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EWCE #1904

Closed Al-Murphy closed 3 years ago

Al-Murphy commented 3 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 3 years ago

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
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: "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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

Al-Murphy commented 3 years ago

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 commented 3 years ago

@nturaga advice

bioc-issue-bot commented 3 years ago

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

Al-Murphy commented 3 years ago

@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!

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: "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.

bioc-issue-bot commented 3 years ago

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

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: "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.

bioc-issue-bot commented 3 years ago

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

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: "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 commented 3 years ago

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 commented 3 years ago

@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

bioc-issue-bot commented 3 years ago

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

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: "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 commented 3 years ago

I tried making some changes to the package to sort the issue but the problem with using the package on Windows seems to persist. Not sure if either you @lshep or @hpages have come across this before? Currently the package won't install on Windows with the following error:

Error: package or namespace load failed for 'ewceData':
 .onLoad failed in loadNamespace() for 'ewceData', details:
  call: fun(libname, pkgname)
  error: no objects found

This is related to the on load function zzz.R which relates to the ExperimentHub functionality to load datasets by dataset(). In this function, it appears the metadata file isn't read correctly on Windows machines hence why it hits the stop("no objects found") condition. The code to load the metadata file is:

objs <- read.csv(system.file("extdata", "metadata.csv",
                               package="ewceData"),
                   stringsAsFactors=FALSE)$Title

It is not clear why this fails only for Windows.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5c2adb900b377f969adc6afaba94bc6f07cc8148

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

Al-Murphy commented 3 years ago

AdditionalPackage: https://github.com/NathanSkene/EWCE

bioc-issue-bot commented 3 years ago

Hi @Al-Murphy, Thanks for submitting your additional package: https://github.com/NathanSkene/EWCE. We are taking a quick look at it and you will hear back from us soon.

mtmorgan commented 3 years ago

Nathan Skene is the maintainer of EWCE, but @Al-Murphy is submitting the package; @Al-Murphy should be the maintainer (cre role)

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fdc3feb009804421ac4b877019ec8d45e25b938a

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

Al-Murphy commented 3 years ago

Hi @mtmorgan. I have updated the maintainer as suggested and references across the two packages and have bumped their versions and pushed the changes. Will the EWCE package be assigned to someone and have a check run similar to the ewceData package? There was an issue with file size with EWCE but I have corrected this in the latest push too.

mtmorgan commented 3 years ago

yes, the EWCE package will be assigned to the current reviewer, and will be built on version bump, once it has been 'moderated'; the maintainer issue was blocking the moderation step, so this will occur when packages are next moderated (usually once every two or three days).

Al-Murphy commented 3 years ago

Hi @mtmorgan, just wondering if packages have been moderated since your last message? EWCE hasn't been assigned and I want to know in case there is something else blocking the moderation step that I can resolve.

mtmorgan commented 3 years ago

@vjcitn is working on this; I think the current stumbling block is resolving the previous EWCE package that we still have a repository for with your new contribution, which might not be derived from git@git.bioconductor.org:packages/EWCE ?

Al-Murphy commented 3 years ago

Ah okay that's no problem. I think it may not have been, EWCE originally went on Bioconductor some time ago and, at the time, I don't think the submission process was the same

bioc-issue-bot commented 3 years ago

Additional Package has been approved for building.

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.

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

Al-Murphy commented 3 years ago

Hi @mtmorgan, @lshep I believe that is the old deprecated version of EWCE that the check was ran against not from the repository I am submitting

vjcitn commented 3 years ago

Yes, there was something about NathanSkene in the repo that was used. I will try to straighten this out.

lshep commented 3 years ago

I think we have corrected the issue. I have just kicked off a manual build for the package and you should have a build report shortly.

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

Al-Murphy commented 3 years ago

That seems odd that it failed on all three OS, it is passing with no warnings or errors locally on my Mac

lshep commented 3 years ago

I can reproduce the linux error locally on my computer. Please make sure that you are using R-devel (R 4.1) and have updated all Bioconductor package dependencies with BiocManager::valid() . I will investigate packages note being available for windows but please fix the linux/mac error

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ffd2c46759f45bbcdafc3b447006777aa9ae9f7d

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

Al-Murphy commented 3 years ago

@lshep can you start antoher manual build on EWCE. The error was caused by something in ewceData which I have fixed and bumped the version of but since no change has been made to EWCE it won't rebuild

lshep commented 3 years ago

done. You should have a new report shortly. I just happened to notice you are writing files to a users home directory by default. That should never be done. Please update the code to use tempdir() or tempfile() by default in the vignettes, examples, tests. The files that are written are 

CellTypeData_kiCortexOnly.rda
CellTypeData_kiCortexOnly_1to1only.rda

and the results of BootstrapPlots directory

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