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 code from vignettes ...
‘permutation_based_testing.Rmd’ using ‘UTF-8’... OK
‘scoring_functions.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
```
biocbuild@kunpeng2 ~/g/CaDrA (devel)> git log -1
commit ae6513e0877d5866fc8240eb123b8bc83af73e19 (HEAD -> devel,
origin/master, origin/devel, origin/HEAD)
Author: RC-88 <lilychau...@gmail.com>
Date: Wed Oct 18 16:14:42 2023 -0400
remove testing for ks_score method due to inconsistent results on linux
and macOS amd64
I will try to debug the disabled code later !
Martin
On Thu, Oct 19, 2023 at 12:21 AM Chau, Reina <rcha...@bu.edu> wrote:
> 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 observed
> input scores (e.g., pathway activity, drug sensitivity, etc.) is greater
> than it would be expected by chance.
>
> Here is a snippet of where the test failed in Mac and Linux ARM64 machine:
>
> # R library
> library(CaDrA)
> library(testthat)
>
> data("sim_FS”)
> data("sim_Scores")
>
> # Set seed
> set.seed(21)
>
> # ks_score
> result <- CaDrA::CaDrA(
> FS = sim_FS,
> input_score = sim_Scores,
> method = "ks_score",
> weights = NULL,
> alternative = "less",
> top_N = 1,
> search_start = NULL,
> search_method = "both",
> max_size = 7,
> n_perm = 10,
> plot = FALSE,
> smooth = TRUE,
> obs_best_score = NULL,
> ncores = 1,
> cache = FALSE,
> cache_path = NULL
> )
>
> testthat::expect_length(result, 4L)
> testthat::expect_type(result, "list")
> testthat::expect_named(result,
>
> c("key","perm_best_scores","obs_best_score","perm_pval"))
> testthat::expect_type(result$key, "list")
> testthat::expect_length(result$key, 11L)
> testthat::expect_named(result$key,
> c("FS", "input_score", "method",
> "custom_function",
> "custom_parameters", "alternative",
> "weights", "top_N",
> "search_start", "search_method",
> "max_size"))
> testthat::expect_type(result$key$FS, "double")
>
> testthat::expect_equal(round(result$perm_best_scores[1:10], 5),
> c('TP_8'=0.34,
> 'TP_10'=0.54,
> 'TP_9'=0.37,
> 'TP_6'=0.40,
> 'TP_9'=0.38,
> 'TP_9'=0.52,
> 'TP_2'=0.44,
> 'TP_2'=0.40,
> 'TP_4'=0.44,
> 'TP_9'=0.49))
>
> testthat::expect_equal(round(result$obs_best_score, 2), c("TP_9"=0.66))
>
> # A smooth factor of 1
> c <- 1
>
> # Add a smoothing factor of 1
> # This is just to not return a p-value of 0
> testthat::expect_equal(
> round((sum(result$perm_best_scores[1:10] >
> result$obs_best_score)+c)/(10+c), 6),
> c(0.090909)
> )
>
> Any helps or directions on how to resolve this problem would be be greatly
> appreciated!
>
> Best,
>
> Reina C.
>
>
> On Oct 18, 2023, at 4:35 PM, Martin Grigorov <martin.grigo...@gmail.com>
> wrote:
>
>
>
> On Wed, Oct 18, 2023 at 11:11 PM Chau, Reina <rcha...@bu.edu> 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 <martin.grigo...@gmail.com>
>> wrote:
>>
>> Hi,
>>
>> On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès <hpages.on.git...@gmail.com>
>> 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
>>>
>>> https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/
>>>
>>> for how to debug Linux ARM64 related issues on a x86_64 host.
>>>
>>> Note that different architectures use slightly different floating point
>>> arithmetic with slightly different precision. This can affect the
>>> results of your numerical calculations. The degree to which they are
>>> affected will vary greatly depending on what calculations you perform
>>> and how you perform them. So it's important to implement things in a way
>>>
>>> that tries to minimize the impact of these variations as much as
>>> possible.
>>>
>>
>> See https://go.dev/ref/spec#Floating_point_operators for some further
>> explanation of the problem and possible fix by explicit rounding (in
>> Golang, but I guess something similar happens in R)
>>
>>
>>>
>>> Best,
>>>
>>> H.
>>>
>>>
>>> On 10/18/23 10:46, Chau, Reina wrote:
>>> > 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 (seehttps://
>>> bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/ andhttps://
>>> bioconductor.org/checkResults/devel/bioc-LATEST/CaDrA/kunpeng2-checksrc.html
>>> )
>>> >
>>> > I did try to figure out what is causing the different results using
>>> this particular platform compare with others but with no resolves.
>>> >
>>> > Hope you can give me some guidance or feedback of why the build is
>>> failing for this particular case.
>>> >
>>> > Thanks so much!
>>> >
>>> > Best,
>>> >
>>> > Reina C.
>>> >
>>> > [[alternative HTML version deleted]]
>>> >
>>> > _______________________________________________
>>> > Bioc-devel@r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Bioconductor Core Team
>>> hpages.on.git...@gmail.com
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>
>
[[alternative HTML version deleted]]
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