[Bioc-devel] R CMD check testthat failure in tokay2 (devel branch)

[Pages, Herve]

Hi Benjamin,

Sorry for the late answer. Looks like things have changed a little bit on the report since your original post. What I see on today's report is a test failure on Windows for the i386 arch only:

  https://bioconductor.org/checkResults/3.9/bioc-LATEST/universalmotif/tokay2-checksrc.html

The universalmotif.Rcheck/tests_i386/testthat.Rout.fail file is:

R version 3.6.0 beta (2019-04-12 r76385) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(universalmotif)
>
> test_check("universalmotif")
-- 1. Error: viewing motif stacks works (@test_view_motifs.R#39)  --------------
could not find function "merge_motifs_get_offset"
1: view_motifs(c(m1, m2)) at testthat/test_view_motifs.R:39
2: lapply(seq_along(mot.mats)[-1], function(x) {
       y <- merge_motifs_get_offset(mot.mats[[1]], mot.mats[[x]], method, min.overlap,
           mot.ics[[1]], mot.ics[[x]], min.mean.ic, normalise.scores)
       merge_add_cols(y)
       y
   })
3: FUN(X[[i]], ...)

== testthat results  ===========================================================
OK: 193 SKIPPED: 2 FAILED: 1
1. Error: viewing motif stacks works (@test_view_motifs.R#39)

Error: testthat unit tests failed
Execution halted


I'm not sure why the merge_motifs_get_offset() function cannot be found when R is running in i386 mode. I see that merge_motifs_get_offset() is implemented in C++ and integrated to the universalmotif package using the Rcpp machinery (with RcppExports.cpp and RcppExports.R files). The package also uses a top-level Makefile and a src/Makevars file. Overall this looks like a relatively complicated setup. Could it be that the issue with the unit test is somehow related to some subtle issue with this setup? Unfortunately I'm not familiar with the Rcpp/RcppExports.cpp/RcppExports.R machinery so I'm not able be provide more help, sorry. Hopefully someone on the list with more experience will be able to help.

Unlikely to be related but FWIW I noted that "[[: not found" is displayed during installation:

  https://bioconductor.org/checkResults/3.9/bioc-LATEST/universalmotif/tokay2-install.html

(once during the "install for i386" step and once during the "install for x64" step). Don't know if that's something that you should worry about or not though...

Best,
H.


On 4/9/19 12:31, Benjamin Tremblay wrote:

Hi,

R CMD check on the tokay2 machine fails due to an error in running tests from testthat in the devel branch of my package universalmotif with no indication as to why. Here is the output from R CMD check:

* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(universalmotif)
  >
  > test_check("universalmotif")
  == testthat results  ===========================================================
  OK: 211 SKIPPED: 1 FAILED: 0
** running tests for arch 'x64' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
And here is the testthat.Rout.fail file:

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.



library(testthat)
library(universalmotif)

test_check("universalmotif")


== testthat results  ===========================================================
OK: 211 SKIPPED: 1 FAILED: 0
Is there any way for me to know what is going on?

Thanks,

Benjamin Tremblay
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