
used to run permutation-based tests to determine whether the strength of the
association between the set of features and the
On Wed, Oct 18, 2023 at 11:11 PM Chau, Reina wrote:
> Thank you both! I will look thru the links and see if I can implement a
> fix.
>
I'd be happy to test any patches if it will be easier for you !
Martin
>
> Best,
>
> Reina C.
>
> On Oct 18, 2023, at 4:03 PM, Martin Grigorov
> wrote:
>
>
Thank you both! I will look thru the links and see if I can implement a fix.
Best,
Reina C.
On Oct 18, 2023, at 4:03 PM, Martin Grigorov wrote:
Hi,
On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès
mailto:hpages.on.git...@gmail.com>> wrote:
Hi Reina,
Note that CaDrA results on Mac ARM64 are
Hi,
On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès
wrote:
> Hi Reina,
>
> Note that CaDrA results on Mac ARM64 are also affected:
> https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/
>
> See Martin Grigorov's blog post here
>
Hi Reina,
Note that CaDrA results on Mac ARM64 are also affected:
https://bioconductor.org/checkResults/devel/bioc-mac-arm64-LATEST/CaDrA/
See Martin Grigorov's blog post here
https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/
for how to debug Linux ARM64 related
Hi Bioconductor Core Team,
I’m the maintainer of CaDrA package, and recently, I notice that my package
built successfully for all platforms except on Kunpeng2 Linux machine (see
https://bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/ and
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