CelliD

[Cortalak]

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• Repository: https://github.com/RausellLab/CelliD

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[bioc-issue-bot]

Hi @Cortalak

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: CelliD
Type: Package
Title: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
Version: 0.99.0
Authors@R: person("Akira", "Cortal", email = "akira.cortal@institutimagine.org",
  role = c("aut", "cre"))
Description: CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. 
  CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. 
  The package can also be used to explore functional pathways enrichment in single cell data. 
Depends:
    R (>= 4.1),
    Seurat,
    SingleCellExperiment
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
Imports:
    RcppArmadillo,
    stats,
    utils,
    Matrix,
    tictoc,
    scater,
    stringr,
    irlba,
    scales,
    data.table,
    glue,
    pbapply,
    umap,
    Rtsne,
    reticulate,
    fastmatch,
    matrixStats,
    ggplot2,
    Rcpp,
    BiocParallel,
    SummarizedExperiment,
    fgsea (>= 1.15.0)
Suggests:
    knitr,
    rmarkdown,
    BiocStyle,
    testthat,
    tidyverse,
    ggpubr,
    destiny,
    ggrepel
VignetteBuilder: knitr
RoxygenNote: 7.1.1
biocViews: RNASeq, SingleCell, DimensionReduction, Clustering, GeneSetEnrichment, GeneExpression, ATACSeq
LinkingTo: Rcpp, RcppArmadillo

[bioc-issue-bot]

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[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: "ERROR, skipped".
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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b80dcaf651bc21d638644c9415f2f3f15ae5b72c

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b21b60044d13ff180d67b90bf688e3fb60f52f3a

[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: "ERROR, 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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: a19c2b2155a3915d50470130fad3a17b9ad5685c

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Cortalak]

Hello @nturaga,

I had my paper recently accepted for publication in a high impact peer-reviewed journal and we would like to include if possible the Bioconductor URL in the abstract rather than the github one.

I was wondering if I had done all the required steps until the personalized review .
If it is the case, it would help me a lot if I can go through the rest of the procedure as soon as possible.

Thank you very much.

Best regards

Akira

[nturaga]

Hi,

During your package review, I realized I could not build your package on my machine locally.

Please help me get past this error as it is not informative at all. Likely, other users will face the same issue.

Quitting from lines 55-60 (BioconductorVignette.Rmd)
Error: processing vignette 'BioconductorVignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://storage.googleapis.com/cellid-cbl/BaronMatrix.rds'
--- failed re-building ‘BioconductorVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘BioconductorVignette.Rmd’

Error: Vignette re-building failed.
Execution halted

[Cortalak]

Hello,

Sorry, It seems that the billing for our google cloud bucket has expired since the last bioconductor build and the rds object cannot be accessed.
I will try to contact the admin to resolve the problem asap and will let you know when it is done.

Thank you for the feedback.

[nturaga]

You can submit such a data set as an ExperimentHub and use it from there. https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html package You don't have to store it on Google cloud and have the link expire. ExperimentHub will give you a constant link that does not expire. Best, Nitesh

…

On Tue, Feb 16, 2021 at 3:50 PM Cortalak ***@***.***> wrote: Hello, Sorry, It seems that the billing for our google cloud bucket has expired since the last bioconductor build and the rds object cannot be accessed. I will try to contact the admin to resolve the problem asap and will let you know when it is done. Thank you for the feedback. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1845 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAU6QSZ76TW3FDOWU2VKCH3S7LLA7ANCNFSM4V5UEXJQ> .

[Cortalak]

Hello,

We have updated the payment for google cloud and the package should now build normally without any new commit.
We also cosidered ExperimentHub but we might make a few changes on the vignette to use in house data in the future.
We would like if possible to wait for that moment to create a ExperimentHub package and keep the flexibility of our own bucket for now as the paper will be published in 2 - 3 weeks and new issue may arise from new users.

Best regards

Akira

[Cortalak]

Hello,

I was just wondering if the package could now be built on your local machine. Did I do everything needed so that the review process can advance?

Thanks

Akira

[nturaga]

I'll take a look at it today.

…

On Thu, Feb 25, 2021 at 5:14 AM Cortalak ***@***.***> wrote: Hello, I was just wondering if the package could now be built on your local machine. Did I do everything needed so that the review process can advance? Thanks Akira — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1845 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAU6QSZC4NA6HO2Y7B4BRCLTAYPKDANCNFSM4V5UEXJQ> .

[Cortalak]

Hello,

I wanted to know if there is there is any advancement on the review process.
we are now editing the proofs of the manuscript in Nature Biotechnology and would like to include if possible in the paper the bioconductor URL rather than the Github repository.

Thanks

Akira

[nturaga]

Hi, Sorry for the delay. I'll be posting a review today.

[nturaga]

R CMD build

ok

R CMD INSTALL

ok

DESCRIPTION

ok

NAMESPACE

• It seems most functions are exported. Are you sure you need all these functions to be available to the user? If you believe all the functions that are exported are needed, ignore this.

R

• RcppExports.R - ok

• When you use stop() it's smart to use a message within the stop('I'm stopping here because....'), give users some idea of why it stopped since all they see is Error:`. https://github.com/RausellLab/CelliD/blob/master/R/check.R#L62.

man

• The documentation for the functions is not extensive, you can consider improving this.

vignettes

• good

General

• Please replace the google buckets with an annotation hub or data experiment package. It is more stable that way.

[Cortalak]

Hello,

Thank you a lot for the review for the data experiment package do I add the package inquiry here or do I open another issue?
I saw that the package with the dependency must be posted first." Start by submitting the package that can be installed without a dependency on any of the other packages you are submitting (this is usually the experiment data package). "

[nturaga]

Hi,

Have you made the changes to the code in the review? I'm happy to accept your package but you'll have to submit at data experiment package later on probably. I'm ok to allow this since you have a time crunch.

[Cortalak]

Hello,

Thank you very much for this exception, We're almost done with the rest of the changes, we will get back to you as soon as it is done.

Akira

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: aa8fb1c4dbe265885d772646aa7fbd3406dc1016

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 47ef3dda679a536f9c225181bc619d64d490fc4d

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Cortalak]

R CMD build

ok

R CMD INSTALL

ok

DESCRIPTION

ok

NAMESPACE

• It seems most functions are exported. Are you sure you need all these functions to be available to the user? If you believe all the functions that are exported are needed, ignore this.

All functions that are exported must indeed be made available to the user.

R

• When you use stop() it's smart to use a message within the stop('I'm stopping here because....'), give users some idea of why it stopped since all they see is Error:`. https://github.com/RausellLab/CelliD/blob/master/R/check.R#L62.

Added informative message for stops

man

• The documentation for the functions is not extensive, you can consider improving this.

Added more extensive description for each functions especially for core functions such as RunMCA

vignettes

• good

replaced the old github installation process with the one with Biocmanager

[Cortalak]

Hello,

I made the changes to assess the different point of the review.

However right now I fail at the build level when I push my changes.

This is due to one of the core dependencies "Seurat" not installing properly due to their corrupted version 4.0.0.
satijalab/seurat#4226
They have just freshly pushed a new version on CRAN which is 4.0.1 and I forced in my DESCRIPTION file the version 4.0.1. However it seems that Bioconductor build check doesn't recognize the newly created version and only finds the 4.0.0.

Shall I just wait a little bit more and retry to push or is there something else I can do?

Thank you very much for your help

Akira

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1de76388d1d49bd7bd37bc362a97bffd1e552203

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 4baac8af3100e50d367de7ad60dd3e581c4845a2

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: e437a1822a393ef965f27930a6a5def443d2f0bb

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Cortalak]

Hello,

The package was finally able to build without error and now the code adresses the issues in the review apart from the experimenthub package.

It should now be ready.

Akira

[nturaga]

Hi,

You have a new issue you have to fix now,

 Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        hyper.R (line 47, column 30)
        hyper.R (line 56, column 14)
        hyper.R (line 57, column 14)
        hyper.R (line 97, column 30)
        hyper.R (line 106, column 14)
        hyper.R (line 107, column 14)

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: be6c96f19fa58610b29045d5c6d6a84fe4d1461b

[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 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
git@git.bioconductor.org:packages/CelliD to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Cortalak]

Hi,

You have a new issue you have to fix now,

 Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
      Found in files:
        hyper.R (line 47, column 30)
        hyper.R (line 56, column 14)
        hyper.R (line 57, column 14)
        hyper.R (line 97, column 30)
        hyper.R (line 106, column 14)
        hyper.R (line 107, column 14)

The sapply have been changed to vapply in the last commit.

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/Cortalak.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(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("CelliD"). The package 'landing page' will be created at

https://bioconductor.org/packages/CelliD

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.