Closed NajlaAbassi closed 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
cc @federicomarini
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.
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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,
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Received a valid push on git.bioconductor.org; starting a build for commit id: 53c242d6e9324daaf32e5253e14e2a5c7172d4e2
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.
I already subscribed to the Bioc-devel mailing list
I can confirm this; please ignore as it should clear up on the next build
Perfect, thanks for confirming this @lshep ! Shall we still re-trigger a new build, or is this now superfluous?
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
stopifnot
calls into one, e.g.,
stopifnot(is.character(collection), identical(length(collection), 1L))
BiocBaseUtils
for checking assertions with e.g.,
isScalarCharacter
instead of the example above.iSEEnrich
.> 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 ──
0 ERRORS | 0 WARNINGS | 6 NOTES
Received a valid push on git.bioconductor.org; starting a build for commit id: 7a930798c5e3637dc38579174b375d656715ec61
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.
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!
Hi Najla, @NajlaAbassi
Thank you for making those changes! Your package has been accepted.
Best regards, Marcel
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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