BiocHail

[vjcitn]

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• Repository: https://github.com/vjcitn/BiocHail

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[bioc-issue-bot]

Hi @vjcitn

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: BiocHail
Date: 2023-03-02
Title: basilisk and hail
Version: 0.99.8
Authors@R: 
    c(person(
        "Vincent", "Carey", role = c("aut", "cre"),
        email = "stvjc@channing.harvard.edu",
        comment = c(ORCID = "0000-0003-4046-0063")
     )
    )
Description: Use hail via basilisk when appropriate, or via reticulate.
    This package can be used in terra.bio to interact with UK Biobank
    resources processed by hail.is.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.2), graphics, stats, utils
Imports: reticulate, basilisk, BiocFileCache
Suggests: knitr, testthat, BiocStyle, ggplot2, DT
VignetteBuilder: knitr
biocViews: Infrastructure
RoxygenNote: 7.2.3
URL: https://github.com/vjcitn/BiocHail
BugReports: https://github.com/vjcitn/BiocHail/issues

[bioc-issue-bot]

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[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/BiocHail 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: 33868831f23888fc298522f1a6e485a65ebd3e83

[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: "WARNINGS, 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/BiocHail 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: 22b74d04be0f4272b14b919873cadad1453296cf

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

[vjcitn]

I am glad to see this is building on linux. I may have to disable macos build ... interactions of java and python and spark may be too delicate for that OS. I am checking a windows system now.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 19640f23d33cc4dc0bbe26751e99f97ccafe8629

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

[ococrook]

Maybe worth checking the environmental variable is pointing to the jdk installation on MAC OS. (Assuming Java is installed)

On MAC OS this is usually somewhere in /Library rather than /usr. This is outside my expertise to make these changes on merida1, however.

[vjcitn]

Thanks. My sense is that this is not going to work on windows note from team; that was 2020 but I tried more recently to no avail. And I don't think it will work on mac unless we downgrade jdk to 11 at latest. I am trying to get time on an intel mac; I have definitely failed with M1. For now I am going to set both macos and win to UnsupportedPlatform in .BBSoptions.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 780d939f92545987dc5a95e8fa12a7c4da3b4655

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

[ococrook]

Is it expected to work on all linux systems? If I can't install it on Fedora I may need to assign the review to someone else

[vjcitn]

I would expect it to run on any reasonably current x86_64 linux system. If you have a problem and post the error messages here I will comment further. It uses basilisk so the first install/execute leads to cached installation of miniconda and all necessary python infrastructure. I am using

openjdk 11.0.18 2023-01-17
OpenJDK Runtime Environment (build 11.0.18+10-post-Ubuntu-0ubuntu120.04.1)
OpenJDK 64-Bit Server VM (build 11.0.18+10-post-Ubuntu-0ubuntu120.04.1, mixed mode, sharing)

and I think JDK <= 11 may be a hard requirement. This could scupper this submission but it has to do with spark versions supported. Here is some relevant discussion with hail support. (If you are working with JDK > 11, it may still work but with warnings...)

[vjcitn]

I guess you can have multiple jdks in linux? So maybe I need to add a requirement and do some configuration.... I seem to have gotten lucky on the BBS

[ococrook]

Thanks @vjcitn, I'll try soon to see if I can get it install and hopefully I don't come up against any challenges if I do, I'll let you know.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b91dde0c24377a9ba63dfbf44329c8c90a7a09dc

[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/BiocHail 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: f7ad123ba674d50a35fb42d6d3f06b45faed05c4

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

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

[hpages]

@vjcitn Could you add a .BBSoptions file to the package to specify the unsupported platforms? E.g.

UnsupportedPlatforms: win, mac

if the package is only going to be supported on Linux. Thanks

[vjcitn]

It runs on intel mac too. I will add the .BBSoptions for win

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

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

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

[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/BiocHail 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: 7740ce3407fc8ef44e076cbac9546b51217b2bc8

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

[vjcitn]

@ococrook I finally made changes to get this to run cleanly on the linux builder. I will have to go into the mac platform to get it to work there; could be a java config step needed. Have you had a chance to try on fedora? It won't work with jdk > 11 AFAIK.

[ococrook]

Hi @vjcitn and @lshep

Unfortuntely, I don't have a way to install this package as my linux computer doesn't have admin rights so can't upgrade to the required dependencies and the package isn't supported on windows. I've had a look through the package and don't see anything to drawn concerns. Though I think someone who can put the package through some more thorough testing would be great to have a look at the package too.

Best wishes, Olly

[vjcitn]

Can I ask which dependencies can't be met? pip install at the user level should succeed to get hail itself in without privileges, and that is taken care of by basilisk. The only other requirement would be java <= 11 and I have to work on configuration for that. That might not be solvable, but admins could install jdk 11 alongside whatever is running and then the configuration could use it. Of course we will try to find another reviewer, sorry to take up your time.

[ococrook]

We're actually stuck at R 4.1.2 or lower still, I can ask admins to see when when updade to 4.2 can happen

[Kayla-Morrell]

@vjcitn - 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. Also, keep in mind that the deadline for packages to be accepted for the upcoming release is April 19th.

DESCRIPTION

• [ ] SUGGESTION: The 'Description:' field is made up by less than 3 sentences. Please consider expanding this field and structure it as a full paragraph.
• [ ] REQUIRED: Update R version dependency from 4.2 to 4.3.0.

NEWS

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

Data

• [ ] REQUIRED: The README.txt should be moved to inst/script/. This is where the documenation should be for any of the data in inst/extdata/.
• [ ] REQUIRED: There needs to be documentation in inst/script/ for myss2.zip.

Vignettes

• [ ] REQUIRED: There should be 'Installation' sections in the vignettes to show users how to download and load the package from Bioconductor.
• [ ] REQUIRED: The final section of the vignettes should be 'Session Information' and include sessionInfo().

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 ?BiocHail.
• [ ] REQUIRED: There should be runnable examples to all man pages that document exported objects.
• [ ] SUGGESTION: Use donttest{} instead of dontrun{}. donttest{} requires valid R code while dontrun{} does not.

R code

• [ ] SUGGESTION: Avoid 1:...; use seq_len() or seq_along().
• [ ] SUGGESTION: Avoid using '=' for assignment and use '<-' instead.
• [ ] SUGGESTION: For formating reasons, consider shorter lines. There are 129 lines that are > 80 characters long.
• [ ] SUGGESTION: For formating reasons, consider 4 spaces instead of tabs. 1 line contains tabs.
• [ ] SUGGESTION: For formating reasons, consider multiples of 4 spaces for line indents. Thre are 201 lines that are not.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b8d4ef9083681fe203c4783337fa5d2a89dc2040

[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: "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/BiocHail 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: bd437706a90f85a25456e3bf586059d07c34a26c

[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/BiocHail 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: 71cc14607934ae2b8ab7fe66d827a5394377a1c7

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

[vjcitn]

I just did another commit after running styler, so now I think all comments have been addressed except the suggestion for making an overview man page. I don't know how to do that with roxygen. Thanks for the review!

[Kayla-Morrell]

@vjcitn - Thank you for making the necessary changes. I have reviewed everything and the package looks good. I'm more than happy to accept it.

Best, Kayla

[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 default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/vjcitn.keys is not empty), then no further steps are required. Otherwise, do the following:

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See further instructions at

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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("BiocHail"). The package 'landing page' will be created at

https://bioconductor.org/packages/BiocHail

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.