Bioconductor / Contributions

Contribute Packages to Bioconductor
135 stars 33 forks source link

TDbasedUFE #2906

Closed tagtag closed 1 year ago

tagtag commented 1 year ago

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]'

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.

bioc-issue-bot commented 1 year ago

Hi @tagtag

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: TDbasedUFE
Type: Package
Title: Tensor Decomposition Bassed Unsupervised Feature Extraction
Version: 0.99.0
Authors@R: 
    person("Taguchi", "Y-h.", ,
    "tag@granular.com", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-0867-8986"))
Description: 
    This is a comprehensive package to perform
    Tensor decomposition based unsupervised feature extraction.
    It can perform unsupervised feature extraction.
    It uses tensor decompission.
    It is  applicable to gene expression, DNA methylation, and 
    histone modification etc.
    It can perform multiomics analysis.
    It is also applicable to single cell omics data sets.
biocViews: 
    GeneExpression, 
    FeatureExtraction, 
    MethylationArray,
    SingleCell
License: GPL-3
Encoding: UTF-8
LazyData: false
URL: https://github.com/tagtag/TDbasedUFE
BugReports: https://github.com/tagtag/TDbasedUFE/issues
Imports: 
    GenomicRanges,
    rTensor,
    readr,
    methods,
    MOFAdata,
    tximport,
    tximportData,
    graphics,
    stats,
    utils
RoxygenNote: 7.2.0
Roxygen: list(markdown = TRUE)
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
bioc-issue-bot commented 1 year ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

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.

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

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS, 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. This link will be 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/TDbasedUFE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

tagtag commented 1 year ago

I have pushed a new one as follows

Enumerating objects: 3, done. Counting objects: 100% (3/3), done. Compressing objects: 100% (2/2), done. Writing objects: 100% (2/2), 215 bytes | 215.00 KiB/s, done. Total 2 (delta 1), reused 0 (delta 0), pack-reused 0 To git.bioconductor.org:packages/TDbasedUFE 51ddf28..c4443ae master -> master

But no replies from bot which usually post that it received a valid push. How long will it take to receive a message from bot here?

lshep commented 1 year ago

I responded to the mailing list as well -- you did not push a version bump. The Bioconductor system only process commits with a valid version bump (to trigger a new build in this process -- and to propagate to users on the daily build system). Please bump the z of version x.y.z -- (e.g. 0.99.1)

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f77448e22faf691563d337d356e65dff49cbb9a

tagtag commented 1 year ago

I responded to the mailing list as well -- you did not push a version bump. The Bioconductor system only process commits with a valid version bump (to trigger a new build in this process -- and to propagate to users on the daily build system). Please bump the z of version x.y.z -- (e.g. 0.99.1)

Thanks and sorry for my stupidness.

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/TDbasedUFE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 1 year ago

@tagtag - 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.

General package development

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TDbasedUFE")

DESCRIPTION

NAMESPACE

Vignettes

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TDbasedUFE")

Man pages

R code

Best, Kayla

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cea6fa3d30df807bcf467a559c68dafb9ecbf854

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/TDbasedUFE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

tagtag commented 1 year ago

@Kayla-Morrell Thank you very much for your excellent comments! I believed that I have addressed all the comments you raised. Only exception is "SUGGESTION: For formatting reasons, consider shorter lines. There are 67 lines that are > 80 characters long." There are still two lines longer than 80 characters, but they include URL longer than 80 characters, which cannot be divided. I am more than happy if you can advice me how to divide URL into two lines in Rmarkdown format. I have also done small modification in R code by which no problem has happened if I executed devtools::check(). I am glad if you can accept this package in your earliest opportunity. I would like to thank you again for your quick and proper evaluation of my package!

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0245a9b5bb5c2769abc989848547556ea80db92d

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/TDbasedUFE to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

tagtag commented 1 year ago

@Kayla-Morrell Since I have noticed that I have failed to correct some of following points other than two URLs that I have mentioned in the above,

SUGGESTION: For formatting reasons, consider shorter lines. There are 67 lines that are > 80 characters long. SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 45 lines that are not.

I have corrected them and pushed version 0.99.3. Now the remaining issues are surely only two long URLs that I do not know how to write them up to 80 characters per one line. I am glad if you can verify this version and accept it!

Kayla-Morrell commented 1 year ago

@tagtag - Thank you for making the necessary changes. I've looked everything over and it looks good. I am more than happy to accept the package.

Best, Kayla

bioc-issue-bot commented 1 year 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.

tagtag commented 1 year ago

@Kayla-Morrell Thank you very much for your prompt evaluation and acceptance of my package. I really appreciate for your every effort to my package! @lshep I am glad if you can include mine into Bioconductor nightly builds in the earliest opportunity!

tagtag commented 1 year ago

@lshep It was some time ago that it was accepted, but the issue is not closed. I am glad if you can inform me when this issue will be closed and the package is released in development ones. Sorry for bothering you in spite of your business.

lshep commented 1 year ago

I'm very sorry for the delay. We have been working on some infrastructure updates that prevented us from ingesting packages into the nightly builds. I believe they are remedied and I will proceed with this later today. Sorry for the inconvenience

tagtag commented 1 year ago

@lshep Thanks for your prompt reply in spite of your business. I am looking forward to hearing from you soon again!

lshep commented 1 year ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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/tagtag.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

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("TDbasedUFE"). The package 'landing page' will be created at

https://bioconductor.org/packages/TDbasedUFE

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.