Bioconductor / Contributions

Contribute Packages to Bioconductor
135 stars 33 forks source link

iSEEfier #3348

Closed NajlaAbassi closed 8 months ago

NajlaAbassi commented 8 months ago

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

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 commented 8 months ago

Hi @NajlaAbassi

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: iSEEfier
Title: Streamlining the creation of initial states for starting an iSEE instance
Version: 0.99.0
Authors@R:
    c(
    person(given = "Najla", family = "Abassi", role = c("aut", "cre"),
 email = "abassi.nejla96@gmail.com", comment = c(ORCID = "0000-0001-8357-0938")
 ),
    person(given = "Federico", family = "Marini", role = c("aut"), 
 email = "marinif@uni-mainz.de", comment = c(ORCID = "0000-0003-3252-7758")
 )
    )
Description: 
    iSEEfier provides a set of functionality to quickly and intuitively create, 
    inspect, and combine initial configuration objects. 
    These can be conveniently passed in a straightforward manner to the function
    call to launch iSEE() with the specified configuration. 
    This package currently works seamlessly with the sets of panels provided by 
    the iSEE and iSEEu packages, but can be extended to accommodate the usage of
    any custom panel (e.g. from iSEEde, iSEEpathways, or any panel developed 
    independently by the user).
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports:
    iSEE,
    iSEEu,
    methods,
    ggplot2,
    igraph,
    rlang,
    stats,
    SummarizedExperiment,
    SingleCellExperiment,
    visNetwork
Suggests:
    knitr,
    rmarkdown,
    scater,
    scRNAseq,
    org.Mm.eg.db,
    scuttle,
    BiocStyle,
    testthat (>= 3.0.0)
biocViews:
    CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, 
    GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, 
    Transcription, Transcriptomics, Visualization
URL: https://github.com/NajlaAbassi/iSEEfier
BugReports: https://github.com/NajlaAbassi/iSEEfier/issues
Config/testthat/edition: 3
VignetteBuilder: knitr
NajlaAbassi commented 8 months ago

cc @federicomarini

bioc-issue-bot commented 8 months ago

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.

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 commented 8 months ago

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: "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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): iSEEfier_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 git@git.bioconductor.org:packages/iSEEfier to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

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

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 53c242d6e9324daaf32e5253e14e2a5c7172d4e2

bioc-issue-bot commented 8 months ago

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: "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.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): iSEEfier_0.99.1.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 git@git.bioconductor.org:packages/iSEEfier to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

NajlaAbassi commented 8 months ago

I already subscribed to the Bioc-devel mailing list

lshep commented 8 months ago

I can confirm this; please ignore as it should clear up on the next build

federicomarini commented 8 months ago

Perfect, thanks for confirming this @lshep ! Shall we still re-trigger a new build, or is this now superfluous?

LiNk-NY commented 8 months ago

Hi @NajlaAbassi

Thank you for your submission. Overall, the package looks to be in good shape. I only made some minor suggestions.

Best regards, Marcel


iSEEfier

DESCRIPTION

NAMESPACE

vignettes

R

tests

> covr::package_coverage(type = "all")
iSEEfier Coverage: 98.91%
R/utils.R: 98.51%
R/iSEEinit.R: 99.13%
R/iSEEnrich.R: 100.00%

BiocCheck results

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES
bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7a930798c5e3637dc38579174b375d656715ec61

bioc-issue-bot commented 8 months ago

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): iSEEfier_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 git@git.bioconductor.org:packages/iSEEfier to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

NajlaAbassi commented 8 months ago

Thank you for your timely positive review @LiNk-NY !

We addressed the points you raised in a separate branch BiocReview, which we just merged in devel (link to the PR for you to check all thins at once: https://github.com/NajlaAbassi/iSEEfier/pull/8).
Please find below our comments, in a point by point fashion.

vignettes

* Minor: Consider wrapping text to fit an 80 character column width.

* It looks good.

We changed the text to fit a 80 character limit.

R

* The documentation text and even code goes past the 80 column width and makes
  it hard to read and review.

Similar to the vignette, the code and documentation were wrapped into lines of 80 characters. BiocCheck is still raising a note for this, but only for a few extra characters and only a few occurrences.

* Combine multiple `stopifnot` calls into one, e.g.,
stopifnot(is.character(collection), identical(length(collection), 1L))
* Consider using `BiocBaseUtils` for checking assertions with e.g.,
  `isScalarCharacter` instead of the example above.

Thanks a lot for pointing out BiocBaseUtils, we rewrote these checks in a more compact manner.

* Tell the user what package needs to be installed in the error message in
  `iSEEnrich`.

Good point, thanks. We updated the error message accordingly.

BiocCheck results

* Consider resolving some of the notes. Overall, it looks good.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES

→ The print() statement is there on purpose to render the htmlWidget output of the function, so we cannot remove it.

→ In the context of that function (glue_initials()), we thought it was meaningful to have the message returned with this combination of conditions.

→ We opted for an indentation of 2 spaces instead of 4, and worked by reflowing the code and comments to reduce its width. Regarding the length of the functions, we felt we could not modularize the routines further, which is why we kept them as they were.

→ Both Federico and I are correctly registered and subscribed to the bioc devel mailing list, this might be a false positive hit that we also get while running the checks locally.


Please let us know if we need to do some additional work. Thank you again for the feedback!

LiNk-NY commented 8 months ago

Hi Najla, @NajlaAbassi

Thank you for making those changes! Your package has been accepted.

Best regards, Marcel

bioc-issue-bot commented 8 months ago

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.

lshep commented 8 months ago

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/NajlaAbassi.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("iSEEfier"). The package 'landing page' will be created at

https://bioconductor.org/packages/iSEEfier

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.