dir.expiry

[LTLA]

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• Repository: https://github.com/LTLA/dir.expiry

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[bioc-issue-bot]

Hi @LTLA

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: dir.expiry
Version: 0.99.0
Date: 2021-02-14
Title: Managing Expiration for Cache Directories
Description: Implements an expiration system for access to versioned directories.
    Directories that have not been accessed by a registered function within a certain time frame are deleted.
    This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.
Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email="infinite.monkeys.with.keyboards@gmail.com")
License: GPL-3
Imports:
    utils,
    filelock
Suggests:
    rmarkdown,
    knitr,
    testthat,
    BiocStyle
biocViews:
    Software,
    Infrastructure
VignetteBuilder: knitr
RoxygenNote: 7.1.1

[LTLA]

This is motivated by the need to clear cached content for basilisk and rebook, and uses code already present in the former.

To preempt any suggestion to use BiocFileCache: yes, I did think about it, but:

• Too may dependencies for features that I didn't need.
• SQL look-up is slow and uses a lock that insufficiently granular.
• Expiry refers to re-downloading rather than deletion.
• Doesn't seem like I'm allowed to store directories rather than files, e.g., bfcremove() doesn't do a recursive removal.

[mtmorgan]

Have you considered submitting this to CRAN since it has not Bioc dependencies (other than for the vignette, is useful outside the Bioc ecosystem, and is not likely to experience the rapid development / bug fix that makes the bioc release model more appealing?

[LTLA]

Hm. I thought you might say that.

Yes, I did think about it, but the CRAN submission process seems incredibly tedious.

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

[nturaga]

Hm. I thought you might say that.

Yes, I did think about it, but the CRAN submission process seems incredibly tedious.

Hi @LTLA Are you not submitting this to CRAN just because it's tedious? I have to agree with Martin here that I'm not able to find relevance for the package in Bioconductor.

According to the package submission pages, a Bioconductor the package should:

• Address areas of high-throughput genomic analysis, e.g., sequencing, expression, and other microarrays, flow cytometry, mass spectrometry, image analysis; see biocViews.
• Interoperate with other Bioconductor packages by re-using common data structures (see S4 classes and methods) and existing infrastructure (e.g., rtracklayer::import() for input of common genomic files).
• Adopt software best practices that enable reproducible research and use, such as full documentation and vignettes (including fully evaluated code) as well as a commitment to long-term user support through the Bioconductor support site.
• Not exist on CRAN. A package can only be submitted to one or the other. Comply with Package Guidelines.
• Your package cannot depend on any package (or a version of a package) that is not (yet) available on CRAN or Bioconductor.

Any thoughts?

[LTLA]

Are you not submitting this to CRAN just because it's tedious?

Well, it's not just the initial submission process. I'm not encouraged by the CRAN guidelines, which recommend that maintainers limit package updates to monthly intervals. dir.expiry is solely designed to provide some infrastructure for rebook (and thus the OSCA books) and basilisk, both of which are difficult downstream dependencies. Historically speaking, updates to both packages on the BBS come in bursts as I try to identify a functional deployment strategy via trial and error.

I suspect that incorporation of dir.expiry into either of these projects will involve a lot of fine-tuning to dir.expiry itself, and I'm not convinced that CRAN will allow me to do that in an expedient manner. Wen I participate in development of other CRAN packages, there always seems to be an inclination to reduce the number of updates, which does not seem very agile.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d1a40cf6259055aba9f7410bbe0a2d6b75a93cd0

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

[nturaga]

Are you not submitting this to CRAN just because it's tedious?

Well, it's not just the initial submission process. I'm not encouraged by the CRAN guidelines, which recommend that maintainers limit package updates to monthly intervals. dir.expiry is solely designed to provide some infrastructure for rebook (and thus the OSCA books) and basilisk, both of which are difficult downstream dependencies. Historically speaking, updates to both packages on the BBS come in bursts as I try to identify a functional deployment strategy via trial and error.

I suspect that incorporation of dir.expiry into either of these projects will involve a lot of fine-tuning to dir.expiry itself, and I'm not convinced that CRAN will allow me to do that in an expedient manner. Wen I participate in development of other CRAN packages, there always seems to be an inclination to reduce the number of updates, which does not seem very agile.

ok @LTLA I'll review the package. It seems that's a fair reason to have it in Bioconductor.

[nturaga]

Review dir.expiry

R CMD build

ok

R CMD INSTALL

ok

DESCRIPTION

ok

NAMESPACE

ok

vignette

Good

R

Good!

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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

https://bioconductor.org/packages/dir.expiry

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.