AnVILWorkflow

[shbrief]

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

• Repository: https://github.com/shbrief/AnVILWorkflow

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

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

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

• [x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.

• [x] 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.

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

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

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• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
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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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1224e0c2e3d5ee170ce007dd37b3ea3b03c24329

[bioc-issue-bot]

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]

@Kayla-Morrell Thanks for trying it out again. Martin could successfully build it locally, so I'm not completely sure what causes the error in your local machine. I updated a few things that can potentially solve the problem. Could you take a look at it now? Thanks!

[Kayla-Morrell]

@shbrief - There is one minor change that I had to make to the vignette code in order to get the package to build. On line 302 of the vignette I had to change tibble::tibble to tibble::tibble() so that it was an actual function call. Now that the package builds locally I can move forward with the review. I'll have it posted in the next couple of days.

Best, Kayla

[Kayla-Morrell]

@shbrief - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

DESCRIPTION

• [ ] REQUIRED: Update R version dependency from 4.1 to 4.3.0.
• [ ] SUGGESTION: We strongly encourage including the 'BugReports:' field which includes a relevant link to GitHub for reporting issues.

NEWS

• [ ] SUGGESTION: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.

Data

• [ ] REQUIRED: We require documentation of files in the inst/extdata/ directory in an inst/script/ directory. The script(s) in this directory can vary. Most importantly there needs to be documentation vary clearly stating how the data was generated and source information. It should include source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data.
• [ ] REQUIRED: Looking at the data files within 'inst/extdata/' I don't see where Table1.pdf is used within the package. If it is not needed it should be removed.

Vignette

• [ ] REQUIRED: There should be an Installation section (besides the load package section) that demonstrates to the user how to install the package from Bioconductor. The code chunk should include eval = FALSE.

Man pages

• [ ] SUGGESTION: We encourage having a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?AnVILWorkflow.
• [ ] REQUIRED: Should the example for availableAnalysis() have the code to check if gcloud is available?
• [ ] REQUIRED: There should be a runnable example in the setCloudEnv() man page.

Unit tests

• [ ] SUGGESTION: Consider adding unit tests. We strongly encourage them. See https://contributions.bioconductor.org/tests.html

R code

• [ ] SUGGESTION: checking R code for possible problems. getOutput: no visible binding for global variable 'workflowName' Undefined global functions or variables: workflowName
• [ ] REQUIRED: Avoid 'cat' and 'print' outside of 'show' methods
• [ ] REQUIRED: Avoid the use of 'paste' in condition signals
• [ ] REQUIRED: Avoid 'suppressWarnings'/'Messages' if possible (found 1 times)
• [ ] SUGGESTION: Consider shorter lines. There are 14 lines that are > 80 characters long.
• [ ] SUGGESTION: Consider multiples of 4 spaces for line indents. There are 84 lines that are not.

Best, Kayla

[Kayla-Morrell]

Hello @shbrief - Checking in to see if there has been any progress made on addressing the points from my review. We like to see changes within 2-3 weeks to be sure the package is actively being worked on. Let me know if you have any questions or need any further clarification.

Best, Kayla

[Kayla-Morrell]

@shbrief - I have not heard back from you in some time. If no changes from the review are made in the next week I'll be closing the issue due to inactivity.

Best, Kayla

[shbrief]

@Kayla-Morrell Hi Kayla, I'll make updates by the end of next week. Thanks for keeping track of it. - Sehyun

[shbrief]

Hey Kayla, I need a little more time to update (~a week). Could you wait? Or would it better to close this and resubmit? Let me know. Thanks!

[Kayla-Morrell]

@shbrief - That's fine, I can wait.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 427b633ddf6fcc4369e664a2a2e04803cd389653

[bioc-issue-bot]

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 55f832a0621296634d90824ce4444a009b19bf57

[bioc-issue-bot]

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 26fc2278ef80944ca47bc2143233df6b7fc8f158

[bioc-issue-bot]

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]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9b62ebd831fe4aaff2062e39fe72c34a73844042

[bioc-issue-bot]

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.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 6192b7e1a49cd1a6eb33032ebc7ccd6087221989

[bioc-issue-bot]

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]

@kayla Here are the updates. Let me know what you think. Thanks!

DESCRIPTION

• [x] REQUIRED: Update R version dependency from 4.1 to 4.3.0. --> It seems like the latest version of R is 4.2.2 now. I updated the dependency to 4.2.0. Let me know if this is not ok.
• [x] SUGGESTION: We strongly encourage including the 'BugReports:' field which includes a relevant link to GitHub for reporting issues. --> BugReports: https://github.com/shbrief/AnVILWorkflow/issues is added

NEWS

• [x] SUGGESTION: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements. --> NEWS file is added

Data

• [x] REQUIRED: We require documentation of files in the inst/extdata/ directory in an inst/script/ directory. The script(s) in this directory can vary. Most importantly there needs to be documentation vary clearly stating how the data was generated and source information. It should include source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data. --> Delete some unnecessary files and add the description on map.tsv file under inst/script/ folder.
• [x] REQUIRED: Looking at the data files within 'inst/extdata/' I don't see where Table1.pdf is used within the package. If it is not needed it should be removed. --> Removed

Vignette

• [x] REQUIRED: There should be an Installation section (besides the load package section) that demonstrates to the user how to install the package from Bioconductor. The code chunk should include eval = FALSE. --> The installation section (with eval=FALSE) is added

Man pages

• [ ] SUGGESTION: We encourage having a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?AnVILWorkflow.
• [x] REQUIRED: Should the example for availableAnalysis() have the code to check if gcloud is available? --> This function is supposed to print out workspaces manually curated by this package, which is saved in the package (inst/extdata/map.tsv). So there is no need to check gcloud availability.
• [x] REQUIRED: There should be a runnable example in the setCloudEnv() man page. --> An example is added

Unit tests

• [ ] SUGGESTION: Consider adding unit tests. We strongly encourage them. See https://contributions.bioconductor.org/tests.html

R code

• [x] SUGGESTION: checking R code for possible problems. getOutput: no visible binding for global variable 'workflowName' Undefined global functions or variables: workflowName --> This variable is removed.
• [x] REQUIRED: Avoid 'cat' and 'print' outside of 'show' methods
• [x] REQUIRED: Avoid the use of 'paste' in condition signals
• [x] REQUIRED: Avoid 'suppressWarnings'/'Messages' if possible (found 1 times)
• [x] SUGGESTION: Consider shorter lines. There are 14 lines that are > 80 characters long. --> Shorten several lines that I think are proper.
• [ ] SUGGESTION: Consider multiples of 4 spaces for line indents. There are 84 lines that are not.

[Kayla-Morrell]

@shbrief - Thank you for making the necessary changes. There is just one change that needs to be made and then I'll be able to accept the package.

DESCRIPTION

• [ ] REQUIRED: The R version should be set to 4.3.0, this is the devel version of R and is the version that will work with Bioconductor 3.17 when it is released.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 70634156cecf7c6d1d80ff25ecbca9246a9d3f13

[bioc-issue-bot]

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]

@Kayla-Morrell R dependence version is updated. Thanks!

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[lshep]

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/shbrief.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("AnVILWorkflow"). The package 'landing page' will be created at

https://bioconductor.org/packages/AnVILWorkflow

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.