Bioconductor
immunogenViewer
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- Repository: https://github.com/kathiwaury/immunogenViewer
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Hi @kathiwaury
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: immunogenViewer
Type: Package
Title: Visualization and evaluation of protein immunogens
Version: 0.99.0
Authors@R: c(person("Katharina", "Waury", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8570-7640")))
Description: Plots protein properties and visualizes position of peptide immunogens within protein sequence.
Allows evaluation of immunogens based on structural and functional annotations to infer
suitability for antibody-based methods aiming to detect native proteins.
License: Apache License (>= 2)
Encoding: UTF-8
LazyData: false
Config/testthat/edition: 3
RoxygenNote: 7.3.1
VignetteBuilder: knitr
Depends:
R (>= 4.0)
Imports:
ggplot2,
httr,
jsonlite,
patchwork,
UniProt.ws
Suggests:
BiocStyle,
knitr,
rmarkdown,
testthat (>= 3.0.0),
DT
biocViews: FeatureExtraction, Proteomics, Software, Visualization
URL: https://github.com/kathiwaury/immunogenViewer
BugReports: https://github.com/kathiwaury/immunogenViewer/issues
I don't think your current custom citation file will display right on our
landing pages as general a citation file must be parsable by
readCitationFile in R. There is also the warning in R CMD check
Found the following CITATION file in a non-standard place:
CITATION.cff
Most likely 'inst/CITATION' should be used instead.
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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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): immunogenViewer_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/immunogenViewer to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 126ef30dcdd5e09acbec0d3910545e36fa7e39fe
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): immunogenViewer_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
[email protected]:packages/immunogenViewer to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: baf9b7ccb608cd8db817a34f40b5bacbefc4eeb5
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): immunogenViewer_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/immunogenViewer to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Hi @kathiwaury,
The package and vignette look good. Only one minor cosmetic detail.
Functions print unnecessary success messages. For example:
> proteinDF <- getProteinFeatures("P55087")
[1] "Successfully created protein dataframe for UniProt P55087."
> proteinDF <- addImmunogen(proteinDF, start=10, end=30, name="A12")
[1] "Successfully added immunogen 'A12' to the protein dataframe."
> proteinDF <- addImmunogen(proteinDF, seq="RFKEAFSKAAQQTKGSYMEVEDNRSQVETDD", name="HPA")
[1] "Successfully added immunogen 'HPA' to the protein dataframe."
This is not really useful. The conventional approach is to raise errors with informative error messages (which you do), but to not print any message in case of success. Exceptions can be made to the "no message on success" rule when one wants to display progress of a long multi-step task. However note that in this case the messages should be displayed with message() instead of print() so that the user can silence the code by wrapping it in suppressMessages().
That will be all! :smiley:
Let me know if you have questions.
Best, H.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2d38335543845c1c30432dd17b21e1447d5f3f20
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: immunogenViewer_0.99.3.tar.gz Linux (Ubuntu 22.04.3 LTS): immunogenViewer_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
[email protected]:packages/immunogenViewer to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @hpages,
Thanks a lot for reviewing!
I have removed the success messages as you suggested. I have also fixed an issue with one of the features and changed names to be more informative in the plot.
All checks ran fine on my side but I get this warning from the Bioconductor Package Builder now:
* Checking vignette directory...
* WARNING: Package listed as VignetteEngine or VignetteBuilder but not currently Suggested.
I have both knitr and rmarkdown listed in the Suggest field, so not really sure how to solve this warning. Could you help with this?
Many thanks,
Kathi
Hi @kathiwaury,
Thanks for making these changes.
I can't reproduce this warning on my laptop where I have the latest version of BiocCheck (1.41.9). Note that the SPB was using BiocCheck 1.41.6 at the time the report was generated, so this strongly suggests that the warning was a false positive that has since been addressed in BiocCheck.
Please remove the LazyData: false line from your DESCRIPTION file.
Once you've done this, the package will be good to go.
Best, H.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5bdf620fea24043d3805501321c80b45768ca609
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: immunogenViewer_0.99.4.tar.gz Linux (Ubuntu 22.04.3 LTS): immunogenViewer_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/immunogenViewer to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @hpages,
the LazyData line is deleted. Happy to hear that the package is good to go. Thanks again!
Best,
Kathi
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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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("immunogenViewer"). The package 'landing page' will be created at
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