Closed PYangLab closed 3 months ago
Hi @PYangLab
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: TransOmicsData
Title: A collection of trans-omics datasets across various biological systems
Version: 0.99.0
Date: 2023-11-25
Authors@R: c(
person(given = "Carissa", family = "Chen", email = "carissa.chen@sydney.edu.au", role="aut"),
person(given = "Di", family = "Xiao", email = "d.xiao@sydney.edu.au", role=c("aut", "cre"))
)
Description: Contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq, from different tissue types and species.
Depends: ExperimentHub
Imports: S4Vectors, utils
License: GPL-3
BugReports: https://support.bioconductor.org/t/TransOmicsData
VignetteBuilder: knitr
Suggests:
BiocStyle,
knitr,
rmarkdown,
RefManageR,
sessioninfo,
testthat
biocViews: ExperimentHub, MassSpectrometryData, RNASeqData, Tissue, SequencingData
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0
Config/testthat/edition: 3
Note: when I R CMD build
your package right now it ERROR with could not find function "listDatasets"
. You should do a library(TransOmicsData)
to load your package before calling your package function in the vignette.
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.
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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/TransOmicsData
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: 8abdce65c74a20e066e081c1166368aa40cf891e
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: macOS 12.7.1 Monterey: TransOmicsData_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData
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: 971770e591a1d663098f391fa1fed4ccc3c17b8a
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: macOS 12.7.1 Monterey: TransOmicsData_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData
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: e186a2e91501624d9dca7952b93a6f20d333c594
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: macOS 12.7.1 Monterey: TransOmicsData_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData
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: 5dad7fcb9a666c14cc0d9a7d765fe94e6933ed73
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: macOS 12.7.1 Monterey: TransOmicsData_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi Ishep, is the doi issued after publishing the package? I'm not sure how to address the warning about the doi.
yes a doi is issued after acceptance. You can ignore that warning for now
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Hi @Kayla-Morrell, thank you for reviewing this package. Are there any updates on this package review?
@carissaynchen - So sorry for the delay, I've been transitioning between jobs. I'll work on getting an initial review posted over the next couple of days.
Best, Kayla
@carissaynchen - 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.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: d8d2437caa5f49cca321d0dc5dc65990884ec35a
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): TransOmicsData_0.99.5.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/TransOmicsData
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi Kayla, I have made the changes below:
General package development
- [X] REQUIRED: File LICENSE is not mentioned in the DESCRIPTION file. Since you are using a standard license you shouldn't need to include the LICENSE file with the package.
DESCRIPTION
- [X] SUGGESTION: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph.
- [X] SUGGESTION: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")'.
- [X] SUGGESTION: Provide 'URL' or 'BugReports' field in DESCRIPTION.
NAMESPACE
- [ ] REQUIRED: Package in Depends field not imported from: 'ExperimentHub'. This package needs to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. I have removed the package ExperimentHub from the Depends field as my function does not require the package.
CITATION
- [ ] SUGGESTION: Include the 'doi' argument in CITATION 'bibentry()'. I will add this when I have been issued a doi.
Vignette
- [X] REQUIRED: There should be an 'Installation' section that demonstrates to the user how to install the package from Bioconductor.
R code
- [X] REQUIRED: In listDatasets, 'read.table()' partial argument match of 'head' to 'header'.
- [ ] SUGGESTION: For formating reasons, consider shorter lines. There are 5 lines that are > 80 characters long.
- [ ] SUGGESTION: For formating reasons, consider multiples of 4 spaces for line indents. There are 2 lines that are not.
Received a valid push on git.bioconductor.org; starting a build for commit id: 1a8569ab9a83259f4b42a78c5da718038c9059df
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): TransOmicsData_0.99.6.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/TransOmicsData
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: af19e92241d3d50288044f24d1603bc9e7391a50
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): TransOmicsData_0.99.7.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/TransOmicsData
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: 3d11c9fb8b2fe78181933e36d908e4b03193cd02
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): TransOmicsData_0.99.8.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/TransOmicsData
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: 4e7c6464402914c0b5fd31f4acb401d1ac98952b
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): TransOmicsData_0.99.9.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/TransOmicsData
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: d0ee40fe895de4a96a39960d2e73dc9c06abad80
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): TransOmicsData_0.99.10.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/TransOmicsData
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @Kayla-Morrell I've been trying to resolve the error with the bioc-devel subscription, and the maintainer has signed up to the mailing list so I'm not sure why the error is unresolved. Is there a way around this?
Just to be clear here, This assumes that the submitter and the maintainer in the package is registered. The currently listed maintainer and maintainer email is: person(given = "Di", family = "Xiao", email = "d.xiao@sydney.edu.au", role=c("aut", "cre")
So it is looking for d.xiao@sydney.edu.au to be registered. Sometime the registration requires confirmation and the confirmation email can end up in the spam folder. I currently do not see this email registered. If you do not see a confirmation email in spam, let us know and we can follow up.
Hi @lshep, could you check again whether d.xiao@sydney.edu.au is registered? we are both receiving the bioc-devel emails now.
yes I can see them
Received a valid push on git.bioconductor.org; starting a build for commit id: dfec4f343f260efdf6bd213c8b7ed61ae2407e9f
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): TransOmicsData_0.99.11.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/TransOmicsData
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
@PYangLab - Thank you for making the necessary changes. I have looked everything over and I'm 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!
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See further instructions at
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(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("TransOmicsData")
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