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AnVILWorkflow #2832

Closed shbrief closed 1 year ago

shbrief commented 2 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 questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 2 years ago

Hi @shbrief

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: AnVILWorkflow
Title: Run workflows implemented in Terra/AnVIL workspace
Version: 0.99.0
Date: 2022-10-7
Authors@R: 
    person(given = "Sehyun",
 family = "Oh",
 role = c("aut", "cre"),
 email = "Sehyun.Oh@sph.cuny.edu",
 comment = c(ORCID = "0000-0002-9490-3061"))
Description: The AnVIL is a cloud computing resource developed in part
    by the National Human Genome Research Institute. The main cloud-based
    genomics platform deported by the AnVIL project is Terra. The 
    AnVILWorkflow package allows remote access to Terra implemented workflows,
    enabling end-user to utilize Terra/ AnVIL provided resources - such as
    data, workflows, and flexible/scalble computing resources - through the 
    conventional R functions.
Depends:
    R (>= 4.1),
Imports:
    AnVIL,
    httr,
    utils,
    methods
Suggests:
    knitr
License: Artistic-2.0
biocViews:
    Infrastructure,
    Software
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
bioc-issue-bot commented 2 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 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

shbrief commented 2 years ago

Hi @Kayla-Morrell ,

I updated my email address to the one used for the bioc-devel mailing list. But I'm unsure how to resolve the other error (* ERROR: At least 80% of man pages documenting exported objects must have runnable examples.), because more than 80% of functions in this package are a wrapper around API calls. Is there any suggestion on this case? Thanks!

Sehyun

Kayla-Morrell commented 2 years ago

Hello @shbrief

There do need to be examples in the man pages for exported objects. Would utilizing something like the following work?

if (AnVIL::gcould_exists()) {
    ## run example code
}

You could also look into donttest{} as a last resort (we prefer runnable, testable code over using donttest{}/dontrun{}). If you must use one of these options we prefer donttest{} because it requires valid R code.

Best, Kayla

shbrief commented 2 years ago

Hi @Kayla-Morrell I fixed all the errors. Could you look at whether it's ready for the next step in review? Thanks!

Kayla-Morrell commented 2 years ago

@shbrief - You need to push a version bump to the git version of the package to kick of a new build report. Without a clean build report I can't continue with my portion of the review. Please see here for how to get this set up.

Best, Kayla

shbrief commented 2 years ago

I have some permission issues accessing upstream. I'll push the new version as soon as I figure this out. Thanks!

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e11d4ec0906fbda7a3f63f72ae872dae899f282d

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 67e7114c571fe8be813dc8043a5dc2c05257e9b0

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3aa378e4294cd2c67d3e1723c98fe90775756ca5

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 68388ecb5530e52908e1e6d34345f71f196cf600

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 86a5490ddcd47ee26a34623660d7920480c6a27d

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 266815847e551e0b3f694ade03d362f2eb159c85

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 57c2b52b484866f9bfaf9a71bdff024f102d6e3d

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 70ff82745ec288f0b9c878933bfebf52cbcc8bff

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b0938924f0fdb1ef6b41f54670a77b0a4c561cf0

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 19e6ecc959f653d3706eaec724f8286148bb1331

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

shbrief commented 2 years ago

Hi @Kayla-Morrell I cleared all the errors/warnings. Please let me know what else needs to be done. Thanks!

Kayla-Morrell commented 2 years ago

@shbrief - When trying to build the package locally I get the following error:

* creating vignettes ... ERROR
--- re-building ‘salmon.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 193-195 (salmon.Rmd)
Error: processing vignette 'salmon.Rmd' failed with diagnostics:
'gcloud auth print-access-token' failed:
  ERROR: (gcloud.auth.print-access-token) Your current active account [shbrief@gmail.com] does not have any valid credentials
    Please run:

      $ gcloud auth login

    to obtain new credentials.

    For service account, please activate it first:

      $ gcloud auth activate-service-account ACCOUNT
  exit status: 1
--- failed re-building ‘salmon.Rmd’

SUMMARY: processing the following file failed:
  ‘salmon.Rmd’

Error: Vignette re-building failed.
Execution halted
bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b8dca5aa420585cf96c5ebf8b54f866ce086a90b

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b60bd46eeda59679952f3894595dbf5dc830a956

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 370c085fd6999d69c1cb74adefec590f51d3d148

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

shbrief commented 2 years ago

Hi @Kayla-Morrell, I think it should work now.

shbrief commented 2 years ago

Will it be possible to include this package in the BioC 3.16 release? @vjcitn @lshep

vjcitn commented 2 years ago

Hi Sehyun -- it may be possible. But I am looking at the vignette as produced on my machine. A key point is

knitr::knit_exit(fully=FALSE)

So most of the vignette is not produced. Is this what you want?

shbrief commented 2 years ago

Oh sorry, I was experimenting with something and accidentally pushed it. I'll fix it now.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1185537aeb116d1c6a1fe9ab8820aa9fae437959

bioc-issue-bot commented 2 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/AnVILWorkflow to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

shbrief commented 2 years ago

@vjcitn Fixed. Let me know if you find any other issues. Thanks!

lshep commented 2 years ago

@Kayla-Morrell is the assigned reviewer and will still have to review and accept

Kayla-Morrell commented 2 years ago

@shbrief - I still need to do a full initial review of this package (besides just a clean build report) which takes time and reviews are not the only thing that I currently work on. This is an especially busy time with the release so please be patient. I will try to get to the review by the end of the day but I do not foresee it being a part of the 3.16 release since the deadline was Wednesday.

Best, Kayla

shbrief commented 2 years ago

@Kayla-Morrell Do you know when you would have time to review this package? I haven't heard anything for a while and just want to make sure I didn't miss any communication. Thanks! - Sehyun

Kayla-Morrell commented 2 years ago

@shbrief - Sorry for the delay, with the release and being out sick last week I'm a bit behind. I will work on getting a review posted early this week.

Kayla-Morrell commented 2 years ago

@shbrief - I still cannot build the package locally in order to do a review. This is the error I get when trying to run R CMD build:

* creating vignettes ... ERROR
--- re-building ‘salmon.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in rm(resp) : object 'resp' not found
Warning in rm(resp) : object 'resp' not found
Quitting from lines 219-221 (salmon.Rmd)
Error: processing vignette 'salmon.Rmd' failed with diagnostics:
'gcloud auth print-access-token' failed:
  ERROR: (gcloud.auth.print-access-token) Your current active account [shbrief@gmail.com] does not have any valid credentials
    Please run:

      $ gcloud auth login

    to obtain new credentials.

    For service account, please activate it first:

      $ gcloud auth activate-service-account ACCOUNT
  exit status: 1
--- failed re-building ‘salmon.Rmd’

SUMMARY: processing the following file failed:
  ‘salmon.Rmd’

Error: Vignette re-building failed.
Execution halted
shbrief commented 1 year ago

It seems like the gcloud enviroment of your local machine is misconfigured - the package is building on the build system and because the build system does not have gcloud installed so no code chunks will be evaluated. Is there a reason you try to build this locally? Could you use the build system instead? Also, just to confirm the configuration issue, could you tell me the output for the following code in your local machine? Thanks!

AnVIL::gcloud_account()
AnVIL::gcloud_project()
Kayla-Morrell commented 1 year ago

@shbrief - Part of the review process is for the reviewer to be able to build and check the package locally. The build system may not have gcloud installed but my local system does and this may be the case for other users. This was my initial result of the code you posted:

> gcloud_exists()
[1] TRUE
> gcloud_account()
[1] "shbrief@gmail.com"

My cloud environment must have been overwritten from an early attempt at building your package. I reset my cloud environment to my account and project and was still unable to build the package. The new error is:

* creating vignettes ... ERROR
--- re-building ‘salmon.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in rm(resp) : object 'resp' not found
Warning in rm(resp) : object 'resp' not found
Quitting from lines 219-221 (salmon.Rmd)
Error: processing vignette 'salmon.Rmd' failed with diagnostics:
Workspace doesn't exit or you don't have access to it.
--- failed re-building ‘salmon.Rmd’

SUMMARY: processing the following file failed:
  ‘salmon.Rmd’

Error: Vignette re-building failed.
Execution halted

Best, Kayla