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allenpvc #751

Closed diogo-branco closed 6 years ago

diogo-branco commented 6 years ago

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

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

I am familiar with the essential aspects of Bioconductor software management, including:

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 6 years ago

Hi @diogo-branco

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: allenpvc
Title: GEO accession data GSE71585 as a SingleCellExperiment
Version: 0.99.0
Authors@R: person("Diogo", "P. P. Branco", email =
        "diogo.pp.branco@gmail.com", role = c("aut", "cre"))
Author: Diogo P. P. Branco
Maintainer: Diogo P. P. Branco <diogo.pp.branco@gmail.com>
Description: Celular taxonomy of the primary visual cortex in adult mice based
    on single cell RNA-sequencing from a study performed by the Allen Institute
    for Brain Science. In said study 49 transcriptomic cell types are
    identified.
License: CC0
NeedsCompilation: no
Depends: R (>= 3.5.0), GEOquery, SingleCellExperiment
Suggests: BiocStyle, ExperimentHub, knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
biocViews: ExperimentData, ExpressionData, SingleCellData, RNASeqData
bioc-issue-bot commented 6 years ago

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

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 commented 6 years ago

@Liubuntu will review this package. I think it would be a useful convenience to have a single function allenpvc() that simply returns eh[["EH..."]].

bioc-issue-bot commented 6 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: "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.

diogo-branco commented 6 years ago

@Liubuntu @mtmorgan Thank you, I will create the allenpvc() function.

Regarding the error on the building: the Package Builder seems to be using BiocVersion 3.7 and not 3.8. This package will only work on version >= 3.8. Is there anything to be fixed on my side in that regard?

mtmorgan commented 6 years ago

the build system should heal itself; @lshep might post here when it is updated.

lshep commented 6 years ago

I apologize for the delay. We are working on the updates - I will post back here when they are complete.

bioc-issue-bot commented 6 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.

Liubuntu commented 6 years ago

Hi @diogo-branco ,

Thank you for your contribution to Bioconductor. Please refer to the following technical review and address any issue. This is my first time reviewing an experiment data package. I will talk to Bioconductor core team about any potential points to add possibly. Please let me know for any questions or concerns. Thanks!

DESCRIPTION

NAMESPACE

R

Vignettes

inst/

Cheers, Qian

diogo-branco commented 6 years ago

Hello @Liubuntu,

Thank you for you review. I will address all the points you have made, but I am unsure about the following:

Please add a section called Installation after Introduction, and show to users how to download and library this package as it is already available in Bioconductor. E.g., to use BiocInstaller function for downloading. BiocInstaller::biocLite("allenpvc")

The package was only submitted to ExperimentHub (by myself) but, from what I could understand from the documentation, that does not mean it is available on Bioconductor, as it needs to load the associated package which is the one being submitted in this issue. Furthermore, running BiocInstaller::biocLite("allenpvc") just returns a warning stating that said package is not available.

Reiterating: I will comply with all the other points but I am confused regarding the one mentioned above.

Best, Branco

Liubuntu commented 6 years ago

I would say as if it is already available in Bioconductor. Because when users are exposed to the vignette, the package should already be available on Bioconductor. Be sure to make the code trunk eval=FALSE for this Installation section.

diogo-branco commented 6 years ago

Thank you for clarifying, I will include the Installation section after Introduction. Is a version bump required for this push to be built by the SPB? I have already added a web hook to the repository.

Liubuntu commented 6 years ago

Yes. Be sure to bump the version whenever you are ready for a new build.

bioc-issue-bot commented 6 years ago

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

40ca492 Minor fixes to comply with reviews from Bioconduct...

bioc-issue-bot commented 6 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.

diogo-branco commented 6 years ago

@Liubuntu I believe I have complied with all the review points in this latest build. Please let me know in case I have overlooked something.

Liubuntu commented 6 years ago

HI @diogo-branco ,

Sorry for the delay. I will look into the updates and get back to you very soon!

Cheers, Qian

Liubuntu commented 6 years ago

Hi @diogo-branco ,

You experiment data package is accepted. Please expect some follow up emails about how to maintain your package. Thanks for your contribution to Bioconductor.

Cheers, Qian

bioc-issue-bot commented 6 years ago

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

mtmorgan commented 6 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/diogo-branco.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 biocLite(\"allenpvc\"). The package 'landing page' will be created at

https://bioconductor.org/packages/allenpvc

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.

lshep commented 5 years ago

Since you have remained unresponsive to emails - this is our last attempt to contact you - Your software package condcomp has been failing in Bioconductor since before the last release. We have tried to contact you to fix the ERRORs but you have remained unresponsive and the repository has been unchanged. If your package is not fixed in the next week we will be deprecating condcomp and allenpvc do to being an unresponsive maintainer.