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zellkonverter #1549

Closed lazappi closed 4 years ago

lazappi commented 4 years ago

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

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bioc-issue-bot commented 4 years ago

Hi @lazappi

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: zellkonverter
Title: Conversion between scRNA-seq objects
Version: 0.99.0
Date: 2020-07-10
Authors@R: 
    c(person(given = "Luke",
   family = "Zappia",
   role = c("aut", "cre"),
   email = "luke@lazappi.id.au",
   comment = c(ORCID = "0000-0001-7744-8565")),
      person(given = "Aaron",
   family = "Lun",
   role = c("aut"),
   email = "infinite.monkeys.with.keyboards@gmail.com",
   comment = c(ORCID = "0000-0002-3564-4813"))
    )
Description:
    The zellkonverter package provides methods to convert between Python AnnData
    objects and SingleCellExperiment objects. These are primarily intended for
    use by downstream Bioconductor  packages that wrap Python methods for
    single-cell data analysis. It also includes functions to read and write
    H5AD files used for saving AnnData objects to disk. 
biocViews: SingleCell, DataImport, DataRepresentation
License: MIT + file LICENSE
Imports: 
    Matrix,
    basilisk,
    reticulate,
    SingleCellExperiment (>= 1.11.6),
    SummarizedExperiment,
    DelayedArray,
    methods,
    S4Vectors,
    utils
Suggests: 
    covr,
    spelling,
    testthat,
    knitr,
    rmarkdown,
    BiocStyle,
    scRNAseq,
    HDF5Array,
    rhdf5
URL: https://github.com/theislab/zellkonverter
BugReports: https://github.com/theislab/zellkonverter/issues
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Language: en-GB
StagedInstall: no
VignetteBuilder: knitr
bioc-issue-bot commented 4 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 4 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, 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/zellkonverter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LTLA commented 4 years ago

Linux and Windows look like Latex errors, dropping the \Figure{} should fix them.

Don't know why Windows fails on identity but not equality. Oh well, we might as well just flip to expect_equal.

Mac is an unknown reason. Don't know why it's borking out, as things are functioning fine on the BBS.

I wonder if we can reproduce the error more simply if @lshep runs (on the command line):

. '/Users/pkgbuild/Library/Caches/basilisk/1.1.8/0/etc/profile.d/conda.sh' 
conda activate

I can only imagine that it's an obtrusive PYTHONPATH, despite the fact that I actually unset the $PYTHONPATH for that subshell.

Edit: Maybe the local Miniconda got corrupted somehow, despite basilisk's defensive checks against incomplete installations. Should also try flushing the cache with basilisk.utils::clearExternalDir().

lazappi commented 4 years ago

I will have a look at the LaTeX error and the test. Any extra info on the conda problem would be helpful.

There's also an error from BiocCheckGitClone about the .Rproj file. Do I need to fix that?

I have updated my email for the mailing list to match my maintainer email (I was already subscribed, just with a different email).

lazappi commented 4 years ago

@lshep I'm having trouble pushing to the Bioconductor git. I checked the BiocCredentials app and I don't have access to the zellkonverter repository. Can you please take a look at that?

lshep commented 4 years ago

Can you show the commands you are trying with output and git remote -v?

lazappi commented 4 years ago

Sorry, I should have posted that the first time.

git remotes

$ git remote -v
origin  git@github.com:theislab/zellkonverter.git (fetch)
origin  git@github.com:theislab/zellkonverter.git (push)
upstream        git@git.bioconductor.org:packages/zellkonverter.git (fetch)
upstream        git@git.bioconductor.org:packages/zellkonverter.git (push)

git push

$ git push upstream master
FATAL: W any packages/zellkonverter l.zappia DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

SSH check (truncated output)


$ ssh -T git@git.bioconductor.org
hello l.zappia, this is git@ip-172-30-0-33 running gitolite3 v3.6.6-6-g7c8f0ab on git 2.24.1

 R      admin/..*
 R      packages/..*
 R      admin/BiocManager
 R      admin/bioconductor.org
...
 R      packages/spikeLI
 R      packages/spkTools
 R W    packages/splatter
 R      packages/spliceR
 R      packages/spliceSites
...
 R      packages/zFPKM
 R      packages/zebrafishRNASeq
 R      packages/zellkonverter
 R      packages/zinbwave
 R      packages/zlibbioc
lshep commented 4 years ago

@nturaga could you investigate?

nturaga commented 4 years ago

@lazappi I have identified the problem with this. I'll get back to you on when you can push successfully.

Thank you for your patience.

nturaga commented 4 years ago

Hi @lazappi , The problem has been fixed. You can commit now.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f73be68ab9452ae5cab2b0238b00949d7b28ac5

bioc-issue-bot commented 4 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, 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/zellkonverter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 4 years ago

I apologize for the delay. I will review the package tonight and have a review tomorrow. In the meantime could you correct the sys file ERROR by adding zellkonverter.Rproj into your .gitignore Thank you

lshep commented 4 years ago

FWIW I'm getting the similar build ERROR's seen on snifter for the lower OS version. I'm reviewing by using the docker right now to bypass this but it might be worth noting somewhere.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 08f3f17f2245ac5bac9e5b237c5894d1c1cf6fc6

lazappi commented 4 years ago

Pushed new .gitignore. No other changes so shouldn't affect checks.

Happy to include whatever note about OS versions is decided for snifter.

So you know I am on leave the next two weeks so might be slow to respond after today.

bioc-issue-bot commented 4 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, 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/zellkonverter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 4 years ago

I only have a few very minor comments.

General

INST

R / man code

Cheers,

lazappi commented 4 years ago

I only have a few very minor comments.

General

  • [ ] Misc files to .gitignore like zellkonverter.Rproj, and codecov.yml. Is the CODE_OF_CONDUCT.md needed to be git tracked as well?

I would like to include CODE_OF_CONDUCT.md on GitHub but can probably put that somewhere else if it's causing issues for Bioconductor. I will look into how essential codecov.yml is. I wonder if there is some way to keep these on GitHub but not push them to Bioconductor?

INST

  • [ ] Please add a inst/scripts that describes how the data in inst/extdata is created. It can be code, sudo code, or text but should be some indication of source and how its used in the package.

Can do.

R / man code

  • [ ] Why is the package man page marked as internal documentation?

Not really sure, I expect it comes from the usethis skeleton. Will look into it.

lshep commented 4 years ago

If the CODE_OF_CONDUCT is needed in there for institution standards no problem we just like to have minimal files on Bioconductor; limiting to only the essential files for a package . If this is too complicated don't worry about it.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 50e00aadf78822b374ae736188045378a018a341

lazappi commented 4 years ago

Updates

General

  • [ ] Misc files to .gitignore like zellkonverter.Rproj, and codecov.yml. Is the CODE_OF_CONDUCT.md needed to be git tracked as well?

I have left these files in the repo for now because I think they are useful:

Happy to discuss further if it would benefit Bioconductor to clean them up.

INST

  • [ ] Please add a inst/scripts that describes how the data in inst/extdata is created. It can be code, sudo code, or text but should be some indication of source and how its used in the package.

Documented in a Markdown file. Let me know if you think there should be more detail than that.

R / man code

  • [ ] Why is the package man page marked as internal documentation?

I have removed the internal keyword because I don't think it's necessary, it just removes the entry from the index (as far as I can tell). As a note though it is recommended in the roxygen documentation https://roxygen2.r-lib.org/articles/rd.html#packages 😸.

Let me know if there is anything else.

LTLA commented 4 years ago

Regarding the files: we could just .Rbuildignore them and then everyone would be happy. This is what (I believe) we do for the iSEE project, which has a lot of top-level crud.

Edit: ... and I notice that we're already doing that, oops.

lshep commented 4 years ago

Yes please

bioc-issue-bot commented 4 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/zellkonverter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LTLA commented 4 years ago

What the!? It built on merida! What magic is this?

lazappi commented 4 years ago

I know! I was just about to ask if something had changed or it just magically started working. 🎩

lshep commented 4 years ago

so fun little fact -- when I set up the builders I originally was having difficulty installing virtualenv and it was recommended to use venv instead. We quickly realized on windows that this had very bad consequences as there are some subtle differences of venv and virtualenv. I didn't think about it until the other night that we updated the virtualenv on windows but never went back and updated it on mac because it seemed to be working okay. I thought maybe it might be something similar and reinstalled with virtualenv this morning.

LTLA commented 4 years ago

It looks like we're in a pretty good state now; are there any further comments?

bioc-issue-bot commented 4 years ago

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

Thank you for contributing to Bioconductor!

mtmorgan commented 4 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/lazappi.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("zellkonverter"). The package 'landing page' will be created at

https://bioconductor.org/packages/zellkonverter

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.