Closed tagtag closed 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
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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?
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)
Received a valid push on git.bioconductor.org; starting a build for commit id: 5f77448e22faf691563d337d356e65dff49cbb9a
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.
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 - 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.
eval = FALSE
in the code chunk:if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TDbasedUFE")
importFrom()
is encouraged over importing an
entire package.eval = FASLSE
in the code chunk.if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TDbasedUFE")
figures/
directory in the man/
directory. I would suggest moving this to an inst/figures/
directory and
changing the file path in the README file.Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: cea6fa3d30df807bcf467a559c68dafb9ecbf854
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 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!
Received a valid push on git.bioconductor.org; starting a build for commit id: 0245a9b5bb5c2769abc989848547556ea80db92d
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 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!
@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
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.
@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!
@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.
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
@lshep Thanks for your prompt reply in spite of your business. I am looking forward to hearing from you soon again!
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