Closed kriemo closed 8 months ago
Hi @kriemo
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: raerdata
Title: A collection of datasets for use with raer package
Version: 0.99.2
Description: raerdata is an ExperimentHub package that
provides a collection of files useful for demostrating
functionality in the raer package. Datasets include
10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome
and RNA-seq data. Additionally
databases of human and mouse RNA editing sites are provided.
Authors@R:
person(given = "Kent",
family = "Riemondy",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-0750-1273"),
email = "kent.riemondy@cuanschutz.edu")
License: MIT + file LICENSE
Imports:
ExperimentHub,
Rsamtools,
SingleCellExperiment,
rtracklayer,
GenomicRanges,
BiocGenerics
Suggests: rmarkdown, knitr, BiocStyle
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Encoding: UTF-8
biocViews: SingleCellData, SequencingData, RNASeqData, ExperimentHub, PackageTypeData, ExpressionData
BugReports: https://github.com/rnabioco/raerdata/issues
URL: https://github.com/rnabioco/raerdata
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 Build System.
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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): raerdata_0.99.2.tar.gz macOS 12.6.5 Monterey: raerdata_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/raerdata
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
AdditionalPackage: https://github.com/rnabioco/raer
Hi @kriemo, Thanks for submitting your additional package: https://github.com/rnabioco/raer. We are taking a quick look at it and you will hear back from us soon.
Additional Package has been approved for building.
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.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: macOS 12.6.5 Monterey: raer_0.99.14.tar.gz Linux (Ubuntu 22.04.2 LTS): raer_0.99.14.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/raer
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Regarding the R CMD CHECK checking compiled code ... WARNING
seen on the package builds. This warning arises from the use of Rhtslib, which includes source code with sprintf
usage. From my understanding this is an expected warning, and is found with all packages that use Rhtslib (https://bioconductor.org/checkResults/3.18/bioc-LATEST/Rhtslib/ ).
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
@kriemo - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review. Keep in mind that the deadline to accept new packages into the Bioconductor 3.18 release is 10/18. Any packages accepted after this date will be included in the next release.
importFrom()
is encouraged over importing an
entire package. However, if there are many functions from a single package
import()
can be acceptable. One should just be selective with the use of
import()
.Best, Kayla
@Kayla-Morrell. Many thanks for the review. I have one quick question before I begin addressing the comments. Is the review in reference to both submitted packages or just the experiment data raerdata
package?
Thanks, Kent
@kriemo - I'm so sorry I missed the additional package line! This would be a review for just raerdata
. If you want to work on addressing that review I can work on getting a review together for rear
and have it posted shortly.
Best, Kayla
ok great, thank you.
Received a valid push on git.bioconductor.org; starting a build for commit id: 8fab809fe2d49f69fe8746652f8ae512b84ca0d4
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): raerdata_0.99.3.tar.gz macOS 12.6.5 Monterey: raerdata_0.99.3.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/raerdata
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
I've made the requested changes to the raerdata
package and fixed most of the suggested formatting notes
I have replaced all imports with importFrom()
I have added an Introduction section with some additional details
I have added an Installation section
I have added unit tests to ensure that the package functions return the expected experimentHub resources
I have reduced the number of lines > 80 characters down to 2 documentation lines, which reference URLs
I have fixed this formatting issue
@kriemo - Below is my review for raer. I'll work on re-reviewing raerdata while you work on addressing these points.
inst/exdata/
data needs accompanying documentation. This
documentation belongs in inst/scripts/
. There should be scripts present that
document very clearly how the data was generated and source information. It
should include source URLs and any key information regarding filtering or
processing. It can be executable code, sudo code, or a text description. Perhaps
your README file in inst/extdata/
should be moved to inst/scripts/
. eval = FALSE
.figures/
directory does not belong in man/
. I would
suggest moving this directory to inst/figures/
.Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: f0b45380e6b76ed3dd0cd946f33cf7a88e71c9a9
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): raer_0.99.15.tar.gz macOS 12.6.5 Monterey: raer_0.99.15.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/raer
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@Kayla-Morrell Many thanks for your prompt review of the raer
package. I believe I have addressed your comments, with the exception of the request to remove the man/figures
directory, which I justify in the notes below. The WARNING from the single package builder is the same warning related to the use of Rhtslib
in the package that I mentioned previously in the issue.
I have moved the README from inst/extdata
to inst/scripts
and updated the README text. I copied the corresponding scripts from raerdata
referenced in the README into inst/scripts
and kept only code relevant for making the files present in the inst/extdata
directory.
I have modified the code to make it executable (lines 183 - 203)
I have added this section (lines 35 - 43)
I have made the sessionInfo an entry in the table of contents and removed the html that made the content a hidden code chunk.
- [ ] REQUIRED: The figures/ directory does not belong in man/. I would suggest moving this directory to inst/figures/.
I would like to request an exemption to this required change. The image files included in man/figures
are referenced as part of the documentation for the package (?raer
) and used by the pkgdown documentation site for the package. The man/figures
directory is a standard directory that is supported by CRAN, and the suggested location for images used in the documentation. https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Figures
The man/figures
directory is also currently used by many Bioconductor packages that use pkgdown for their documentation: (e.g. results from a BioC code search for packages that reference an man/figures/logo.png file)
I have moved the illustrator file (raer-logo.ai
) to inst/misc
as this is not necessary for pkgdown or the R documentation.
I have reduced the number of lines > 80 from 323 lines to 70 lines. Most of the remaining lines > 80 characters are in .Rd documentation files.
I have reduced the number of line indents not multiples of 4 spaces from 217 lines to 115 lines. Most of the remaining problematic lines idents are in .Rd documentation files.
@kriemo - Thank you for making all the necessary changes. I have re-reviewed both raer and raerdata and everything looks good. I'm more than happy to accept the packages.
Best, Kayla
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.
Great, thank you so much for all of your help!
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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
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(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("raer")
. The package 'landing page' will be created at
https://bioconductor.org/packages/raer
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.
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