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mapper #3419

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haihuilab opened this issue May 14, 2024 · 5 comments
Open
10 tasks done

mapper #3419

haihuilab opened this issue May 14, 2024 · 5 comments
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1. awaiting moderation submitted and waiting clearance to access resources 3d. needs interop Package must explicitly use Bioconductor structures and methods 3e. pending pre-review changes review has indicated blocking concern that needs attention

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@haihuilab
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haihuilab commented May 14, 2024

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

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

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

  • 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.

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

  • 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.

  • I am familiar with the Bioconductor code of conduct and
    agree to abide by it.

I am familiar with the essential aspects of Bioconductor software
management, including:

  • The 'devel' branch for new packages and features.
  • The stable 'release' branch, made available every six
    months, for bug fixes.
  • Bioconductor version control using Git
    (optionally via GitHub).

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
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Dear @haihuilab,

The package version number, '1.99.1', does not start
with 0. Expecting format: '0.99.z' for new packages. Starting
with non-zero x of 'x.y.z' format is generally only allowed if
the package has been pre-released.

We recommend fixing the version number. See Bioconductor version numbers
Please also consider running BiocCheck::BiocCheck('new-package'=TRUE) on your package
to look for other Bioconductor package requirements.

@bioc-issue-bot
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Hi @haihuilab

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: mapper
Title: A wrapper of `purrr` and `furrr` packages for easy parallel mapping in R (mapper)
Version: 1.99.1
Maintainer: Haihui Zhang <zhanghaihui@pku.edu.cn>
Authors@R: 
    person("Haihui", "Zhang", , "zhanghaihui@pku.edu.cn", role = c("aut", "cre"),
 comment = c(ORCID = "0009-0006-4619-4500"))
Description: You just need to change `map` function to `mapper` function (and also other mapping functions) for parallel calculation.
License: MIT + file LICENSE
VignetteBuilder: knitr
biocViews: Software, StatisticalMethod, Visualization
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports: 
    furrr,
    future,
    magrittr,
    parallel,
    purrr
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3

@bioc-issue-bot bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label May 14, 2024
@bioc-issue-bot bioc-issue-bot mentioned this issue May 14, 2024
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@haihuilab
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Thank you so much! I have changed the version to 0.99.0

@lshep
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lshep commented May 17, 2024

You need to resubmit as a new issue so that other prechecks will also pass

@bioc-issue-bot bioc-issue-bot mentioned this issue May 17, 2024
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@lshep
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lshep commented May 20, 2024

The package documentation is not sufficient for Bioconductor standards. There are no man pages and the vignette needs much more detail on what the package does and providing examples. There is also no interopability with existing Bioconductor classes. Please show how this would work into a Bioconductor workflow/pipeline with existing Bioconductor class structures. See http://contributions.bioconductor.org/develop-overview.html . The vignette should also include an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope.

@lshep lshep added 3e. pending pre-review changes review has indicated blocking concern that needs attention 3d. needs interop Package must explicitly use Bioconductor structures and methods labels May 20, 2024
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