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

[emmachenlingo]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

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

Confirm the following by editing each check box to '[x]'

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

• [x] I am familiar with the Bioconductor code of conduct and agree to abide by it.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

[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 bioc-devel@r-project.org 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", , "emmachentar@live.com", 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.