omicRexposome

[carleshf]

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• Repository: https://github.com/isglobal-brge/omicRexposome

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[bioc-issue-bot]

Hi @carleshf

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: omicRexposome
Title: Exposome and omic data associatin and integration
Version: 0.99.2
Authors@R: c(person("Carles", "Hernandez-Ferrer", , "carles.hernandez@isglobal.org", c("aut", "cre")),
    person("Juan R.", "González", ,"juanr.gonzalez@isglobal.org", role = "aut"))
Maintainer: Carles Hernandez-Ferrer <carles.hernandez@isglobal.org>
Description: What the package does (one paragraph).
License: MIT
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Depends:
    R (>= 3.0),
    Biobase
Imports:
    rexposome,
    snpStats,
    limma,
    sva,
    ggplot2,
    ggrepel,
    PMA,
    omicade4,
    ggplot2,
    qqman,
    gridExtra
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    BRGEdata

[mtmorgan]

The Description: field is incomplete and the vignette contains a few commands with little text -- are you sure your package is ready for submission?

[carleshf]

I've just pushed several changes (+ version bump) according to this last comment.

But I do not see any message here with each one of the commits (in the other package, rexposome I see here the commits I did). Is that usual?

[carleshf]

Dear @mtmorgan ,

I do not understand what is happening here. As you can see, the webhood is properly set:

But any one of the commits done to the repository has an effect in this issue. What can I do?

C.

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[mtmorgan]

I think the package was still in the 'waiting moderation' stage so that the commits were being ignored. It should build now.

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170419091943.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

b2bca28 Test BioC issue

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170419095814.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

92c55e1 Updated doc. Updated documentation and examples ...

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170419120348.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

8e5467b Update examples Updated examples that crashed dur... 30cd270 Improved example in 'assocES'

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170419143539.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

0e92ac3 Validated warnings. Only one BioC warning should ...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170419145803.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

4ef2ed4 Full update of NAMESPACE Properly generation of '...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170419153230.html

[mtmorgan]

Sorry for my very slow review

DESCRIPTION, NAMESPACE

• Spell check this and all documents.
• For the Description: field, provide a more extensive description of what the package does. Mention if there are other similar packages.
• Review the biocViews terms, for instance 'tatisticalMethod' is not a term.

vignette

• generally good
• No need for the html version of the vignette to be under version control; remove it.
• Use standard Biocondcutor installation instructions rather than devtools; biocLite() installs dependencies so update this sentence.
• include a final code chunk with sessionInfo().

R

• Biobase::ExpressionSet() is being replaced by SummarizedExperiment; consider updating your code to accept either.
• spell check warning and error messages, e.g., 'No samles in common...'
• avoid using @ for slot access; write (internal-only) plain-old functions as accessors.

• avoid highly nested calls, e.g.,

  res <- data.frame(do.call(rbind, lapply(1:length(names(object)), function(ii) {

  which are hard to read and debug.

data / extdata

• the size of the data objects mean that the package exceeds Biocondcutor guidelines (package size no more than 4MB); create more modes example data or separate the data as an Experiment data package (with vignette) and add as an 'Additional package'
• verify that the data in inst/extdata is actually used in your package

man

• provide more extensive documentation for the exp_r, gexp_r, and other data objects, indicating what data it represents, how it was created, what the most important features of it are.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

dd20a9e Added 'show.effect'.

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170515134641.html

[mtmorgan]

Looks like your package is not building; so I take it this is still a work in progress...?

[carleshf]

Dear @mtmorgan ,

I'm currently working on the rexposome review (that is a bit extensive). Since rexposome is a dependence of omicRexposome (and I'm moving some function from one to the other) I thin that is better if I finish the changes on rexposome before going to omicRexposome. Is it fine?

[mtmorgan]

Yes, please be sure when your revisions to omicRexposome are complete to post a summary here, so that I know to continue my review.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

51c9b17 Solved type in crossomics. 86bd1e9 Updated plotIntegration + vignette 8f7f675 Updated omicRexposome - documentation, examples an...

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170717084643.html

[carleshf]

AdditionalPackage: https://github.com/isglobal-brge/brgedata

[bioc-issue-bot]

Hi @carleshf,

Starting build on additional package https://github.com/isglobal-brge/brgedata.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your additional package repository will NOT trigger a new build.

The DESCRIPTION file of this additional package is:

Package: BRGEdata
Title: Exposures, Gene Expression and Methylation data for ilustration purpouses
Version: 0.0.91
Authors@R: c(person("Carlos", "Ruiz-Arenas", email = "carlos.ruiz@isglobal.org", role = c("aut", "cre")),
person("Carles", "Hernandez-Ferrer", email = "carles.hernandez@isglobal.org", role = "aut"),
person("Juan R.", "Gonzalex", email = "juanr.gonzalez@isglobal.org", role = "aut"))
Description: This package contains seeveral sets of omics data including Gene 
Expression (ExpressionSet), Methylation (MethylationSet) and loss of Y data. 
This data is used in vignettes and exaples at MEAL, snpFier, MADloy and 
omicRexposome.
Depends: R (>= 3.4),
Biobase,
MultiDataSet
Imports: SummarizedExperiment
Suggests: rexposome,
minfi,
MultiAssayExperiment
License: MIT
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/brgedata_buildreport_20170717095139.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

7dbb85f Version bump.

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170717095434.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

46794d4 Removed LOY datasets. Checked description.

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/brgedata_buildreport_20170718102200.html

[carleshf]

Dear @mtmorgan ,

We are having some troubles to understand what is happening with the additional experimental package (BRGEdata). We have seen in the build-report that PackageFileSize: -1.00 KiB. This is strange since it contains several completed omic data-sets.

We used the lfs feature from GitHub to store this package, could this be the root of the problem? If yes, can you provide us with instructions to properly deploy the package in Bioconductor's testing servers?

Kind regards, C.

[mtmorgan]

Yes this looks like a problem on our end; we'll investigate.

[mtmorgan]

Can you please increment the version of your package, to trigger a new build?

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

ce17dbd solved bug when null model selected for associatio...

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170819174341.html

[mtmorgan]

remember that only CRAN and Bioconductor dependencies are allowed.

[carleshf]

Dear @mtmorgan,

Follows my comments on omicRexposomereview (also about the last fail in the build).

DESCRIPTION, NAMESPACE

• Spell check this and all documents.

I spell checked all the documents.

• For the Description: field, provide a more extensive description of what the package does. Mention if there are other similar packages. Review the biocViews terms, for instance 'tatisticalMethod' is not a term.

I updated the description of the package. Follows current one:

omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

I also updated the biocViews section. The new selected terms are: WorkflowStep, MultipleComparison, Visualization, GeneExpression, DifferentialExpression, DifferentialMethylation, GeneRegulation, Epigenetics, Proteomics, Transcriptomics, StatisticalMethod, Regression

vignette

• generally good
• No need for the html version of the vignette to be under version control; remove it.

The HTML version was removed.

• Use standard Bioconductor installation instructions rather than devtools; biocLite() installs dependencies so update this sentence. include a final code chunk with sessionInfo().

I do not know the time where I should change from devtools to biocLite since the package is still in ISGlobal GitHub repository.

As you suggested I change this line.

I also added the sessionInfo() at the end of the vignette.

R

• Biobase::ExpressionSet() is being replaced by SummarizedExperiment; consider updating your code to accept either.

Changed assocES to association and updated crossomics Now they work on MultiDataSet objects, that can store both eSet-like and SummarizedExperiment-like objects.

• spell check warning and error messages, e.g., 'No samles in common...'

I think I spell checked all the messages and warnings.

• avoid using @ for slot access; write (internal-only) plain-old functions as accessors.

As suggested I removed most all used of @. I keep three:

1. I keep one occurrence in getIntegration, since its usage is in the implementation of a getter.

2. Two occurrences in the two integration methods that ensure the name of a list stored in ResultSet.

   • avoid highly nested calls, e.g.,

     res <- data.frame(do.call(rbind, lapply(1:length(names(object)), function(ii) {

     which are hard to read and debug.

I updated some functions to avoid this highly nested calls: plot_integration_mcca and snpToContinuous.

data / extdata

• The size of the data objects mean that the package exceeds Biocondcutor guidelines (package size no more than 4MB); create more modes example data or separate the data as an Experiment data package (with vignette) and add as an 'Additional package' verify that the data in inst/extdata is actually used in your package

We have created an experiment package called BRGEdata that contains the different omic data-sets and the exposome-set used by omicRexosome and MEAL package.

Then three new objects were created and save in omicRexposome, to be used in methods' examples.

man

provide more extensive documentation for the exp_r, gexp_r, and
other data objects, indicating what data it represents, how it was
created, what the most important features of it are.

All the data-sets were removed and moved to BRGEdata experimental data package. Unfortunately, I still don't know how to properly link the LFS repository to this issue.

Then minimal data-sets were generated and included in omicRexposome (asr, mds, crs) for example purposes.

Checks

Result of R CMD check

R CMD check results
0 errors | 1 warning  | 0 notes

R CMD check succeeded

[mtmorgan]

I think the lfs issue on our end is solved, and the the data package requires a version bump.

[mtmorgan]

Not sure where we stand on this? I think BRGEdata needs a version bump to trigger a build.

[mtmorgan]

Any update, or shall I close this issue?

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

548b308 Updated version

[bioc-issue-bot]

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: "skipped, TIMEOUT, 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 following build report for more details:

http://bioconductor.org/spb_reports/brgedata_buildreport_20170909133728.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

b0e6804 Removed methy samples. Updated BRGEdata.R.

[bioc-issue-bot]

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: "skipped, 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 following build report for more details:

http://bioconductor.org/spb_reports/brgedata_buildreport_20170922140232.html

[carleshf]

Dear @mtmorgan ,

I updated the BRGEdata package, making it a bit less heavy. but, unfortunately, I think it sill not being clone properly.

When looking at the build report I see that its size is -1.00 KiB:

Package: brgedata
--
Version: 0.99.3
RVersion: 3.4
BiocVersion: 3.6
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data brgedata
BuildTime: 4 minutes 37.84 seconds
CheckCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R  CMD check --no-vignettes --timings  --no-multiarch  None  &&   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD  BiocCheck --build-output-file=R.out --new-package None
CheckTime: 0 minutes 0.39 seconds
BuildBinCommand: /Users/pkgbuild/packagebuilder/workers/build-universal.sh None libdir
BuildBinTime: 0 minutes 0.81 seconds
Status: skipped
PackageFile:
PackageFileSize: -1.00 KiB
BuildID:: brgedata_20170922175419
PreProcessing: Accessing  git_info. Starting Git clone. Installing dependencies. Installing  package: brgedata. Starting Build package. Starting Check package.  Starting Build package.
PostProcessing: Accessing  git_info complete. Finished Git clone. Installing dependency status: 0.  Installing package status: 0. Build Package status: 0. Checking Package  status: 1. Build Package status: 1.
InstallCommand:      source("http://bioconductor.org/scratch-repos/pkgInstall.R")

Both omicRexposome and BRGEdata passes standard R CMD check and BiocCheck locally.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

fab7171 Updated association to also include SVA pipeline... ba75623 Updated SVA Now "association" implements isva (fa...

[bioc-issue-bot]

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: "skipped, TIMEOUT". 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 following build report for more details:

http://bioconductor.org/spb_reports/omicRexposome_buildreport_20170928083715.html

[mtmorgan]

Thanks for your revisions; I think the timeout is not important for the package review process, and I'll mark this package as 'accepted'.