CCAFE

[wolffha]

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

• Repository: https://github.com/wolffha/CCAFE

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

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

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

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

• 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.

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

• 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.

• 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:

• The 'devel' branch for new packages and features.
• The stable 'release' branch, made available every six
  months, for bug fixes.
• 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]

Hi @wolffha

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: CCAFE
Type: Package
Title: Case Control Allele Frequency Estimation
Version: 0.99.0
Authors@R: c(person("Hayley", "Wolff", email = "[email protected]", role = c("cre", "aut")))
Description: Functions to reconstruct case and control AFs from summary statistics. 
    One function uses OR, NCase, NControl, and SE(log(OR)). 
    The second function uses OR, NCase, NControl, and AF for the whole sample. 
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.2
Imports: 
    dplyr
Depends: 
    R (>= 4.4.0)
Suggests: 
    testthat (>= 3.0.0),
    rmarkdown,
    markdown,
    knitr,
    tidyverse,
    DescTools,
    cowplot
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://github.com/wolffha/CCAFE/
BugReports: https://github.com/wolffha/CCAFE/issues
biocViews: GenomeWideAssociation, ComparativeGenomics, Genetics, Preprocessing, SNP, Software, WholeGenome

[lshep]

We prefer to have a clean upload to Bioconductor. Please remove pkgdown/docs
directories from default branch until uploaded to Bioconductor.

We like to see interopability with standard Bioconductor
classes. If no direct interaction with a class structure is appropriate please
show how this can be utilized in a Bioconductor pipeline to be used in
correlation with other packages.

All dependencies must be on CRAN or Bioconductor. Currently when I try to build
the package

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

--- re-building ‘CCAFE_Extra_Details.Rmd’ using rmarkdown
--- finished re-building ‘CCAFE_Extra_Details.Rmd’

--- re-building ‘CaseControlAF.Rmd’ using rmarkdown

Quitting from lines 198-200 [unnamed-chunk-4] (CaseControlAF.Rmd)
Error: processing vignette 'CaseControlAF.Rmd' failed with diagnostics:
there is no package called 'CaseControlAF'
--- failed re-building ‘CaseControlAF.Rmd’

--- re-building ‘CaseControlAF_Extra_Details.Rmd’ using rmarkdown

Quitting from lines 39-43 [unnamed-chunk-2] (CaseControlAF_Extra_Details.Rmd)
Error: processing vignette 'CaseControlAF_Extra_Details.Rmd' failed with diagnostics:
there is no package called 'CaseControlAF'
--- failed re-building ‘CaseControlAF_Extra_Details.Rmd’

SUMMARY: processing the following files failed:
  ‘CaseControlAF.Rmd’ ‘CaseControlAF_Extra_Details.Rmd’

Error: Vignette re-building failed.
Execution halted