Contributions iSEEhub

trafficstars

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

Repository: https://github.com/iSEE/iSEEhub/

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] 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.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] 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.
[x] 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:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] 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.

Aug 16 '22 10:08 kevinrue

Hi @kevinrue

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: iSEEhub
Title: iSEE for the Bioconductor ExperimentHub
Version: 0.99.0
Date: 2022-07-29
Authors@R: 
    c(person("Kevin", "Rue-Albrecht", , "[email protected]",
   role = c("aut", "cre"),
   comment = c(ORCID = "0000-0003-3899-3872")))
Description: This package defines a custom landing page for an iSEE app
    interfacing with the Bioconductor ExperimentHub. The landing page allows
    users to browse the ExperimentHub, select a data set, download and cache it,
    and import it directly into a Bioconductor iSEE app.
License: Artistic-2.0
URL: https://github.com/iSEE/iSEEhub
BugReports: https://support.bioconductor.org/t/iSEEhub
biocViews: Software,
    Infrastructure,
    DataImport,
    SingleCell,
    ImmunoOncology
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
Depends:
    SummarizedExperiment,
    SingleCellExperiment,
    ExperimentHub
Imports:
    AnnotationHub,
    BiocManager,
    DT,
    iSEE,
    methods,
    rintrojs,
    S4Vectors,
    shiny,
    shinydashboard,
    shinyjs,
    utils
Suggests:
    BiocStyle,
    BioPlex,
    bodymapRat,
    CLLmethylation,
    CopyNeutralIMA,
    covr,
    curatedAdipoArray,
    curatedAdipoChIP,
    curatedMetagenomicData,
    curatedTCGAData,
    DuoClustering2018,
    easierData,
    emtdata,
    FieldEffectCrc,
    GSE103322,
    GSE13015,
    GSE62944,
    HDCytoData,
    HMP16SData,
    HumanAffyData,
    imcdatasets,
    knitr,
    mcsurvdata,
    MetaGxBreast,
    MetaGxOvarian,
    MetaGxPancreas,
    MethylSeqData,
    muscData,
    ObMiTi,
    quantiseqr,
    RefManageR,
    restfulSEData,
    RLHub,
    rmarkdown,
    sesameData,
    sessioninfo,
    SimBenchData,
    SingleCellMultiModal,
    spatialDmelxsim,
    STexampleData,
    TabulaMurisData,
    TENxVisiumData,
    testthat (>= 3.0.0),
    tissueTreg,
    VectraPolarisData
Config/testthat/edition: 3
VignetteBuilder: knitr

Aug 16 '22 10:08 bioc-issue-bot

Do you really want all these in Suggests:

Packages suggested but not available:
  'BioPlex', 'bodymapRat', 'CLLmethylation', 'CopyNeutralIMA', 'covr',
  'curatedAdipoArray', 'curatedAdipoChIP', 'curatedMetagenomicData',
  'curatedTCGAData', 'DuoClustering2018', 'easierData', 'emtdata',
  'FieldEffectCrc', 'GSE103322', 'GSE13015', 'GSE62944', 'HDCytoData',
  'HMP16SData', 'HumanAffyData', 'imcdatasets', 'mcsurvdata',
  'MetaGxBreast', 'MetaGxOvarian', 'MetaGxPancreas', 'MethylSeqData',
  'muscData', 'ObMiTi', 'quantiseqr', 'restfulSEData', 'RLHub',
  'sesameData', 'SimBenchData', 'SingleCellMultiModal',
  'spatialDmelxsim', 'STexampleData', 'TabulaMurisData',
  'TENxVisiumData', 'tissueTreg', 'VectraPolarisData'

maybe Enhances would be better? For Check to succeed without changing environment, all those are needed?

Aug 20 '22 10:08 vjcitn

Enhances sounds like a suitable choice. I never fully understood the exact purpose of Enhances, and many times in the past Suggests was recommended to me for various scenarios, which is why it was my first choice here too.

None of the packages (well, perhaps one for unit testing) are needed for check to succeed, as the packages are only loaded (in some cases, installed) during the runtime of the shiny app, which doesn't happen during check, build, or test.

I'll move them all to Enhances ASAP and see what effect it has on Check.

Thanks

Aug 22 '22 10:08 kevinrue

https://github.com/Bioconductor/Contributions/issues/2749#issuecomment-1221274695

Fixed in https://github.com/iSEE/iSEEhub/pull/22

Aug 22 '22 13:08 kevinrue

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

Aug 26 '22 12:08 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 [email protected]:packages/iSEEhub to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 26 '22 12:08 bioc-issue-bot

FYI, I've already discussed the following error on the BioC Slack:

    * ERROR: Remove install() calls (found 1 times)

See https://community-bioc.slack.com/archives/C0207H5QC3X/p1660313871200209

Aug 26 '22 15:08 kevinrue

Hi @kevinrue I'm currently on holidays but will post my review as soon as I'm back (10th September).

Aug 30 '22 13:08 nilseling

btw, note: we've pushed two new versions that haven't triggered new builds

Sep 12 '22 19:09 kevinrue

Have you bumped the package version? In the linked Github repo I don't see new changes and the version is still at 0.99.1.

Sep 13 '22 08:09 nilseling

Yeah, so when i bumped the version to 0.99.1 nothing happened. Then I thought Charlotte bumped it to 0.99.2 but you make me realise that the PR hasn't been merged yet, it's only open at the moment.

Sep 13 '22 09:09 kevinrue

OK, so there's something funky about the PR for 0.99.2, github action is throwing an error for something that worked before and that the PR is not touching, possibly something about the repositories where packages are installed from. In any case, you can review 0.99.1 in the meantime, because 0.99.2 is only bringing minor aesthetic fixes. We might even pack fixes following your review in that PR, depending on timings.

Sep 13 '22 09:09 kevinrue

Sounds good, that's also what I wanted to suggest as I don't have major comments anyway.

First of all, thanks for submitting iSEEhub. The package is in a great shape and there are only a few things that I noticed:

[x] R CMD build should pass without errors, warnings and notes: Please address the last NOTEs by selectively importing capture.output, code, hr, installed.packages, modalDialog, removeModal and showModal.
[x] Checking the discussion on Slack, I think the ERROR: Remove install() calls (found 1 times) can be ignored.

Documentation

[x] The vignette is lacking an Introduction section. Even though iSEEhub is an extension to iSEE, you should consider adding a short introduction to explain its use cases. Please also motivate its inclusion in Bioconductor as link between iSEE and ExperimentHub.

The CITATION file

[ ] The CITATION file contains invalid DOIs. Exclude of adapt the file until the DOIs are active.

R code

[x] Add a validity check that ehub is actually an ExperimentHub object.

Shiny apps

[x] The tour doesn't seem to point at the right locations (e.g. when selecting the Info tab, the Launch button cannot be found)

Unit test

[x] Looks good but there is still one test failing.

Sep 13 '22 09:09 nilseling

Sounds all good. As it happened, I've just merged 0.99.2 before noticing your review. So:

We'll make another PR (0.99.3) to incorporate changes following your review.
Bumping 0.99.2 still didn't trigger another build of the single package builder. Not sure what I'm missing

Sep 13 '22 11:09 kevinrue

Did you git push upstream main:master?

Sep 13 '22 11:09 nilseling

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.

i feel such a newb right now xD

Sep 13 '22 13:09 kevinrue

Received a valid push on git.bioconductor.org; starting a build for commit id: 8ffd53419cd256834d8a773e5a633f04b152e31a

Sep 13 '22 13:09 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 [email protected]:packages/iSEEhub to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sep 13 '22 13:09 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: c193740de69420f3f3a89b63789cde25cc1d9a8b

Sep 13 '22 15:09 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 [email protected]:packages/iSEEhub to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sep 13 '22 15:09 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: d61891e8681f731ef5181d91f565680acab85bb4

Sep 14 '22 09:09 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 [email protected]:packages/iSEEhub to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sep 14 '22 09:09 bioc-issue-bot

Target achieved; only one ERROR left, which we agreed to ignore:

* Checking parsed R code in R directory, examples, vignettes...
    * ERROR: Remove install() calls (found 1 times)

Probably worth bringing in a core team member at this point to establish this as a precedent of non-core package being allowed this ERROR, and possibly turning it into a WARNING?

Thanks for the review!

Sep 14 '22 09:09 kevinrue

I have now accepted the package for inclusion in Bioconductor allowing the BiocManager::install() call as an exception.

Sep 19 '22 08:09 nilseling

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

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

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

https://bioconductor.org/packages/iSEEhub

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.

Sep 26 '22 13:09 lshep

Contributions Contributions copied to clipboard

iSEEhub

Documentation

The CITATION file

R code

Shiny apps

Unit test

Contributions
Contributions copied to clipboard