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2 years ago Dear @ethevenot,
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ethevenot
Dear Bioconductor team,
Please find below the GitHub link to the "phenomis" package that we would like to submit to Bioconductor.
The package provides methods for the post-processing (quality control, normalization), univariate hypothesis testing, clustering, and annotation of omics single or multiple datasets. It is mainly focused on metabolomics data but applications to proteomics and transcriptomics data are described in the vignette.
The package complements the "ropls" and "biosigner" Bioconductor packages, which focus on downstream multivariate analysis and feature selection. These 3 packages therefore enables to design comprehensive statistical and annotation workflows, as described in the vignette for single and multiple omics data sets. All of these 3 packages support the SummarizedExperiment and MultiAssayExperiment formats, but also the ExpressionSet and MultiDataSet formats.
We thank you in advance for reviewing the package.
Best Regards,
Etienne.
The remaining notes from the checks are commented below:
I. R CMD check: 1 note
1) N checking for non-standard things in the check directory Found the following files/directories: 'met_dataMatrix.tsv' 'met_sampleMetadata.tsv' 'met_variableMetadata.tsv' 'metabo' 'pro_dataMatrix.tsv' 'pro_sampleMetadata.tsv' 'pro_variableMetadata.tsv' 'prometis'
This files/directories are generated in the examples of the "writing" method (note that the \dontrun{} has been modified to \donttest{} according to the Bioconductor guidelines).
II. R CMD BiocCheck: 8 notes
1) NOTE: Consider adding these automatically suggested biocViews: Sequencing, Coverage, KEGG
"BatchEffect" has been included as previously suggested. These remaining suggestions, however, are not relevant.
2) NOTE: Avoid 'cat' and 'print' outside of 'show' methods
There is no call to 'cat'. The very few calls to 'print' provide useful summaries which cannot be provided by the 'message' function.
3) NOTE: Avoid the use of 'paste' in condition signals
The very few uses of 'paste' provide the users with useful hints to address the raised issues.
4) NOTE: Recommended function length <= 50 lines.There are 56 functions > 50 lines.
We did our best to shorten the function code.
5) NOTE: Usage of dontrun{} / donttest{} found in man page examples.12% of man pages use one of these cases.
Annotating examples requiring to query the ChEBI database may take about 1 min and fail if the database is unavailable for some reason. In addition, examples with the "writing" method have been flagged with 'donttest' to avoid writing on the user file disk.
6) NOTE: Consider shorter lines; 830 lines (7%) are > 80 characters long.
Again, we did our best to follow this recommendation.
7) NOTE: Consider multiples of 4 spaces for line indents; 5006 lines (44%) are not.
I must admit that I am used to the 2 spaces which I find provides a clear view of the indentations (and is the default with RStudio). Because I do not think that there is an automated way to swith all the code to 4 spaces, I would prefer to stick to this display in the package if possible
8) NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials).
I am member of the Bioc-Devel mailing list as a maintainer of the ropls and biosigner Bioconductor packages.
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
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[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.
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