iSEEtree

[RiboRings]

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

• Repository: https://github.com/microbiome/iSEEtree

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[bioc-issue-bot]

Hi @RiboRings

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: iSEEtree
Version: 0.99.0
Authors@R: 
    person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
 email = "[email protected]",
 comment = c(ORCID = "0000-0002-8732-7692"))
Title: Interactive visualisation for microbiome data
Description:
    iSEEtree is an extension of iSEE for the TreeSummarizedExperiment.
    It leverages the funcionality from the miaViz package for microbiome data
    visualisation to create panels that are specific for
    TreeSummarizedExperiment objects. Not surprisingly, it also depends on the
    generic panels from iSEE.
biocViews: Microbiome, Software, Visualization, DataImport
License: Artistic-2.0
Encoding: UTF-8
Depends:
    R (>= 4.0),
    iSEE
Imports:
    methods,
    miaViz,
    S4Vectors,
    shiny,
    shinyWidgets,
    SingleCellExperiment,
    SummarizedExperiment,
    TreeSummarizedExperiment
Suggests:
    BiocStyle,
    knitr,
    mia,
    RefManageR,
    remotes,
    rmarkdown,
    scater,
    testthat (>= 3.0.0),
    utils,
    vegan
URL: https://github.com/RiboRings/iSEEtree
BugReports: https://github.com/RiboRings/iSEEtree/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
VignetteBuilder: knitr
Config/testthat/edition: 3

[RiboRings]

Tagging @kevinrue

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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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 the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): iSEEtree_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/iSEEtree to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[RiboRings]

Hi! I'm having a hard time connecting to the Bioconductor.org via ssh to push changes. I activated BiocCredentials account and checked that SSH is correct but still connection fails. Would you have any tip how to fix this issue?

> git remote -v
origin	[email protected]:microbiome/iSEEtree.git (fetch)
origin	[email protected]:microbiome/iSEEtree.git (push)
upstream	[email protected]:packages/iSEEtree.git (fetch)
upstream	[email protected]:packages/iSEEtree.git (push)

> git fetch --all
Fetching origin
Fetching upstream
ssh: connect to host git.bioconductor.org port 22: Operation timed out
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: could not fetch upstream

[kevinrue]

When did you set up the credentials and when did you test?

It's been too long for me to remember but I suspect that Bioconductor has an automated script that runs on a schedule, probably daily, meaning that you may need to give it a bit of time.

Don't take my word for it, I'm genuinely trying to remember!

[RiboRings]

Thanks! I tested immediately after activating it, I'll try tomorrow.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 4ca123970cb2900d13b810b080712790a3113bdc

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: iSEEtree_0.99.2.tar.gz Linux (Ubuntu 22.04.3 LTS): iSEEtree_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/iSEEtree to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[PeteHaitch]

Hi @RiboRings,

Thank you for submitting iSEEtree to Bioconductor.

I've completed my checklist review of iSEEtree and overall the package is in good shape and close to being ready for acceptance. The main issue is in improving the vignette. The vignette is the first thing many potential users will look at, so you want to explain when they might want to use iSEEtree and how it relates to other Bioconductor packages they may already be familiar with.

In my checklist review below I have separated the issues into Required and Recommended points that I would ask you to address before the package can be accepted. Would you please provide line-by-line comments to my initial review so that I know what changes I'm looking for in my re-review.

Cheers, Pete

---

Required

• [ ] The vignette must have an Introduction section. This should include motivation for inclusion to Bioconductor.
  • [ ] Currently, the vignette doesn't really tell someone when they would want to use iSEEtree or how it differs from or extends iSEE. To my mind, you've got 2 sorts of users: (1) those familiar with microbiome packages (mia, TreeSummarizedExperiment, etc.) but not with iSEE and (2) users who are new to microbiome work but perhaps familiar with iSEE from other types of omics data. I think the vignette should point to the extensive iSEE documentation for new users in category (1) and the relevant documentation for new users in category (2).
  • [ ] I come from category (2) and had no real idea what I was looking at when I read the vignette and launched the app, so its also important to some explanation of the new panels to the vignette.
• [ ] Installation instructions should be the officially supported Bioconductor instructions rather than remotes::install_github()-based ones.
• [ ] Man page for iSEEtree::iSEE should document Usage, Arguments, Details, Value, etc. like is done for ?iSEE::iSEE. This might be achieved by cross-linking or otherwise re-using documentation from iSEE (see https://roxygen2.r-lib.org/articles/reuse.html)
• R CMD build reports 2 notes on my system (see below):
  • [ ] I think the first is noting that a LICENSE file isn't required for a package with a Artistic-2.0 license (e.g., core Bioconductor packages with this license, such as https://github.com/Bioconductor/IRanges/, don't include that file).
  • [ ] For the second, have you asked the iSEE whether they'd consider exporting this function?

  * checking top-level files ... NOTE
File
  LICENSE
  * checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘iSEE:::.selectInputHidden’
  See the note in ?`:::` about the use of this operator.

• [ ] The runnable examples on each man page aren't always focused on the documented function. E.g., ?AbundanceDensityPlot doesn't explicitly include that function anywhere in its example. I appreciate that some (if not all) of the exported functions are documenting iSEE panels that on their own may not be functional or useful, but perhaps there's a way to better tailor the examples to the specific function.

Recommended

• [ ] Suggest running spelling::spell_check_package() because I spotted a few typos when reading the documentation.
• [ ] Not clear to me why these chunks are in the vignette. I suggest removing them.
  • [ ] createVignettechunk isn't evaluated or echoed; why is it there?
  • [ ] reproduce1 chunk is redundant because date is automatically added to rendered vignette by BiocStyle
  • [ ] reproduce2 chunk and the startTime <- Sys.time() in vignetteSetup chunk: timing info isn't relevant to user
• [ ] BiocCheck::BiocCheck() recommends some biocViews terms that you might consider (e.g., GUI, ShinyApps)
• [ ] Good job adding unit tests. You could take a look at output of covr::report() to identify areas that may benefit from testing.

[RiboRings]

Hi! Thank you for the thorough feedback! I will work on those points hopefully in a couple of weeks.

Regarding .selectInputHidden, a PR is open in iSEE: https://github.com/iSEE/iSEE/pull/656

[kevinrue]

Regarding .selectInputHidden, a PR is open in iSEE: https://github.com/iSEE/iSEE/pull/656

I completely forgot about that one 🥹

I think the PR covers the technical bit of exporting, but best practice still require a tiny comment about the export in the man page. I'm about to be offline for a week, and this summer is incredibly packed for me, but this export is part of a much larger need to export a whole series of methods needed by various extension packages. iSEE's API for extensions has been growing faster than we've been able to properly document it, so some of the methods are still internal when they should be exported (and renamed without a dot prefix)

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 827151c5fe2fd6b21f6ea53fc92270243da9d9e9

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: iSEEtree_0.99.4.tar.gz Linux (Ubuntu 22.04.3 LTS): iSEEtree_0.99.4.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/iSEEtree to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[RiboRings]

Hi @PeteHaitch!

The package is ready for the next round of review. Below I will mention how the changes map to your feedback

The vignette must have an Introduction section. This should include motivation for inclusion to Bioconductor.

Now the vignettes contain an introduction section and a description of the panels. New users are redirected to the main documentations of iSEE and mia.

Installation instructions should be the officially supported Bioconductor instructions rather than remotes::install_github()-based ones.

Now both the readme and the get started page give Bioconductor installation instructions.

Man page for iSEEtree::iSEE should document Usage, Arguments, Details, Value, etc. like is done for iSEE::iSEE.

Now the vignettes of iSEEtree::iSEE inherit the sections from iSEE::iSEE.

R CMD build reports 2 notes on my system

The LICENSE note was fixed. The .selectInputHidden note is in the agenda but will probably be solved at a later point depending on the iSEE schedule.

The runnable examples on each man page aren't always focused on the documented function.

Now every vignette shows how to view the slots and start iSEE with initial custom panel specifically for the corresponding function. For example: https://microbiome.github.io/iSEEtree/reference/AbundanceDensityPlot.html

Suggest running spelling::spell_check_package()

For me it didn't find any mistake.

Not clear to me why these chunks are in the vignette

I removed them

BiocCheck::BiocCheck() recommends some biocViews terms that you might consider

I added them. However, the recommendations are not always the same when I run the check.

Good job adding unit tests

I added more. Some method like .createObservers are difficult to test because they require an interactive session. Others are tested but not all their parts are detected by codecov.

[PeteHaitch]

Thank you for responding to the review and making many of the requested changes, @RiboRings.

It seems like you might be confused about the difference between a vignette (a file with Bioconductor-specific requirements) and other documentation (e.g., README.Rmd It looks like you've made your changes only to the README.md but not to the actual vignette (vignettes/iSEEtree.Rmd). That is, the vignette still does not contain an Introduction section and still needs the below points from the initial review to be addressed:

• [ ] Not clear to me why these chunks are in the vignette. I suggest removing them.
  • [ ] createVignettechunk isn't evaluated or echoed; why is it there?
  • [ ] reproduce1 chunk is redundant because date is automatically added to rendered vignette by BiocStyle
  • [ ] reproduce2 chunk and the startTime <- Sys.time() in vignetteSetup chunk: timing info isn't relevant to user

Please fix these.

spelling::spell_check_package() does give a bunch of false-positives but reals ones include:

> spelling::spell_check_package()
compositional              README.md:22,90
contructor                 RDAPlot.Rd:9
funcionality               description:2

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9cd27668d141b0d664078c2b3973e80726ea2de8

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: iSEEtree_0.99.5.tar.gz Linux (Ubuntu 22.04.3 LTS): iSEEtree_0.99.5.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/iSEEtree to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[RiboRings]

Thanks @PeteHaitch for clearing that out!

I moved the introduction to the vignette and reorganised it so that it's hopefully easier to follow.

I am getting this warning on Bioconductor server, not sure yet what's the reason: WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested.

I checked and both knitr and rmarkdown are under Suggested in DESCRIPTION.

[PeteHaitch]

Thank you for making those changes, @RiboRings.

I'm now happy to accept iSEEtree into Bioconductor. Congratulations and thank you for your contribution!

Regarding the warning you are receiving from BiocCheck::BiocCheck() (WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested.) - I can reproduce it but I don't understand it either. I see another developer has also been recently confused by this (https://github.com/Bioconductor/Contributions/issues/3379#issuecomment-2244550550). @LiNk-NY Could you please explain what's happening here? Is it a false positive?

[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.

[LiNk-NY]

Could you please explain what's happening here? Is it a false positive?

Thanks @PeteHaitch , yes, it was a false positive. It should be fixed in version 1.41.7.

[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/RiboRings.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("iSEEtree"). The package 'landing page' will be created at

https://bioconductor.org/packages/iSEEtree

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.