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Submission of the new "phenomis" package for postprocessing and univariate analysis of omics data
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/odisce/phenomis
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Hi @ethevenot
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: phenomis
Type: Package
Title: Postprocessing and univariate analysis of omics data
Version: 0.99.0
Date: 2022-06-27
Authors@R: c(
person(given = "Etienne A.", family = "Thevenot",
email = "[email protected]",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-1019-4577")),
person(given = "Natacha", family = "Lenuzza",
email = "[email protected]",
role = "ctb"),
person(given = "Alyssa", family = "Imbert",
email = "[email protected]",
role = "ctb"),
person(given = "Pierrick", family = "Roger",
email = "[email protected]",
role = "ctb"),
person(given = "Eric", family = "Venot",
email = "[email protected]",
role = "ctb"),
person(given = "Sylvain", family = "Dechaumet",
email = "[email protected]",
role = "ctb")
)
Description: The 'phenomis' package provides methods to perform post-processing (i.e. quality control
and normalization) as well as univariate statistical analysis of single and multi-omics data sets.
These methods include quality control metrics, signal drift and batch effect correction,
intensity transformation, univariate hypothesis testing, but also clustering (as well as
annotation of metabolomics data). The data are handled in
the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment
for single and multi-omics datasets, respectively; the alternative ExpressionSet
and MultiDataSet formats are also supported for convenience). As a result, all methods
can be readily chained as workflows. The pipeline can be further enriched by multivariate
analysis and feature selection, by using the 'ropls' and 'biosigner' packages, which support
the same formats. Data can be conveniently imported from and exported to text files. Although
the methods were initially targeted to metabolomics data, most of the methods can be
applied to other types of omics data (e.g., transcriptomics, proteomics).
biocViews:
BatchEffect, Clustering, MassSpectrometry, Metabolomics, Normalization, Proteomics, QualityControl, StatisticalMethod, Transcriptomics
Depends:
SummarizedExperiment
Imports:
Biobase,
biodb,
biodbChebi,
data.table,
futile.logger,
ggplot2,
ggrepel,
graphics,
grDevices,
grid,
htmlwidgets,
igraph,
limma,
methods,
MultiAssayExperiment,
MultiDataSet,
PMCMRplus,
plotly,
ranger,
RColorBrewer,
ropls,
stats,
tibble,
tidyr,
utils,
VennDiagram
Suggests:
BiocGenerics,
BiocStyle,
biosigner,
CLL,
knitr,
omicade4,
rmarkdown,
testthat
VignetteBuilder: knitr
License: CeCILL
Encoding: UTF-8
LazyLoad: yes
URL: https://doi.org/10.1038/s41597-021-01095-3
RoxygenNote: 7.2.0
This is what the first comment was edited with; please create NEW issues to provide your content in response to review.
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.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 0e7fa92c0b54e34f78109d167c72d495782ece84
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5ffdd67e52339656d88cae7f63f4d7a638d75b1b
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7772f461daaef15dcab21a884625b32281802fde
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear Bioconductor Team,
I keep receiving this warning regarding the size of the vignette, although the size I have is 3.3 MB. I do not know why there is a difference (linux vs windows?), what is the actual size of the vignette on your side (the warning only says "above 5MB"), and how I could reduce the size (the vignette does not appear particularly big on my size). I have already reduced the number of figures and their sizes. I would appreciate some help from your side. I thank you very much in advance. Best Regards, Etienne.
Received a valid push on git.bioconductor.org; starting a build for commit id: b440ef267058148d848a32326031bbaa51ae18df
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: c303a9a1d8f42cc84807838182f902184b363470
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: b87ee923c86b1c169cbeaf69d0531278c89dd615
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 34fa0fc669cf8d80c49391b7ef35dac7ed521394
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @ethevenot Please issue a new build report by bumping the version number.
There are many NOTEs you can fix in the build report quite easily.
Review
DESCRIPTION
ok
NAMESPACE
ok
NEWS
ok
vignette
Good!
Tests
Good!
R
-
End user messages as given in the NOTEs on the 'BiocCheck::BiocCheck()' function should be corrected.
-
Good examples cases!
-
BiocCheck complains about the spacing in the code, but you can ignore this. It's well written. If you are able to follow it, that's fine.
-
Lots of "magic numbers" in the function arguments. Be sure to explain why some values are set the way they are as defaults for the arguments.
Received a valid push on git.bioconductor.org; starting a build for commit id: f9707bbf8ef79a00fcf54b573d112e836d130563
Dear Bioconductor reviewer,
We are pleased to submit our revised version of the package in addition to our responses to your comments below.
We thank you in advance for reviewing this revised package and we hope that this new version will now be accepted in Bioconductor.
Etienne Thévenot.
Responses to the comments:
- There are many NOTEs you can fix in the build report quite easily.
The code has been reformatted thoroughly to address all NOTEs. In particular the largest functions have been refactorized, the 80 character line rule was followed in all possible cases, and the messages have been cleaned.
The three remaining NOTES from the 'BiocCheck::BiocCheck()' function are discussed below:
1.1) NOTE: Recommended function length <= 50 lines. There are 69 functions > 50 lines.
All functions larger than 200 lines have been refactorized to facilitate the reading of the code. The longest function has now < 185 lines.
1.2) NOTE: Usage of dontrun{} / donttest{} found in man page examples. 12% of man pages use one of these cases.
There are 4 calls to donttest (2 in the examples from the annotating method and 2 in the examples from the writing method), which are motivated by the following reasons: "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.
1.3) NOTE: Consider shorter lines; 359 lines (3%) are > 80 characters long.
All files were manually parsed to shorten the lines. The remaining lines which are > 80 characters long often result from the usage of the package name in front of the function name to facilitate the reading of the code (package_name::function_name).
- Lots of "magic numbers" in the function arguments. Be sure to explain why some values are set the way they are as defaults for the arguments.
All method/function documentations were checked and completed, e.g. to detail the meaning of parameters or their default values which may be less familiar to people outside the metabolomics/proteomics community (in particular in the 'annotating', 'inspecting', and 'reducing' methods).
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/phenomis to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @lshep / @vjcitn FWIW, I can no longer change the label to "Accepted" on this package.
Please do so. It passes all the checks, and the code is in good standing. I am ready to accept this package.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("phenomis"). The package 'landing page' will be created at
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