[Bioc-devel] Testing the srnadiff package with R CMD check takes lots of time

[Matthias Zytnicki]

Dear Vincent,


I thank you very much for your help.


I never had this "subscript out of bounds" error, and the BioC testing platform either.

Yet, as you suggested, solving this problem (which I still do not exactly know how to reproduce) could maybe solve the other problem as an unexpected but lucky side-effect?


Thanks again,


Matthias.

________________________________
From: Vincent Carey <stvjc using channing.harvard.edu>
Sent: Thursday, December 19, 2024 5:13:17 PM
To: Matthias Zytnicki
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] Testing the srnadiff package with R CMD check takes lots of time

I tried running your tests (checked out from github repo at

commit e580d52d7242693b79ec6b8483d68a65d6fb9e02 (HEAD -> master,
origin/master, origin/HEAD)
Author: Matthias Zytnicki <matthias.zytnicki using inra.fr>
Date:   Mon Mar 6 21:35:41 2023 +0100

    version bump

and ran into some serious issues -- a very long stream of

> test_that("Running implemented constructor", {
+     object <- srnadiffExp(bamFiles, sampleInfo, annotReg)
+     expect_is(object, "srnadiffExp")
+  .... [TRUNCATED]
── Warning: Running implemented constructor
────────────────────────────────────────────────────────────────────────────
subscript out of bounds (index 1 >= vector size 1)
Backtrace:
    ▆
 1. └─srnadiff::srnadiffExp(bamFiles, sampleInfo, annotReg) at
test_AllClass.R:21:5
 2.   └─srnadiff:::computeNormFactors(object using coverages)
 3.     └─srnadiff:::rcpp_normalization(cvg, librarySize)

── Warning: Running implemented constructor
────────────────────────────────────────────────────────────────────────────
subscript out of bounds (index 2 >= vector size 1)
Backtrace:
    ▆
 1. └─srnadiff::srnadiffExp(bamFiles, sampleInfo, annotReg) at
test_AllClass.R:21:5
 2.   └─srnadiff:::computeNormFactors(object using coverages)
 3.     └─srnadiff:::rcpp_normalization(cvg, librarySize)

Admittedly this is not the right environment to reproduce what you are
seeing but
perhaps it is somewhat helpful.  Have you tried running the tests in
the bioc BBS container?
see https://github.com/bioconductor/bioconductor_salt/pkgs/container/bioconductor_salt

R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;
 LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] srnadiff_1.19.2 testthat_3.2.2  rmarkdown_2.29

loaded via a namespace (and not attached):
  [1] later_1.4.1                 BiocIO_1.16.0
  [3] bitops_1.0-9                filelock_1.0.3
  [5] tibble_3.2.1                XML_3.99-0.17
  [7] rpart_4.1.23                startup_0.23.0


On Mon, Dec 2, 2024 at 3:13 PM Matthias Zytnicki
<matthias.zytnicki using inrae.fr> wrote:
>
> Dear everyone,
>
>
> I have difficulties trying to decrease the time spent to check my package, srnadiff (for reproducibility, you can get the GitHub repo from https://github.com/mzytnicki/srnadiff, on the devel branch).
>
>
> I tried to reduce the tests to 2 files (for reproducibility: test_annotation.R and test_pvalues.R).
>
>
> When I use devtools::check(), the "checking tests" step takes 29 minutes.  With all the files, it takes more than one hour. Same goes with R CMD check on the built package. On the BioC check platform, it reaches the time limit.
>
>
> When I use devtools::test(), the same tests takes 8 seconds.
>
>
> Now, on the computer of my colleague, trying to reproduce the BioC environment variables, the whole devtools::check takes a few minutes.
>
>
> I am puzzled by the discrepancy, and would like to reduce this time.
>
> Does anyone have a suggestion about how I could proceed?
>
>
> I used profvis with the command  p <- profvis::profvis({foo <- devtools::check()})
>
> It seems that most of the time is spent on ".Call" (with no other sub-function called), and I cannot interpret this.
>
>
> I thank you very much for your help.
>
>
> Best regards,
>
>
> Matthias.
>
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>
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