CelliD #1845

Cortalak · 2021-01-11T14:20:58Z

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bioc-issue-bot · 2021-01-11T14:20:59Z

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 · 2021-01-15T21:17:47Z

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bioc-issue-bot · 2021-01-15T21:32:54Z

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 · 2021-01-18T15:21:03Z

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

bioc-issue-bot · 2021-01-19T13:54:55Z

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 · 2021-01-20T09:54:19Z

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

bioc-issue-bot · 2021-01-20T10:51:22Z

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 · 2021-01-20T12:29:35Z

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

bioc-issue-bot · 2021-01-20T13:10:06Z

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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

Cortalak · 2021-02-08T12:27:25Z

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 · 2021-02-16T19:34:44Z

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 · 2021-02-16T20:50:08Z

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 · 2021-02-16T22:00:54Z

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 · 2021-02-17T09:17:37Z

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 · 2021-02-25T10:14:43Z

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 · 2021-02-25T20:30:40Z

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 · 2021-03-09T10:56:29Z

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 · 2021-03-12T18:31:55Z

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

nturaga · 2021-03-12T20:37:47Z

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 · 2021-03-17T11:10:54Z

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 · 2021-03-17T13:07:57Z

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 · 2021-03-17T13:21:45Z

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 · 2021-03-18T14:21:30Z

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

bioc-issue-bot · 2021-03-18T14:25:23Z

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 · 2021-03-18T15:38:01Z

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

bioc-issue-bot · 2021-03-18T15:43:03Z

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 · 2021-03-18T16:08:37Z

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 · 2021-03-18T16:19:16Z

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 · 2021-03-19T09:24:05Z

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

bioc-issue-bot · 2021-03-19T09:55:34Z

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 · 2021-03-19T17:42:51Z

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

bioc-issue-bot · 2021-03-19T18:09:48Z

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 · 2021-03-22T08:08:39Z

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

bioc-issue-bot · 2021-03-22T11:33:11Z

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 · 2021-03-22T15:29:45Z

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 · 2021-03-23T17:20:26Z

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 · 2021-03-23T19:24:55Z

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

bioc-issue-bot · 2021-03-23T20:00:55Z

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 · 2021-03-23T20:16:53Z

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 · 2021-03-26T18:06:41Z

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

Thank you for contributing to Bioconductor!

vjcitn · 2021-03-30T10:13:43Z

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:

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.

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Jan 11, 2021

bioc-issue-bot added 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place and removed 1. awaiting moderation submitted and waiting clearance to access resources labels Jan 15, 2021

bioc-issue-bot assigned nturaga Jan 15, 2021

bioc-issue-bot added the ERROR label Jan 15, 2021

bioc-issue-bot added the TIMEOUT label Jan 20, 2021

bioc-issue-bot added OK and removed TIMEOUT ERROR labels Jan 20, 2021

bioc-issue-bot added ERROR and removed OK labels Mar 18, 2021

bioc-issue-bot added OK and removed ERROR labels Mar 22, 2021

nturaga added 3a. accepted will be ingested into Bioconductor daily builder for distribution and removed 2. review in progress assign a reviewer and a more thorough review of package code and documentation taking place labels Mar 26, 2021

vjcitn closed this as completed Mar 30, 2021

CelliD #1845

CelliD #1845

Comments

Cortalak commented Jan 11, 2021

bioc-issue-bot commented Jan 11, 2021

bioc-issue-bot commented Jan 15, 2021

bioc-issue-bot commented Jan 15, 2021

bioc-issue-bot commented Jan 18, 2021

bioc-issue-bot commented Jan 19, 2021

bioc-issue-bot commented Jan 20, 2021

bioc-issue-bot commented Jan 20, 2021

bioc-issue-bot commented Jan 20, 2021

bioc-issue-bot commented Jan 20, 2021

Cortalak commented Feb 8, 2021 • edited Loading

nturaga commented Feb 16, 2021

Cortalak commented Feb 16, 2021

nturaga commented Feb 16, 2021 via email

Cortalak commented Feb 17, 2021 • edited Loading

Cortalak commented Feb 25, 2021

nturaga commented Feb 25, 2021 via email

Cortalak commented Mar 9, 2021

nturaga commented Mar 12, 2021

nturaga commented Mar 12, 2021

R CMD build

R CMD INSTALL

DESCRIPTION

NAMESPACE

R

man

vignettes

General

Cortalak commented Mar 17, 2021

nturaga commented Mar 17, 2021

Cortalak commented Mar 17, 2021

bioc-issue-bot commented Mar 18, 2021

bioc-issue-bot commented Mar 18, 2021

bioc-issue-bot commented Mar 18, 2021

bioc-issue-bot commented Mar 18, 2021

Cortalak commented Mar 18, 2021 • edited Loading

R CMD build

R CMD INSTALL

DESCRIPTION

NAMESPACE

R

man

vignettes

Cortalak commented Mar 18, 2021 • edited Loading

bioc-issue-bot commented Mar 19, 2021

bioc-issue-bot commented Mar 19, 2021

bioc-issue-bot commented Mar 19, 2021

bioc-issue-bot commented Mar 19, 2021

bioc-issue-bot commented Mar 22, 2021

bioc-issue-bot commented Mar 22, 2021

Cortalak commented Mar 22, 2021

nturaga commented Mar 23, 2021

bioc-issue-bot commented Mar 23, 2021

bioc-issue-bot commented Mar 23, 2021

Cortalak commented Mar 23, 2021

bioc-issue-bot commented Mar 26, 2021

vjcitn commented Mar 30, 2021

Cortalak commented Feb 8, 2021 •

edited

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Cortalak commented Feb 17, 2021 •

edited

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Cortalak commented Mar 18, 2021 •

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