AnVILPublish

[mtmorgan]

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

• Repository: https://github.com/mtmorgan/AnVILPublish

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 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 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 help with submitting your package, please subscribe and post questions
to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @mtmorgan

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: AnVILPublish
Title: Publish Packages and Other Resources to AnVIL Workspaces
Version: 0.99.0
Authors@R: 
    person(
        given = "Martin",
        family = "Morgan",
        role = c("aut", "cre"),
        email = "Martin.Morgan@RoswellPark.org",
        comment = c(ORCID = "0000-0002-5874-8148")
    )
Description:
    Use this package to create or update AnVIL workspaces from
    resources such as R / Bioconductor packages. The metadata about
    the package (e.g., select information from the package DESCRIPTION
    file and from vignette YAML headings) are used to populate the
    'DASHBOARD'. Vignettes are translated to python notebooks ready
    for evaluation in AnVIL.
License: Artistic-2.0
Imports:
    AnVIL,
    httr,
    rmarkdown,
    whisker,
    tools,
    utils,
    stats,
Suggests:
    knitr,
    BiocStyle,
    BiocManager
biocViews: Infrastructure, Software
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
VignetteBuilder: knitr

[bioc-issue-bot]

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]

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/AnVILPublish 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: fce9bbb382d2109f3da2aae87bf29dbf48aeb18e

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

[lshep]

Please see initial review:

Description

• There doesn't seem to be data but we recommend LazyData: true be remove from the DESCRIPTION file. We have rarely found it useful and that it can actually slow the installation process.

.github/workflows

• Will information in this need to be updated frequently by maintainer or by user? Seems to have hard coded data like R version that may become stale?

Vignette

• Update installation to include Bioconductor official repository for stable copy and github for devel

• AnVILPublish::add_user is not an exported function? Did this change name to AnVILPublish::add_access? Also the above tested worked great with BiocFileCache, is there a user you can think of that I can test this function?

• What is the default access level when a workspace/notebook is created? It seems like it already had Bioconductor_User, is this because I am part of that group?

Cheers,

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2de2d65f718bdb6498cbf8b18c808a78b32756c3

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

[mtmorgan]

Thanks for the comments! Checked boxes represent updates made.

Description

• There doesn't seem to be data but we recommend LazyData: true be remove from the DESCRIPTION file. We have rarely found it useful and that it can actually slow the installation process.

.github/workflows

• Will information in this need to be updated frequently by maintainer or by user? Seems to have hard coded data like R version that may become stale?

Vignette

• Update installation to include Bioconductor official repository for stable copy and github for devel

• AnVILPublish::add_user is not an exported function? Did this change name to AnVILPublish::add_access? Also the above tested worked great with BiocFileCache, is there a user you can think of that I can test this function?

• What is the default access level when a workspace/notebook is created? It seems like it already had Bioconductor_User, is this because I am part of that group?

  The Bioconductor_User was added by default on creation or update of a workspace, but I have changed this (and the documentation, e.g., in the vignette) so that add_access() needs to be run explicitly. By default, only the person running as_workspace() will have access.

The build report ERROR is as before, a concern about runnable examples, but the functionality should not be run during testing or via example().