Question

`R CMD check` failure on Linux for compartmap

0

Entering edit mode

martin.grigorov ▴ 10

@6f6493f5

Last seen 10 months ago

Bulgaria

Hi,

The checks of compartmap fail on Linux due to missing Suggest declarations for csaw, BiocStyle and SingleCellExperiment:

* checking data for non-ASCII characters ... WARNING
  Error loading dataset 'k562_scatac_chr14':
   Error in .requirePackage(package) : 
    unable to find required package 'csaw'

  Error loading dataset 'ss3_umi_sce':
   Error in .requirePackage(package) : 
    unable to find required package 'SingleCellExperiment'

  The dataset(s) may use package(s) not declared in Depends/Imports.
* checking data for ASCII and uncompressed saves ... OK
* checking files in "vignettes" ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
scCompartments    81.621  1.832  83.454
getDenoisedMatrix  7.197  0.272   7.468
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in "inst/doc" ... OK
* checking running R code from vignettes ...
  "compartmap_vignette.Rmd" using "UTF-8"... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building "compartmap_vignette.Rmd" using rmarkdown

Quitting from lines 2-16 (compartmap_vignette.Rmd)
Error: processing vignette 'compartmap_vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building "compartmap_vignette.Rmd"

SUMMARY: processing the following file failed:
  "compartmap_vignette.Rmd"

Error: Vignette re-building failed.
Execution halted

I've opened a Pull Request with a fix.

Regards,

Martin

compartmap • 820 views

ADD COMMENT • link 2.3 years ago martin.grigorov ▴ 10

score 0 · Answer 1 · 2023-08-02

0

Entering edit mode

James W. MacDonald 68k

@james-w-macdonald-5106

Last seen 14 hours ago

United States

It tells you what the problem is, in the error message.

Error: processing vignette 'compartmap_vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'

Install BiocStyle.

ADD COMMENT • link 2.3 years ago James W. MacDonald 68k

0

Entering edit mode

Thank you for your response, James!

BiocStyle is installed:

> BiocManager::install("BiocStyle")
Bioconductor version 3.18 (BiocManager 1.30.21.1), R 4.3.1 (2023-06-16)
Old packages: 'PathNetData'
Update all/some/none? [a/s/n]: n
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocStyle'

It is part of the builder setup steps.

But if a dependency does not declare explicitly that it needs it then it is not visible/usable to the package.

See _R_CHECK_SUGGESTS_ONLY_=true for more details.

ADD REPLY • link 2.3 years ago martin.grigorov ▴ 10