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scToppR
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- Repository: https://github.com/bryanwgranger/scToppR
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Hi @bryanwgranger
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: scToppR
Title: API Wrapper for ToppGene
Version: 0.99.10
Authors@R:
person("Bryan", "Granger", , "[email protected]", role = c("aut", "cre"), comment=c(ORCID="0009-0008-6663-3755"))
Description: scToppR provides an easy-to-use API wrapper for the ToppGene web platform, used for gene ontology and functional enrichment research. The package also integrates visualization tools, making it a convenient tool directly connecting ToppGene to code-based workflows in R. The tool can also easily save results into different formats.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports:
dplyr,
forcats,
ggplot2,
httr,
rjson,
stringr,
openxlsx,
viridis,
patchwork,
utils
Depends:
R (>= 4.3.0)
LazyData: false
Suggests:
knitr,
rmarkdown
VignetteBuilder: knitr
biocViews: Pathways, SingleCell
BugReports: https://github.com/BioinformaticsMUSC/scToppR
URL: https://github.com/BioinformaticsMUSC/scToppR
I'm concerned that the usage of the ToppGene website is not better advertised or explained within the package or package documentation. It should be stated up front in the vignette, man page, and any function that is collecting data from the site that the data might actually be usable and that you would need to check with the "third party" term and conditions.
Currently the package vignettes are focused on using data from Seurat Data objects that are not currently common Bioconductor workflow. It is fine to keep these but it will also be a requirement to show how this can work with and utilize a common Bioconductor class structure for this type of data.
Yes, apologies! Thank you for the feedback, I am finishing up the changes to the code and will be able to commit the changes in the next day or two. When I do, I will explain more here as well.
Hello, I have made some updates to scToppR:
That's a good point about making sure it's very clear that the data being used is from ToppGene and should adhere to their terms of use. Accordingly, I've added text in the README, a package startup message on attaching, the man file for toppFun(), and the toppFun() function (by printing a message when running it) itself to remind users that all data being used is governed by ToppGene's terms of use.
Additionally, I have also added a new vignette using a standard Bioconductor class, using DESeq2 to analyze the 'airway' dataset. From there, the toppFun() function can be run directly on the results, which are in a DESeqResults object.
I have pushed all changes to the Github repository here. I'm not sure if I need to be pushing the changes at this stage during review to the git.bioconductor.org repo (if that exists), and I'm having trouble doing so. But if I need to, I will address that asap.
Thanks again for your feedback, please let me know if these changes address your concerns.
I'm trying to build this locally and get the following error:
R CMD build scToppR
* checking for file 'scToppR/DESCRIPTION' ... OK
* preparing 'scToppR':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘differential_expression_airway.Rmd’ using rmarkdown
Quitting from lines 24-50 [setup] (differential_expression_airway.Rmd)
Error: processing vignette 'differential_expression_airway.Rmd' failed with diagnostics:
Could not find a root 'DESCRIPTION' file that starts with '^Package' in
'/home/lorikern/biocm/packages/scToppR/'.
ℹ Are you in your project directory and does your project have a 'DESCRIPTION'
file?
--- failed re-building ‘differential_expression_airway.Rmd’
--- re-building ‘differential_expression_seurat.Rmd’ using rmarkdown
Quitting from lines 25-30 [setup] (differential_expression_seurat.Rmd)
Error: processing vignette 'differential_expression_seurat.Rmd' failed with diagnostics:
Could not find a root 'DESCRIPTION' file that starts with '^Package' in
'/home/lorikern/biocm/packages/scToppR/'.
ℹ Are you in your project directory and does your project have a 'DESCRIPTION'
file?
--- failed re-building ‘differential_expression_seurat.Rmd’
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 28-32 [setup] (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Could not find a root 'DESCRIPTION' file that starts with '^Package' in
'/home/lorikern/biocm/packages/scToppR'.
ℹ Are you in your project directory and does your project have a 'DESCRIPTION'
file?
--- failed re-building ‘introduction.Rmd’
SUMMARY: processing the following files failed:
‘differential_expression_airway.Rmd’
‘differential_expression_seurat.Rmd’ ‘introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Sorry about that! I've found the error causing that and have updated the vignettes so they should build properly. I tested this in a different environment, and it should work now.
I'm not sure how this got through moderation initially as the version number is not Bioconductor standard for incoming packages. A Bioconductor incoming submission should have a 0.99.0 version number; have you published this package elsewhere before that requires you to keep 1.0.0?
It is not published elsewhere, that's an oversight. It was originally 0.99.0 and passed moderation that way, but I changed it last week so a colleague could install from github to test it out. I've now changed it back to 0.99.0.
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
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 24.04.1 LTS): scToppR_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/scToppR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hello, according to the build report there was 1 WARNING and 1 ERROR.
-WARNING: "No Bioconductor dependencies detected." scToppR does not require any Bioconductor dependencies, but it can work with standard Bioconductor classes and can be integrated into workflows using other packages easily. I think it will also benefit the Bioconductor community as it is, and there is opportunity to develop more secondary aspects of the package (e.g. plotting using specific Bioconductor packages).
-ERROR: "Subscribe to the Bioc-devel mailing list by going to https://stat.ethz.ch/mailman/listinfo/bioc-devel" I have now subscribed to the Bioc-devel mailing list.
I am hoping that the warning is ok and the error has been fully resolved and that this can move onto the next review stage.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Hey @bryanwgranger! Thanks for the package submission. Before I dig deeper into checking the package, some of the first things I notice are that the package is lacking unit tests. Normally, we use a framework such as testthat for this. I also noticed that there are no instructions on how to install the package from bioconductor.
Received a valid push on git.bioconductor.org; starting a build for commit id: 8eb4c4e788b8137a2223287c398290046cde4780
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: Linux (Ubuntu 24.04.1 LTS): scToppR_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/scToppR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hey @svalvaro, thank you for the feedback! I have added the instructions for installing from bioconductor. I am also working on unit tests and will have those pushed within a few days.
@bryanwgranger just checking in on further updates. May we expect updates soon?
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
Thank you for your interest in Bioconductor.
Hello, I would like to resubmit scToppR - I've updated a few elements that needed it, and I am able to now commit to maintaining the package. Is this possible?
Are the git histories consistent that a git push is possible on the version at git.bioconductor.org or would it have to be reset (if divergent histories requiring a force push)
Yes the git histories are consistent, and I've pushed the updated package to git.bioconductor.org.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Dear @bryanwgranger ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
@bryanwgranger could you please push another commit with a version bump so that the package can be rebuilt on our system
Received a valid push on git.bioconductor.org; starting a build for commit id: 5207bed0d4a95fd3bceaa085e4a7b0f80717449b
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: "skipped, 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: ERROR before build products produced.
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/scToppR 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: c792a1db872fd78947c02f43bb4705174a0c16bf
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: Linux (Ubuntu 24.04.3 LTS): scToppR_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/scToppR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.