OmicGsea R package submission

[xuz1]

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

• Repository: https://github.com/xuz1/OmicGsea

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 @xuz1,

The package DESCRIPTION must contain valid biocViews.

The following are not valid biocViews terms and should be removed
GeneOntology, MSigDB, Geneexpression
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 @xuz1

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: OmicGsea
Type: Package
Title: Geneset Enrichment Analysis for Complex Omics Data
Version: 0.99.0
Authors@R:
  c(person("Zongli","Xu",email="[email protected]",role=c("cre","aut")),
   person("Alison","Motsinger-Reif",email="[email protected]",role="aut"),
    person("Liang", "Niu", role="aut",email="[email protected]"))
Description: OmicGsea R Package utilizing efficient methods that account for complex relationships in omics datasets, including probe correlations and varying probe counts per gene. This package supports the analysis of DNA methylation, gene expression, copy number variation (CNV), and other genomic data across multiple species.
License: Artistic-2.0
biocViews: GeneSetEnrichment, Pathways, Gene Ontology, KEGG, MSigDB, 
        DNA Methylation, Gene expression, Microarray
Depends: utils,stats,parallel,Matrix
Suggests: msigdbr, org.Hs.eg.db, org.Mm.eg.db, minfi, knitr, rmarkdown, GO.db
Imports:  dqrng,AnnotationDbi,poolr,BiasedUrn
VignetteBuilder: knitr
Encoding: UTF-8
URL: https://github.com/Bioconductor/OmicGsea
BugReports: https://github.com/Bioconductor/OmicGsea/issues
git_url: https://git.bioconductor.org/packages/OmicGsea
NeedsCompilation: no

[xuz1]

I fixed all bugs, could you move it forward to submit it to biocondoctor. Thanks.

[lshep]

Why not use the KEGGREST package to retrieve information?

If you are downloading files from the internet, you should use a caching mechanism so that the package can still be used if the serve is down or offline (see BiocFileCache).

Also when running check I get the following ERROR. All dependencies that are needed to run should be listed as suggests in the package description.

> ### ** Examples
> 
> anno=getIlluminaAnnotation(arrayType="EPIC")
Error in getIlluminaAnnotation(arrayType = "EPIC") : 
  IlluminaHumanMethylationEPICanno.ilm10b4.hg19 required but not installed
Execution halted

Could you expand your vignette introduction to include a comparison to the existing packages for enrichment analysis. There are currently many package in Bioconductor so emphasizing what makes your unique and a comparison to existing will be necessary.

Your vignette does not meet Bioconductor standards. Trying to cheat the system by making the sections eval=TRUE and then putting all the runnable code in an eva=FALSE conditional is not acceptable. Please run all code.