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TaxSEA
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- Repository: https://github.com/feargalr/TaxSEA
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Hi @feargalr
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: TaxSEA
Type: Package
Title: Taxon Set Enrichment Analysis
Version: 0.99.0
Authors@R: c(person("Feargal", "Ryan",
email = "[email protected]",
role = c("aut", "cre"),comment = c(ORCID = "0000-0002-1565-4598")))
Description: TaxSEA is an R package for Taxon Set Enrichment Analysis, which
utilises a Kolmogorov-Smirnov test analyses to
investigate differential abundance analysis output for whether there
are alternations in a-priori defined sets of taxa from five previously
published databases (BugSigDB, MiMeDB, GutMGene, mBodyMap and GMRepoV2).
TaxSEA takes as input a list of taxonomic identifiers (e.g. species names,
NCBI IDs etc.) and a rank (E.g. fold change, correlation coefficient).
TaxSEA be applied to any microbiota taxonomic profiling technology
(array-based, 16S rRNA gene sequencing, shotgun metagenomics &
metatranscriptomics etc.) and enables researchers to rapidly contextualize
their findings within the broader literature to accelerate interpretation
of results.
License: GPL-3
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
RoxygenNote: 7.2.3
biocViews: Microbiome, Metagenomics, Sequencing, GeneSetEnrichment, RNASeq
URL: https://github.com/feargalr/taxsea
BugReports: https://github.com/feargalr/taxsea/issues
Suggests:
knitr,
rmarkdown
Imports:
ggplot2,
stats,
utils
Please get rid of the empty export in the namespace
Plesae change the name of the vignette file to something more meaningful than
my-vignette generic names are not recommended to avoid load conflicts. We
recommend the name of the package TaxSEA.Rmd.
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
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 24.04.1 LTS): TaxSEA_0.99.0.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
[email protected]:packages/TaxSEA to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Thanks BioC team. A query about one of the warnings. This package is designed to complement several existing BioC packages (e.g. bugsigdbr, ANCOMBC etc.) but it doesn't depend on them as it has other standalone functionality too. However, I get a warning in the check. I wanted to ask how you'd like me to handle that? I could list a package as a dependency, although as an enhance might be more accurate? Thanks!
"WARNING: No Bioconductor dependencies detected. Note that some infrastructure packages may not have Bioconductor dependencies. For more information, reach out to the Bioconductor community and/or consider a CRAN submission."
@feargalr - Apologizes for the late response. I would say to not worry about this warning for now and work on the ERRORs that are produced instead. When I review the package I will determine if this warning is something that should be addressed.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7c43132b34e5f0284b6ae12e3077adaa11c7472e
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 24.04.1 LTS): TaxSEA_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
[email protected]:packages/TaxSEA 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: cbe356fc7d293609dfc90959c210f1f2d4b1c9d8
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 24.04.1 LTS): TaxSEA_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
[email protected]:packages/TaxSEA to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi BioC team, just wondering if possible to get a status update on this? The manuscript has been accepted and would love to drop in the link to BioC if possible. Thanks
@feargalr - 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
- [ ] REQURIED: README file should also include instructions on how to install from Bioconductor.
DESCRIPTION
- [ ] REQURIED: Update R version dependency from 4.4.0 to 4.5.0.
NAMESPACE
- [ ] REQUIRED: Namespace in Imports field not imported from: 'ggplot2'. All declared Imports should be used.
- [ ] SUGGESTION: Undefined global functions or variables. Consider adding 'importFrom("utils", "URLencode")' to your NAMESPACE file.
Vignette
- [ ] REQUIRED: All code chunks should be executable and not include 'eval = FALSE'.
- [ ] SUGGESTION: We strongly encourage the use of 'BiocStyle' for formatting.
- [ ] REQUIRED: There should be an installation section that demonstrates to the user how to install the package from Bioconductor.
- [ ] SUGGESTION: We strongly encourage the use of table of contents.
Unit tests
- [ ] SUGGESTION: Consider adding unit tests. We strongly encourage them.
R code
- [ ] SUGGESTION: Avoid 1:...; use seq_len() or seq_along()
- [ ] SUGGESTION: Avoid using '=' for assignment and use '<-' instead.
- [ ] SUGGESTION: Avoid redundant 'stop' and 'warn*' in signal conditions.
- [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 21 lines that are > 80 characters long.
- [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 93 lines that are not.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: 2b57a6aa9728cb3c264c1f869cd5f69d4f8a3722
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 24.04.1 LTS): TaxSEA_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
[email protected]:packages/TaxSEA to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thanks for the review @Kayla-Morrell :) Have addressed all requirements and almost all of the suggestions as per above. Let me know what else you need from me.
@feargalr - Thank you for making the necessary changes. I have reviewed them and everything looks good. 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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(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("TaxSEA"). The package 'landing page' will be created at
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