[Bioc-devel] Build error for CaDrA package on kunpeng2 Linux machine
Martin Grigorov
m@rt|n@gr|gorov @end|ng |rom gm@||@com
Fri Oct 20 14:51:47 CEST 2023
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 to replace the "manual" calculations with fma() [2] or
disable it at compile time
1. https://accurate-algorithms.readthedocs.io/en/latest/ch03fma.html
2. https://www.oreilly.com/library/view/c-in-a/0596006977/re80.html
Martin
On Thu, Oct 19, 2023 at 4:49 PM Chau, Reina <rchau88 using bu.edu> wrote:
> 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 <martin.grigorov using gmail.com>
> wrote:
>
> 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 using kunpeng2 ~/g/CaDrA (devel)> git log -1
> commit ae6513e0877d5866fc8240eb123b8bc83af73e19 (HEAD -> devel,
> origin/master, origin/devel, origin/HEAD)
> Author: RC-88 <lilychau999 using 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 <rchau88 using 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.grigorov using gmail.com>
>> wrote:
>>
>>
>>
>> On Wed, Oct 18, 2023 at 11:11 PM Chau, Reina <rchau88 using 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.grigorov using gmail.com>
>>> wrote:
>>>
>>> Hi,
>>>
>>> On Wed, Oct 18, 2023 at 10:48 PM Hervé Pagès <hpages.on.github using 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 using r-project.org mailing list
>>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>> --
>>>> Hervé Pagès
>>>>
>>>> Bioconductor Core Team
>>>> hpages.on.github using gmail.com
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>
>>
>
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