jfanale26 commented 1 year ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Repository: https://github.com/zhou-lab/CytoMethIC

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:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six months, for bug fixes.
[x] Bioconductor version control using Git (optionally via GitHub).

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.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3ab7c34f273177843065530e887865e9dc64bbf1

bioc-issue-bot commented 5 months ago

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 22.04.3 LTS): CytoMethIC_0.99.17.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a6f991643c4278b773b778f8c213963b98ad32fc

bioc-issue-bot commented 5 months ago

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): CytoMethIC_0.99.18.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jfanale26 commented 5 months ago

@jianhong The warning should be fixed, let me know what our next steps are.

jianhong commented 5 months ago

Package 'CytoMethIC' Review

Amost there. There are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

General package development

[ ] Important: NEWS file is not updated and the content is not correlated with the update of the package.

R code

[ ] Important: input validation are not fully covered. For example, betas in function cmi_classify. Should that must be a matrix? And there is no input check for impute_mean function.

Documentation

[ ] Note: Vignette should use BiocStyle package for formatting.
- rmd file vignettes/CytoMethIC.Rmd

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f0660cb869cfc1c567f6f9b9c555da4361860007

bioc-issue-bot commented 5 months ago

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 22.04.3 LTS): CytoMethIC_0.99.19.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7a23521a1469dbb3e6b245181061e263ead064f4

bioc-issue-bot commented 5 months ago

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): CytoMethIC_0.99.20.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f3d3e0be2beec32a06e0d07358c12a8e0ce8682b

bioc-issue-bot commented 5 months ago

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): CytoMethIC_0.99.21.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jfanale26 commented 5 months ago

Thank you for the speedy review, @jianhong. We have amended all of the comments you made:

Important: NEWS file is not updated

We have added the most recent build to NEWS.

Important: input validation are not fully covered.

We have added input validation for the cmi_classify function, see lines 112-118 of CytoMethIC.R. Please note that the impute_mean function has been removed, as the updated function no longer uses it.

Note: Vignette should use BiocStyle package for formatting.

We have changed the output of the Rmd file to BiocStyle::html_document. See lines 4-6 of CytoMethIC.Rmd.

Please let us know what else needs to be done.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f007bc6cace94125c5e4138f2211a1625a6ee358

bioc-issue-bot commented 5 months ago

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 git@git.bioconductor.org:packages/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 420a9e80f0622fa63fc0edcb79d1826ac72476f3

bioc-issue-bot commented 5 months ago

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): CytoMethIC_0.99.23.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e09ab1c3646135f8266091ffb72aa2c54382122d

bioc-issue-bot commented 5 months ago

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): CytoMethIC_0.99.24.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6e2f230dcea2870da1ae34fc7931cae6a904b653

bioc-issue-bot commented 5 months ago

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): CytoMethIC_0.99.25.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jianhong commented 5 months ago

The new function cmi_checkVersion. You may want to simply the function by something like:

rv <- R.Version()
message(
        "CytoMethIC requires matched versions of ",
        "R, sesame, sesameData and ExperimentHub.\n",
        "Here is the current versions installed:\n",
         "Bioconductor: ", version(), "\n",
        "CytoMethIC: ", packageVersion("CytoMethIC"), "\n",
        "sesame: ", packageVersion("sesame"), "\n",
        "sesameData: ", packageVersion("sesameData"), "\n",
        "ExperimentHub: ", packageVersion("ExperimentHub"), "\n"
)

jianhong commented 5 months ago

Also, please double check your documentations. There are some minor typos.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 91f81855fbda9a57f0b73ae28db898afd1d419b2

bioc-issue-bot commented 5 months ago

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): CytoMethIC_0.99.26.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/CytoMethIC to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jfanale26 commented 5 months ago

@jianhong we have fixed cmi_checkVersion and proofread for typos. Let us know what else should be done.

jianhong commented 5 months ago

Please always update your NEWS file to the newest updates once you changed anything.

jfanale26 commented 5 months ago

Pushed NEWS file update, but did not build on system. @jianhong

jianhong commented 5 months ago

@jfanale26 I will make it as accepted now. Certainly, we kindly request that you remember to update your NEWS file whenever you make any changes. Your attention to this matter is greatly appreciated.

bioc-issue-bot commented 5 months ago

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.

jfanale26 commented 5 months ago

@jianhong, thank you so much for all of the help in getting this package ready for release! We will be sure to update NEWS as we make changes.

lshep commented 5 months ago

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/jfanale26.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("CytoMethIC"). The package 'landing page' will be created at

https://bioconductor.org/packages/CytoMethIC

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.

Bioconductor / Contributions

CytoMethIC #3097

Package 'CytoMethIC' Review

General package development

R code

Documentation