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EWCE #1904

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9 tasks done
Al-Murphy opened this issue Feb 22, 2021 · 138 comments
Closed
9 tasks done

EWCE #1904

Al-Murphy opened this issue Feb 22, 2021 · 138 comments

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@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 22, 2021

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 understand that by submitting my package to Bioconductor,
    the package source and all review commentary are visible to the
    general public.

  • I have read the Bioconductor Package Submission
    instructions. My package is consistent with the Bioconductor
    Package Guidelines.

  • 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.

  • My package addresses statistical or bioinformatic issues related
    to the analysis and comprehension of high throughput genomic data.

  • I am committed to the long-term maintenance of my package. This
    includes monitoring the support site for issues that users may
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@bioc-issue-bot bioc-issue-bot commented Feb 22, 2021

Hi @Al-Murphy

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: ewceData
Title: The ewceData package provides reference data required for ewce
Version: 0.99.1
Authors@R: 
    c(person(given = "Alan",
 family = "Murphy",
 role = c("cre"),
 email = "alanmurph94@hotmail.com",
 comment = c(ORCID = "0000-0002-2487-8753")),
    person(given = "Nathan",
 family = "Skene",
 role = c("aut"),
 email = "nathan.skene@gmail.com",
 comment = c(ORCID = "0000-0002-6807-3180")))       
Description: This package provides reference data required for ewce. Expression 
  Weighted Celltype Enrichment (EWCE) is used to determine which cell 
  types are enriched within gene lists. The package provides tools 
  for testing enrichments within simple gene lists (such as human 
  disease associated genes) and those resulting from differential 
  expression studies. The package does not depend upon any particular 
  Single Cell Transcriptome dataset and user defined datasets can be 
  loaded in and used in the analyses.
URL: https://github.com/neurogenomics/ewceData
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1)
Imports: 
    ExperimentHub,
    utils
Suggests: 
    knitr,
    BiocStyle,
    ggplot2,
    cowplot,
    rmarkdown,
    testthat (>= 3.0.0)
biocViews: ExperimentData, ExperimentHub, ExpressionData, Genome, Proteome, MicroarrayData, 
  SequencingData, SingleCellData, RNASeqData
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
VignetteBuilder: knitr
Config/testthat/edition: 3

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@bioc-issue-bot bioc-issue-bot commented Feb 23, 2021

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

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@bioc-issue-bot bioc-issue-bot commented Feb 24, 2021

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

@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 24, 2021

The error seems to be down to a ggplot object part of the data object ctd (ctd[[1]]$plotting$ggdendro_vertical) I can't seem to reproduce this error locally and looking online the only related issue seems to be here: https://stackoverflow.com/questions/60187844/error-in-getas-characterfun-mode-function-envir-envir-object-guid. @lshep have you encountered an issue like this before? Sorry it's hard to correct since it isn't failing locally.

The error:
[[1]]$plotting$ggdendro_vertical Error in get(as.character(FUN), mode = "function", envir = envir) : object 'guide_none' of mode 'function' was not found Calls: <Anonymous> ... lapply -> FUN -> f -> lapply -> FUN -> match.fun -> get Execution halted

@lshep
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@lshep lshep commented Feb 24, 2021

Please note you are also getting ERROR's for not being signed up for the mailing list and having some files that should not be git tracked.
I am able to reproduce this locally, Please make sure you are testing with R-devel (R4.1) and Bioconductor 3.13. If this is already the case make sure all dependencies are up-to-date with BiocManager::valid() or BiocManager::install() # choose a if any are out of date to update all

@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 25, 2021

Thanks @lshep, that all makes sense and I have sorted all the errors and have bumped the version and pushed to my git repository. However, when I try and push upstream to bioconductor, I get the following error:

To git.bioconductor.org:packages/ewceData.git
! [remote rejected] main -> main (hook declined)
error: failed to push some refs to 'git@git.bioconductor.org:packages/ewceData.git'

@lshep
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@lshep lshep commented Feb 25, 2021

Please show the full command with output. I assume you followed the instructions to set up the remotes but please be sure there is a upstream remote that points to git@git.bioconductor.org:packages/ewceData.git you can check this with git remote -v . github changed the default branch naming master to main however our build system still uses master. Two thoughts, 1. make sure to git fetch --all before trying to push and 2. make sure to explicitly state the branch you would like to push to git push upstream master

@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 25, 2021

I believe the upstream is set to bioconductor git, see the output of git remote -v:

origin https://github.com/neurogenomics/ewceData.git (fetch) origin https://github.com/neurogenomics/ewceData.git (push) upstream git@git.bioconductor.org:packages/ewceData.git (fetch) upstream git@git.bioconductor.org:packages/ewceData.git (push)

Based on your advice, I reran git fetch --all:

Fetching origin
Fetching upstream

and then tried to push, I use main rather than master so I used git push upstream main but still got:

Total 0 (delta 0), reused 0 (delta 0)
remote: FATAL: W refs/heads/main packages/ewceData Al-Murphy DENIED by fallthru
remote: error: hook declined to update refs/heads/main
To git.bioconductor.org:packages/ewceData.git
! [remote rejected] main -> main (hook declined)
error: failed to push some refs to 'git@git.bioconductor.org:packages/ewceData.git'

@lshep
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@lshep lshep commented Feb 25, 2021

Again -- our default branch is not main... please do git push upstream master The command is saying push this branch I am on to the remote upstream onto the branch master.

@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 25, 2021

Sorry I missed what you meant about master/main, I thought you could still use either (as per this documentation). I tried using master rather than main and I'm still getting an error:

git push upstream master

error: src refspec master does not match any
error: failed to push some refs to 'git@git.bioconductor.org:packages/ewceData.git'

Should I rename my main branch as master or would that make any difference?

Also note I ran git merge origin/main rather than master earlier when setting up the git Bioconductor upstream, again per the document. I'm not sure if this is affecting things?

@lshep
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@lshep lshep commented Feb 25, 2021

You should be able to leave yours as main while pushing to our master. Could you try
git push upstream main:master

@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 25, 2021

That failed and I also tried forcing it which didn't seem to work either:

git push upstream main:master                           
To git.bioconductor.org:packages/ewceData.git
 ! [rejected]        main -> master (non-fast-forward)
error: failed to push some refs to 'git@git.bioconductor.org:packages/ewceData.git'
hint: Updates were rejected because a pushed branch tip is behind its remote
hint: counterpart. Check out this branch and integrate the remote changes
hint: (e.g. 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

git push -f upstream main:master
Total 0 (delta 0), reused 0 (delta 0)
remote: Error: Illegal version bump from '0.99.1' to '0.9.1'.
remote: 
remote: Check http://bioconductor.org/developers/how-to/version-numbering/
remote: for details.
remote: 
To git.bioconductor.org:packages/ewceData.git
 ! [remote rejected] main -> master (pre-receive hook declined)
error: failed to push some refs to 'git@git.bioconductor.org:packages/ewceData.git'

@lshep
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@lshep lshep commented Feb 25, 2021

@nturaga advice

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@bioc-issue-bot bioc-issue-bot commented Feb 25, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: c69c7012261f6267fd4e3e374cb14e97ef06b3be

@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 25, 2021

@lshep, @nturaga no need to look into this anymore, I removed the upstream branch and then re-initiated it and it seems to be working find now. Thanks for the help!

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@bioc-issue-bot bioc-issue-bot commented Feb 25, 2021

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

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@bioc-issue-bot bioc-issue-bot commented Feb 25, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 76deb36b06196b67a4829afd39f9ec88ff83a0a1

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@bioc-issue-bot bioc-issue-bot commented Feb 25, 2021

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

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@bioc-issue-bot bioc-issue-bot commented Feb 25, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: e3b1cf772bbcd9ad241a393fffbdbef6a833d230

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@bioc-issue-bot bioc-issue-bot commented Feb 25, 2021

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

@Al-Murphy
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@Al-Murphy Al-Murphy commented Feb 25, 2021

Hey @lshep, the remaining issue is

Quitting from lines 91-99 (ewceData.Rmd) 
Error: processing vignette 'ewceData.Rmd' failed with diagnostics:
could not find function "cortex_mrna"
--- failed re-building 'ewceData.Rmd'

which relates to cortex_mrna <- cortex_mrna() in the vignette and is Windows specific. This is odd since I have already libraried the package and my load function from ExperimentHub is working correctly for the other operating systems. A re you aware of some naming errors with ExperimentHub on Windows that I could be committing here?

@lshep
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@lshep lshep commented Feb 26, 2021

@hpages do you know of any stipulations regarding windows for this use case?

In the meantime I will review based on the other two platforms. Cheers

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@bioc-issue-bot bioc-issue-bot commented Feb 27, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: bc3515a757b3bbaeb1e99a917d51d98f62681cac

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@bioc-issue-bot bioc-issue-bot commented Apr 14, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 4dcf3d25a1625b4b944955253156689483a3fee2

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@bioc-issue-bot bioc-issue-bot commented Apr 14, 2021

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

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@bioc-issue-bot bioc-issue-bot commented Apr 14, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: c3c4d3dc713c9e1c8e5d67e166f4f32b07438ee5

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@bioc-issue-bot bioc-issue-bot commented Apr 14, 2021

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

@Al-Murphy
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@Al-Murphy Al-Murphy commented Apr 14, 2021

Hi @lshep, is it acceptable to use a donttest wrapper for two examples in my exported functions? I will still have greater than 80% with running examples but this will greatly improve my runtime.

@lshep
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@lshep lshep commented Apr 14, 2021

Are there other tests or anything for the functions that would be in the donttest? I think that would be reasonable as long as the majority are run.

@Al-Murphy
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@Al-Murphy Al-Murphy commented Apr 14, 2021

Yep unit tests still cover 80+% of the code so they would be covered. I think with dontest checks that it's valid R code anyway. Thanks!

@lshep
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@lshep lshep commented Apr 14, 2021

Yes that is acceptable then

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@bioc-issue-bot bioc-issue-bot commented Apr 14, 2021

Received a valid push on git.bioconductor.org; starting a build for commit id: 4fd2bd628efa9efe9ecd83ffb5a8ff1e93b2de18

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@bioc-issue-bot bioc-issue-bot commented Apr 14, 2021

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

@Al-Murphy
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@Al-Murphy Al-Murphy commented Apr 14, 2021

Hi @lshep , is the warning for a run time over 20 minutes on Windows acceptable? Note that the run time is below 10 for Linux and I assume the same on Mac.

@lshep
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@lshep lshep commented Apr 15, 2021

Yes this is acceptable. I try and review your packages over the next few days.

@Al-Murphy
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@Al-Murphy Al-Murphy commented Apr 15, 2021

Thank you! I won't be making any changes in the meantime then

@lshep
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@lshep lshep commented Apr 15, 2021

I can hold off if you would like to still make changes?

@Al-Murphy
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@Al-Murphy Al-Murphy commented Apr 15, 2021

No no I have no more changes I want to make, sorry I was just confirming for you so you know things won't change while you are in the middle of a review!

@lshep
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@lshep lshep commented Apr 21, 2021

Thank you for taking the time to apply the changes. The packages are in an acceptable state for inclusion into Bioconductor.

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@bioc-issue-bot bioc-issue-bot commented Apr 21, 2021

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

Thank you for contributing to Bioconductor!

@Al-Murphy
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@Al-Murphy Al-Murphy commented Apr 22, 2021

Thank you @lshep for all your help and work on this, I realise it wasn't the easiest of packages!

Thanks,
Alan.

@vjcitn
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@vjcitn vjcitn commented Apr 24, 2021

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/Al-Murphy.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("ewceData"). The package 'landing page' will be created at

https://bioconductor.org/packages/ewceData

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.

@vjcitn vjcitn closed this as completed Apr 24, 2021
@vjcitn
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@vjcitn vjcitn commented Apr 24, 2021

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/Al-Murphy.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("EWCE"). The package 'landing page' will be created at

https://bioconductor.org/packages/EWCE

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.

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