xanibas commented 3 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/xanibas/granulator

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[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.
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bioc-issue-bot commented 3 years ago

Hi @xanibas

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: granulator
Type: Package
Title: Granulator: Rapid benchmarking of methods for in silico deconvolution of bulk RNA-seq data 
Version: 0.99.0
Authors@R: 
  c(person(given = "Sabina",
 family = "Pfister",
 role = c("aut", "cre"),
 email = "sabina.pfister@novartis.com"),
    person(given = "Vincent",
 family = "Kuettel",
 role = "aut"),
    person(given = "Enrico",
 family = "Ferrero",
 role = "aut"))
Description: granulator is an R package for the estimation of cell type proportions from heterogeneous tissues 
    based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing 
    interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution 
    of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.
Depends: R (>= 4.0)
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown
VignetteBuilder: knitr
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
biocViews: RNASeq, GeneExpression, DifferentialExpression, Transcriptomics, StatisticalMethod, Regression
Imports: 
    stats, 
    dplyr, 
    tidyr,
    purrr, 
    tibble,
    magrittr, 
    dtangle,
    e1071, 
    limSolve, 
    MASS, 
    nnls, 
    parallel, 
    epiR,  
    ggplot2, 
    ggplotify,
    cowplot,
    pheatmap, 
    grDevices,
    rlang

bioc-issue-bot commented 3 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 3 years ago

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

xanibas commented 3 years ago

hey @LiNk-NY ,

I'm tagging @lshep as I'm having the same issue in the previous submission attempt: https://github.com/Bioconductor/Contributions/issues/2036

after version bump and succesfull push, no automatic build is triggered: https://github.com/xanibas/granulator/commit/5ee0c397b2d3ca01542969c8b2f771c8c2801e53

git remote -v
origin git@github.com:xanibas/granulator.git (fetch) origin git@github.com:xanibas/granulator.git (push) upstream git@git.bioconductor.org:packages/granulator.git (fetch) upstream git@git.bioconductor.org:packages/granulator.git (push)

git fetch -v --all Fetching origin Enter passphrase for key '....': From github.com:xanibas/granulator = [up to date] master -> origin/master Fetching upstream Enter passphrase for key '....': From git.bioconductor.org:packages/granulator = [up to date] master -> upstream/master

lshep commented 3 years ago

While we debug we will have to do manual builds of the package. @nturaga could you set up the log monitoring we discussed to see if you get an error message from the internal codes so we can trace why its rejecting the call to the API to trigger a build? @Kayla-Morrell while I'm out next week you may have to trigger some manual builds for this package

bioc-issue-bot commented 3 years ago

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

nturaga commented 3 years ago

I'm hesitant to set up logs, because on looking back at the response I got from it trying the API_ENDPOINT manually, it's not very useful.

ln [14] response.content
Out[8]: b'OK not building existing package'

In [15]: response.status_code
Out[15]: 200

I also retraced my steps when we did set it up. The logging code is implemented and ready, but we decided to disable it because it wasn't adding any value.

Also, how did the build go through just now?? (looking above)

lshep commented 3 years ago

I manually kicked off a build

lshep commented 3 years ago

And the ERROR code is not helpful to you but helpful to me -- it is recognizing granulator as an existing package

lshep commented 3 years ago

Ok I think I figured out what the issue was; There was multiple previous submissions so the code was not able to trace it back to the correct issue. I believe I have corrected. @xanibas Could you try another version bump to see if it is automatically triggered now? Sorry for all this confusion

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f622ed8b3477ed12727f0f510741fcf7dce067e2

bioc-issue-bot commented 3 years ago

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/granulator to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

xanibas commented 3 years ago

Thank you @lshep , issue is solved now!

LiNk-NY commented 3 years ago

Hi Sabina, @xanibas

Thank you for your submission and for making the changes to improve your package. We appreciate it. There are a few points still outstanding from BiocCheck that can be easily resolved. Thank you for your patience and attention.

Best, Marcel

granulator #2065

DESCRIPTION

Add a BugReports field
Update R version to >= 4.1
LazyData should be set to FALSE

NAMESPACE

Looks good.
Consider re-exporting the %>% if you expect users to use your functions that way.

vignettes

Avoid using print for inspecting an object. Simply use correl$summary, for example.

R

Remove the redundant paste0 on line 112 of R/deconvolute.R as pointed out by BiocCheck

tests

Please add unit tests to ensure that your functionality is robust and less prone to bugs and errors.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 883adff942764a35ff37456fb6388a1660474cf9

bioc-issue-bot commented 3 years ago

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/granulator to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 56a65dc3f5ca19b2b2302a780337b0d558e5f992

bioc-issue-bot commented 3 years ago

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/granulator to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: edc8471f5ce0c855828b11463e73789ab62d5826

bioc-issue-bot commented 3 years ago

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

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e9a8e058ae79213b1b8da3e6ab48d50a78b3dbe9

bioc-issue-bot commented 3 years ago

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/granulator to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2083c9cffc64617ff636eb297ea4dcc550410424

bioc-issue-bot commented 3 years ago

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/granulator to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

xanibas commented 3 years ago

Hey Marcel @LiNk-NY ,

thank you for the quick reply. I have adressed all issues you have raised (see comments below).

The build fails on Mac, but it seems a Mac font installation issue: Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : no font could be found for family "Arial" which causes GeometryDoesNotContainImage and fails to build the vigentte.

Best, Sabina

Hi Sabina, @xanibas

Thank you for your submission and for making the changes to improve your package. We appreciate it. There are a few points still outstanding from BiocCheck that can be easily resolved. Thank you for your patience and attention.

Best, Marcel

granulator #2065

DESCRIPTION

Add a BugReports field

Update R version to >= 4.1

LazyData should be set to FALSE

done.

NAMESPACE

Looks good.

Consider re-exporting the %>% if you expect users to use your functions that way.

I made all outputs in the matrix or data.frame format. I prefer to leave it to the user to decide how they want to manipulate them in downstream analysis.

vignettes

Avoid using print for inspecting an object. Simply use correl$summary, for example.

done.

R

Remove the redundant paste0 on line 112 of R/deconvolute.R as pointed out by BiocCheck

done.

tests

Please add unit tests to ensure that your functionality is robust and less prone to bugs and errors.

done, added tests for data loading and all processing/plotting functions.

LiNk-NY commented 3 years ago

Hi Sabina, @xanibas

Thank you for making those changes. The package is ready to go. You can optionally reduce the size of the repository (86 Mb) with the BFG repo cleaner. It seems quite large due to committing a large .RData | 41c3a874 (76.1 MB) file. Please let us know if you do decide to use the tool.

Best regards, Marcel

xanibas commented 3 years ago

Hey Marcel @LiNk-NY ,

indeed I got rid of quite some big datasets. I can use BFG, but whouldn't be a simple clean of the git history suffice? https://gist.github.com/stephenhardy/5470814

(given that it's the first release, I don't really need to keep track of how the package was created)

Let me know which way you prefer...

Best, Sabina

LiNk-NY commented 3 years ago

Hi Sabina, @xanibas

That is the nuclear option if you don't mind losing your git history. We would prefer to preserve the git history but it is entirely up to you. If you do change the history, we would need someone to do the force push to the git.bioconductor.org repository (which you may not be able to do and after you force push to GitHub, of course).

Best, Marcel

xanibas commented 3 years ago

Hey Marcel @LiNk-NY ,

I want throguh with cleaning the history as it was quite messy and force push to the origin. Will start tracking the commits from this version on.

The force push to the upstream is indeed being blocked: remote: FATAL: + refs/heads/master packages/granulator xanibas DENIED by fallthru remote: error: hook declined to update refs/heads/master To git.bioconductor.org:packages/granulator.git ! [remote rejected] master -> master (hook declined) error: failed to push some refs to 'git.bioconductor.org:packages/granulator.git'

Are you able to do it from your side?

Thanks for the help, Sabina

LiNk-NY commented 3 years ago

Hi Sabina, @xanibas Please force push only to your GitHub repository. We can take care of the rest. Is it ready? Best, Marcel

xanibas commented 3 years ago

yes, the github repositroy is up to date now

LiNk-NY commented 3 years ago

Hi Sabina, @xanibas Nitesh updated the BioC git repository. The package is ready to go now. Thanks for your submission! Best, Marcel

bioc-issue-bot commented 3 years ago

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

Thank you for contributing to Bioconductor!

vjcitn commented 3 years ago

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/xanibas.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("granulator"). The package 'landing page' will be created at

https://bioconductor.org/packages/granulator

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.

Bioconductor / Contributions

granulator #2065

granulator #2065

DESCRIPTION

NAMESPACE

vignettes

R

tests

granulator #2065

DESCRIPTION

NAMESPACE

vignettes

R

tests