(inactive) mixOmics

[mixOmicsTeam]

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

• Repository: https://github.com/mixOmicsTeam/mixOmics/tree/BioC/mixOmics Please note that we have 3 branches.
  • Master is the current mixOmics package on CRAN.
  • Devel is the version in development
  • BioC is the branch we are submitting to Bioconductor

mixOmics has been on CRAN since 2009 and we finally decided to convert to bioC. It is a big move for us and we are aware that our current submission needs further improvements. We hope to be able to stage some of our developments gradually. The future improvements we envisage in particular are to set up setGeneric and setMethods functions to fit in MultiAssayExperiments. We have not been successful so far and we need more time. We hope that mixOmics will benefit the bioC community and attract more users! You can see our engagement and commitment with the computational biology community at www.mixOmics.org

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.

• [see below] 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.

Please note the following:

• R CMD check --as-cran gives 3 NOTES, all OK for bioconductor
  • R CMD BiocCheck gives:
  • 1 ERROR (remove package from CRAN as our package still needs to be live on CRAN
  • 1 WARNING: that we cannot address because it's relative to when we use the cpus argument in some of our functions, let me know if there is a work around this
• 4 NOTES: those include unit tests and aesthetics of the code. Our package includes > 100 R functions and we are unsure how to implement the unit tests at this stage. We welcome any feedback from you.

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

Yes! see www.mixOmics.org, mixOmics is an R toolkit for omics data integration.

• [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.

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 help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Dear @mixOmicsTeam ,

I could not find a DESCRIPTION file in the default branch of the GitHub repository at https://github.com/mixOmicsTeam/mixOmics . This repository should contain an R package.

I am closing this issue. Please try again with a new issue.