Closed BioinfoUSAL closed 1 year ago
Hi @BioinfoUSAL
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: Rvisdiff
Type: Package
Version: 0.99.0
Date: 2023-08-04
Title: Interactive Graphs for Differential Expression
Description: Creates a muti-graph web page which allows the interactive exploration of differential expression results. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.
License: GPL-2 | GPL-3
Depends: R (>= 4.4.0)
Imports: edgeR, DESeq2, limma, SummarizedExperiment, utils
Suggests: knitr, rmarkdown, airway
VignetteBuilder: knitr
NeedsCompilation: no
biocViews: Software, Visualization, RNASeq, DataRepresentation,
DifferentialExpression
Authors@R: c(
person("Carlos", "Prieto", email = "cprietos@usal.es", role = "aut", comment = c(ORCID = "0000-0003-2064-4842")),
person("David", "Barrios", email = "metal@usal.es", role = c("cre","aut"), comment = c(ORCID = "0000-0003-4465-0200"))
)
Thanks for this submission. The vignette does not meet the conditions of the contributions guidelines. Please explain the use of the tool and its relationship to Bioconductor. Try to imagine a newcomer to your package who needs to get the flavor of it, and who can be inspired to try it out by what you write.
We have updated the vignette with a new description and detailed examples of use. It shows the connection with Differential Expression packages of bioconductor and explains the main features of the package.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
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
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
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: "ERROR, skipped". 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: 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
git@git.bioconductor.org:packages/Rvisdiff
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The current Bioconductor builders only support R 4.3; is R 4.4 a necessary requirement as it is not scheduled to be release by CRAN until next Spring? Our devel builder will not have R 4.4 until after the October Bioconductor release.
Thanks for the comment, the package supports older R versions. R dependency has been updated to 4.3.0.
Can you please follow the instructions for pushing to git.bioconductor.org to trigger a new build report. See previous post
Received a valid push on git.bioconductor.org; starting a build for commit id: aef7aedd849956e0709e1369b7bee37fc8cf37a7
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: "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 Bioconductor Build System: macOS 12.6.5 Monterey: Rvisdiff_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): Rvisdiff_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/Rvisdiff
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: f89b6f22e19b71b8023a090493c9efeff63e9d82
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: macOS 12.6.5 Monterey: Rvisdiff_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): Rvisdiff_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/Rvisdiff
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
[ ] I see quite a few checks on the input data, however, these should be tested more thoroughly (see also comment below). E.g., running the DEreport
example and setting names(dr)[6] <- "padjj"
already breaks the volcano and MA plot. Implementing a proper validity check on what edgeR/DESeq2/limma
outputs would look like should catch this, and perhaps provide the user with an informative message on what's wrong/how to fix it.
[ ] Complementary to the above, it might be helpful to expose some key arguments to the user, e.g., to let users provide the names of columns containing (adjusted) p-values etc.
[ ] File/directory paths should be constructed using file.path()
as opposed to paste0(..., "/...")
to be OS-agnostic, e.g., in createHTML()
.
[ ] Consider adding a package help-(man-)page (to be viewed via ?Rvisdiff
) summarizing the packages functionality.
[ ] In the vignette, consider using BiocStyle
functions to hyperlink external packages in order to direct users to these directly, e.g., `r BiocStyle::Biocpkg("edgeR")`
.
[ ] Similarly, considering using code-style in order to distinguish/highlight anything R-related (package/function/argument/variable name), including Rvisdiff; this aids general readability.
[ ] Please keep tracking changing in the NEWS file; it's still listing version 0.99.0 only.
[ ] In the README, please provide Bioconductor installation instructions using BiocManager::install()
.
[ ] Please consider implementing more comprehensive unit testing; current coverage is fairly minimal (~37% coverage with 1 hit/line according to devtools::test_coverage()
).
Received a valid push on git.bioconductor.org; starting a build for commit id: fff5ea3cda62ec8f7fdf92c4a34913b95bd3e3b5
We have introduce input checks in the code. Input parameters have been updated to adjust column names. Directory paths are now constructed with file.path function. We have created a help man page and add code style to help functions. News file has been updated, README file has been modified with BiocManager install and new unit tests have been added.
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: macOS 12.6.5 Monterey: Rvisdiff_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): Rvisdiff_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/Rvisdiff
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Great, thanks for addressing these quickly and comprehensively! One last thing:
Imports
: (i.e., depends) on all of edgeR
, limma
, and DESeq2
. However, my understanding is that DEreport()
would work on any of these, independent of the users preferred framework.Suggests:
instead (see here for details), i.e., only demanding users to have one of these frameworks installed vs. all possibilities?DEreport()
is being run on.Received a valid push on git.bioconductor.org; starting a build for commit id: b0965d9c5d8fb31c17732cef1165e23398fe0c09
Dear Helena, thanks for your useful comments. We have updated dependencies to enable optional installations.
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: macOS 12.6.5 Monterey: Rvisdiff_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): Rvisdiff_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
git@git.bioconductor.org:packages/Rvisdiff
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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.
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/BioinfoUSAL.keys is not empty), then no further steps are required. Otherwise, do the following:
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("Rvisdiff")
. The package 'landing page' will be created at
https://bioconductor.org/packages/Rvisdiff
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.
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]'
[x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x] I am familiar with the Bioconductor code of conduct and agree to abide by it.
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.