Polytect: an automatic clustering and labeling method for multi-color digital PCR data

[emmachenlingo]

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• Repository: https://github.com/emmachenlingo/Polytect

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[bioc-issue-bot]

Dear @emmachenlingo,

The package DESCRIPTION must contain valid biocViews.

The following are not valid biocViews terms and should be removed
dPCR
If you would like to request a term be added please email the
[email protected] mailing list and provide details on
why and where in the hierarchy you think it should be added.

Please fix your DESCRIPTION. See current biocViews
Please also remember to run BiocCheck::BiocCheck('new-package'=TRUE) on your package
before submitting a new issue. BiocCheck will look for other
Bioconductor package requirements.

[bioc-issue-bot]

Hi @emmachenlingo

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: Polytect
Title: An R package for digital data clustering
Version: 0.99.0
Authors@R: 
    person("Yao", "Chen", , "[email protected]", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0001-8172-3996"))
Description: An automatic clustering and labeling method for multi-color digital PCR data to classify partitions into groups based on subpopulations generated by flowPeaks.
biocViews: dPCR, Clustering
License: MIT
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Depends: 
    R (>= 3.5.0)
Imports: 
    mvtnorm,
    sn,
    dplyr,
    flowPeaks,
    ggplot2,
    tidyverse,
    cowplot,
    mlrMBO,
    DiceKriging
Suggests: 
    testthat (>= 3.0.0),
    knitr,
    rmarkdown
VignetteBuilder: knitr

[emmachenlingo]

I have changed the biocViews to an existing one. thanks!

[lshep]

When I perform a R CMD build it is ERRORing. Please ensure R CMD build, R CMD check and BiocCheck are run without ERROR, Warning, or Notes

 R CMD build Polytect 
* checking for file 'Polytect/DESCRIPTION' ... OK
* preparing 'Polytect':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from lines 68-81 [flowpeaks and merge] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
could not find function "polytect_clust"
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted

[lshep]

Also...

Could you provide a comparison to existing Bioconductor packages with similar
functionality in the vignette in addition to the generic comparison statement.

Please remove vignette/introduction.pdf and Polytect_manual.pdf. Vignette pdf
and man page compilations are generated automatically when R CMD build is run.