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chevreul
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/whtns/chevreul/
Confirm the following by editing each check box to '[x]'
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[x] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
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[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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Hi @whtns
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:
Type: Package
Package: chevreul
Title: Tools for managing SingleCellExperiment objects as projects
Version: 0.99.0
Authors@R: c(
person("Kevin", "Stachelek", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2085-695X")),
person("Bhavana", "Bhat", , "[email protected]", role = "aut")
)
Description: Tools for managing SingleCellExperiment objects as projects.
Includes functions for analysis and visualization of single-cell data.
Also included is a shiny app for visualization of pre-processed scRNA data.
License: MIT + file LICENSE
URL: https://github.com/whtns/chevreul,
https://whtns.github.io/chevreul/
Date: 2024-03-05
BugReports: https://github.com/cobriniklab/chevreul/issues
Depends:
R (>= 4.4.0),
SingleCellExperiment,
scater,
shiny (>= 1.6.0),
shinydashboard
Imports:
SummarizedExperiment,
annotables (>= 0.1.91),
clustree,
ComplexHeatmap (>= 2.5.4),
DataEditR (>= 0.0.9),
DBI,
dplyr,
DT,
ensembldb,
fs,
future,
glue,
ggplotify,
ggpubr,
httr,
janitor,
magrittr,
megadepth,
methods,
patchwork,
plotly,
rlang,
RSQLite,
shinyFiles,
shinyhelper,
shinyjs,
shinyWidgets,
tidyr,
unglue,
waiter,
wiggleplotr (>= 1.13.1),
purrr,
batchelor,
stringr,
tibble,
ggplot2,
scran,
AnnotationDbi,
EnhancedVolcano,
EnrichmentBrowser,
harmony,
scuttle,
grDevices,
graphics,
stats,
utils,
pillar,
cluster,
circlize,
bluster,
EnsDb.Hsapiens.v86,
EnsDb.Mmusculus.v79,
scales,
readr,
velociraptor,
LoomExperiment,
chevreuldata,
S4Vectors,
base,
grid,
forcats
Suggests:
BiocStyle,
knitr,
monocle3 (>= 0.2.1),
RefManageR,
rmarkdown,
testthat (>= 3.0.0)
VignetteBuilder:
knitr
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
biocViews: Coverage, RNASeq, Sequencing, Visualization, GeneExpression, Transcription, SingleCell
Config/testthat/edition: 3
All package dependencies must be on CRAN or Bioconductor. annotables is currently not on CRAN or Bioconductor and must not be used or referenced in the package.
I assume chevreuldata will be submitted once this issue can accept additional packages. I glanced at that github repo. All Bioconductor packages must include a vignette.
Thank you for taking a look at these packages. I removed the annotables dependency in chevreul and added a vignette in chevreuldata. I'd greatly appreciate further review.
adding an explicit reference to accompanying data package chevreuldata
AdditionalPackage: https://github.com/whtns/chevreuldata
Can't build unless issue is open and past pre-review stage, or issue is closed and 'TESTING' label is present.
A few questions:
Can default for saving or writing files be a tempdir() unless specified by a user?
Insteading of defining ~/.cache/ which isn't necessarily a default for all operating systems can you use tools::R_user_dir(which="cache") or rappdirs::user_cache_dir which would grab an appropriate path for a given OS.
Why is a chmod explicit set_permission_call necessary?
It looks like you import httr::GET but is it utilized anywhere?
Thank you for continuing to share feedback/shortcomings. I addressed the points you raised above in my last commit.
Can default for saving or writing files be a tempdir() unless specified by a user? I've removed any hardcoded filepaths previously used for saving
Insteading of defining ~/.cache/ which isn't necessarily a default for all operating systems can you use tools::R_user_dir(which="cache") or rappdirs::user_cache_dir which would grab an appropriate path for a given OS. I've replaced references to caches with rappdirs::user_cache_dir
Why is a chmod explicit set_permission_call necessary? removed
It looks like you import httr::GET but is it utilized anywhere? removed
When I try to run R CMD build I'm getting the following
R CMD build chevreul
* checking for file 'chevreul/DESCRIPTION' ... OK
* preparing 'chevreul':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘chevreul.Rmd’ using rmarkdown
--- finished re-building ‘chevreul.Rmd’
--- re-building ‘integration.Rmd’ using rmarkdown
Quitting from lines at lines 71-77 [unnamed-chunk-2] (integration.Rmd)
Error: processing vignette 'integration.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘integration.Rmd’
--- re-building ‘preprocessing.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
--- finished re-building ‘preprocessing.Rmd’
--- re-building ‘shiny_app.Rmd’ using rmarkdown
--- finished re-building ‘shiny_app.Rmd’
--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Quitting from lines at lines 144-145 [unnamed-chunk-5] (visualization.Rmd)
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘visualization.Rmd’
SUMMARY: processing the following files failed:
‘integration.Rmd’ ‘visualization.Rmd’
Error: Vignette re-building failed.
It looks like you are hard linking to a file on your system that would not exist for a user.
I'm sorry I can't identify the source of the errors listed above in my current branch. I incremented the package version. Can you confirm that the check and build is run against the devel branch? thanks,
Yes it is
lorikern@jbcj433:~/PkgReview/PreReview/chevreul(devel)$ git remote -v
origin https://github.com/whtns/chevreul/ (fetch)
origin https://github.com/whtns/chevreul/ (push)
lorikern@jbcj433:~/PkgReview/PreReview/chevreul(devel)$ git pull
remote: Enumerating objects: 7, done.
remote: Counting objects: 100% (7/7), done.
remote: Compressing objects: 100% (2/2), done.
remote: Total 7 (delta 5), reused 7 (delta 5), pack-reused 0
Unpacking objects: 100% (7/7), 620 bytes | 38.00 KiB/s, done.
From https://github.com/whtns/chevreul
e4d2858..da02a9c sce -> origin/sce
Already up to date.
lorikern@jbcj433:~/PkgReview/PreReview/chevreul(devel)$ cd ..
lorikern@jbcj433:~/PkgReview/PreReview$ R CMD build chevreul
* checking for file 'chevreul/DESCRIPTION' ... OK
* preparing 'chevreul':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘chevreul.Rmd’ using rmarkdown
--- finished re-building ‘chevreul.Rmd’
--- re-building ‘integration.Rmd’ using rmarkdown
Quitting from lines 71-77 [unnamed-chunk-2] (integration.Rmd)
Error: processing vignette 'integration.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘integration.Rmd’
--- re-building ‘preprocessing.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
--- finished re-building ‘preprocessing.Rmd’
--- re-building ‘shiny_app.Rmd’ using rmarkdown
--- finished re-building ‘shiny_app.Rmd’
--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Quitting from lines 144-145 [unnamed-chunk-5] (visualization.Rmd)
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘visualization.Rmd’
SUMMARY: processing the following files failed:
‘integration.Rmd’ ‘visualization.Rmd’
Error: Vignette re-building failed.
Execution halted
Ah, thank you very much. I had a mismatch between local and remote branches. The branch you are pulling is origin/sce in the above snippet. I've updated the local and remote branches and incremented version again. Can you try building again? Sorry for the trouble.
skevin@cobrinik-srt:~/rpkgs/chevreul$ git status
On branch devel
Changes to be committed:
(use "git restore --staged <file>..." to unstage)
deleted: docs/articles/Heatmap2.0.PNG
deleted: docs/articles/PlotCoverage2.0.PNG
deleted: docs/articles/violinPlot.PNG
skevin@cobrinik-srt:~/rpkgs/chevreul$ ..
skevin@cobrinik-srt:~/rpkgs$ R CMD build chevreul
* checking for file 'chevreul/DESCRIPTION' ... OK
* preparing 'chevreul':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'chevreul_0.99.2.tar.gz'
Same
R CMD build chevreul
* checking for file 'chevreul/DESCRIPTION' ... OK
* preparing 'chevreul':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘chevreul.Rmd’ using rmarkdown
--- finished re-building ‘chevreul.Rmd’
--- re-building ‘integration.Rmd’ using rmarkdown
Quitting from lines 71-77 [unnamed-chunk-2] (integration.Rmd)
Error: processing vignette 'integration.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘integration.Rmd’
--- re-building ‘preprocessing.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
--- finished re-building ‘preprocessing.Rmd’
--- re-building ‘shiny_app.Rmd’ using rmarkdown
--- finished re-building ‘shiny_app.Rmd’
--- re-building ‘visualization.Rmd’ using rmarkdown
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Warning in grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per page
Quitting from lines 144-145 [unnamed-chunk-5] (visualization.Rmd)
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
--- failed re-building ‘visualization.Rmd’
SUMMARY: processing the following files failed:
‘integration.Rmd’ ‘visualization.Rmd’
Error: Vignette re-building failed.
Execution halted
In the vignette this seems to have to do with the plot_violin function. For what its worth it is also reproducible if I use devtools to load the package and just try to run that example as well
> load_all(".")
ℹ Loading chevreul
> chevreul_sce <- chevreuldata::human_gene_transcript_sce()
snapshotDate(): 2024-05-28
see ?chevreuldata and browseVignettes('chevreuldata') for documentation
loading from cache
> plot_violin(chevreul_sce, plot_var = "batch", features = "NRL")
Error in .Call2("C_h5getdimscales", filepath, name, scalename, PACKAGE = "HDF5Array") :
file '/dataVolume/storage/single_cell_projects/sc_cone_devel/sc_cone_devel_organoid/20181001-DS-organoid-Hs_proj/output/velocyto/20181001-DS-organoid-Hs_proj.loom' does not exist
Ok, I think I've resolved this problem. The example dataset (in accompanying experimenthub package chevreuldata) includes a SingleCellLoomExperiment assay for use with the velociraptor package. Because the source loom file is inaccessible on any other system even unrelated functions break. Because I don't know best practices to share loom files in this manner I've removed that assay from the dataset and excluded those functions from vignettes and examples.
You should not disable these examples and vignettes. If the data isn't loading, you should check out LoomExperiment where this class is defined and figure out the proper way. Exported functions need to be run/tested somewhere in the code base.
Ok thanks, I recognize the submission requirement to have included functions documented with examples. I've removed any dependency on LoomExperiment or velociraptor from the package
monocle3 does not appear to be on CRAN or Bioconductor. Bioconductor packages require all dependencies to be on CRAN or Bioconductor. You must remove the dependency from your package or request the monocle3 maintainers to officially submit the package.
Thank you, we've removed all references to monocle3 and dropped the package dependency in DESCRIPTION
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
[email protected]:packages/chevreul to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I am submitting an additional experimentHub data package, chevreuldata. See #3491. I'm also pinging author @Bavanaa. This is a dependency for the above package chevreul
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Repository: https://github.com/whtns/chevreuldata
Confirm the following by editing each check box to '[x]'
[ x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.
[x ] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x ] I understand Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[ x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[ x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
[x ] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.
[x ] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
[ x] The 'devel' branch for new packages and features. [ x] The stable 'release' branch, made available every six months, for bug fixes. [ x] Bioconductor version control using Git (optionally via GitHub).
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.
Please see https://github.com/Bioconductor/Contributions#submitting-related-packages and use AdditionalPackage: https://github.com/whtns/chevreuldata
Hi @whtns, Thanks for submitting your additional package: https://github.com/whtns/chevreuldata. We are taking a quick look at it and you will hear back from us soon.
Additional Package has been approved for building.
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.
Additional Package has been approved for building.
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.
Additional Package has been approved for building.
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.
Additional Package has been approved for building.
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.
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
[email protected]:packages/chevreuldata to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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
[email protected]:packages/chevreuldata to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Additional Package has been approved for building.
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.