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limpca
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/ManonMartin/limpca
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Hi @ManonMartin
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: limpca
Type: Package
Title: An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods
Version: 0.99.0
Authors@R: c(person("Bernadette", "Govaerts", role = c("aut", "ths"),
email = "[email protected]"),
person("Sebastien","Franceschini", role = "ctb",
email="[email protected]"),
person("Robin","van Oirbeek", role = "ctb",
email="[email protected]"),
person("Michel","Thiel", role = "aut",
email="[email protected]"),
person("Pascal","de Tullio", role = "dtc",
email="[email protected]"),
person("Manon","Martin", role = c("aut", "cre"),
email="[email protected]",
comment = c(ORCID = "0000-0003-4800-0942")),
person("Nadia", "Benaiche", role = "ctb",
email = "[email protected]"))
Description: >
This package has for objectives to provide a method to make Linear Models
for high-dimensional designed data. limpca applies a GLM (General Linear Model)
version of ASCA and APCA to analyse multivariate sample profiles generated
by an experimental design. ASCA/APCA provide powerful visualization
tools for multivariate structures in the space of each effect of
the statistical model linked to the experimental design and contrarily
to MANOVA, it can deal with mutlivariate datasets having more variables
than observations. This method can handle unbalanced design.
License: Artistic-2.0
Encoding: UTF-8
LazyData: FALSE
VignetteBuilder: knitr
Imports: ggplot2, stringr, plyr, ggrepel, reshape2,
grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci,
tidyverse, methods, stats
Suggests:
BiocStyle, pander,
rmarkdown, car, gridExtra, knitr
biocViews: StatisticalMethod, PrincipalComponent, Regression, Visualization, ExperimentalDesign, MultipleComparison
RoxygenNote: 7.2.3
Roxygen: list(markdown=TRUE)
BugReports: https://github.com/ManonMartin/limpca/issues
URL: https://github.com/ManonMartin/limpca,
https://manonmartin.github.io/limpca/
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.
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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 Build System.
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.
The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: limpca_0.99.0.tar.gz Linux (Ubuntu 22.04.2 LTS): limpca_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/limpca 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: d74d421923ba3448eb99ca852f0a6b3d94c8ac59
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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 Bioconductor Build System: macOS 12.6.5 Monterey: limpca_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): limpca_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/limpca to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The remaining warning is due to missing values field in 3 man pages (man/limpca.Rd, man/trout.Rd, man/UCH.Rd), but they concern data or package description, so in my opinion no value field is necessary.
Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
Thank you for your interest in Bioconductor.
Dear @ManonMartin ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
cannot build unless issue is open and has the 'pre-review' label or '2. review in progress' label, or is closed and has the 'TESTING' label.
Could you please provide an abstract/intro section in your vignette that provides motivation for inclusion in Bioconductor and when appropriate a review and comparison to existing Bioconductor packages with similar functionality or scope
Sorry for the extended time taken to reply. The introduction of the UCH vignette has been modified accordingly to motivate the inclusion of limpca to Bioconductor.
Received a valid push on git.bioconductor.org; starting a build for commit id: ac28232f1ad23e436c8facad63adc0de088fd053
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): limpca_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
[email protected]:packages/limpca to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Before a reviewer is assigned for an in-depth review of the package, please see the following comments:
Build Report
- [ ] Please clean up Warnings and NOTES
NEWS
- [ ] Please have a valid NEWS entry. A section must be populated by at least one item.
ie:
# limpca 0.0.99
- submitted to bioconductor
Citation File
- [ ] is not formatted correctly
> readCitationFile("CITATION")
Error in tools:::.parse_CITATION_file(file, meta$Encoding) :
non-ASCII input in a CITATION file without a declared encoding
>
General
- [ ] Please show interop with standard Bioconductor packages.
Received a valid push on git.bioconductor.org; starting a build for commit id: 25426d3cd5cca49b6d14f6efee78be376a68503c
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): limpca_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
[email protected]:packages/limpca to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi, thank you for these remarks. there is the progress so far:
- [x] Please clean up Warnings and NOTES The WARNINGS and most of the NOTES have been addressed
- [x] Please have a valid NEWS entry. A section must be populated by at least one item. a NEWS entry has been added
- [x] Citation File is not formatted correctly The problem comes from two accented characters, but it works with UTF-8 encoding (the defined encoding in the DESCRIPTION file). I would rather keep the accent in the bib entry but if it must pass with ASCII encoding I can remove it.
# Not working
utils::readCitationFile("inst/CITATION")
# Working
utils::readCitationFile("inst/CITATION", meta = packageDescription("limpca", encoding = NA))
- [ ] Please show interop with standard Bioconductor packages. I still have to work on that point
Received a valid push on git.bioconductor.org; starting a build for commit id: 8dce21ad63bd9b5ce2ea3648de3ceed47e519afc
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): limpca_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
[email protected]:packages/limpca to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi,
interoperability has been added trough the function data2LmpDataList: it can convert a SummarizedExperiment to a list (lmpDataList) formatted to run the core functions of the package.
Likely the Citation file will not display correctly on the package landing page. We use default setting when extracting and it is currently not possible to customize.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: 752973743811727a91f47dc9e9783b414699b5c5
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): limpca_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
[email protected]:packages/limpca to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thanks @ManonMartin for submitting limpca to Bioconductor.
A quick note before I take a closer look at the package: Bioconductor packages should always be installed with BiocManager::install() (see for example https://bioconductor.org/packages/release/bioc/html/BiocIO.html). So the Installation section in the vignette should have something like this in an non-evaluated (eval=FALSE) code chunk:
```{r installation, eval=FALSE}
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("limpca")
```
Also please keep in mind that we strongly advice against installing packages directly from GitHub as it tends to mix up package versions that belong to different versions of Bioconductor, which usually doesn't end well.
Thanks, H.
Thank you for the preliminary note. Should I already update the installation instructions if the package is not (yet) on Bioconductor? Of course if the package is accepted, I will completely remove the GitHub installation instructions.
Yes please. We expect that issues reported during the review process get addressed before the package can be accepted. Thanks for your understanding.