Closed GuangchuangYu closed 8 months ago
Hi @GuangchuangYu
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: ggsc
Title: Visualizing single cell data
Version: 0.99.1
Authors@R: c(
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
person("Shuangbin", "Xu", email = "xshuangbin@163.com", role = "aut", comment = c(ORCID="0000-0003-3513-5362"))
)
Description: Useful functions to visualize single cell data.
Imports:
methods,
dplyr,
SingleCellExperiment,
SummarizedExperiment,
ggplot2,
rlang,
cli,
scattermore,
SeuratObject,
Seurat,
tidydr,
tidyr,
tibble,
utils,
yulab.utils
Suggests:
knitr,
rmarkdown,
prettydoc,
aplot,
BiocParallel,
scran,
scater,
igraph,
shadowtext,
ggnewscale,
ggforce,
STexampleData
biocViews: GeneExpression, SingleCell, Software, Spatial, Transcriptomics,
Visualization
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.3.tar.gz macOS 12.6.5 Monterey: ggsc_0.99.3.tar.gz
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Please correct the Errors, Warnings, and Notes in the build report before a more in depth review will take place. Please also note and correct the message
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
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The sp package is now running under evolution status 2
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The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: ggsc_0.99.5.tar.gz Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.5.tar.gz
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@lshep We have fixed all the issues to satisfy BiocCheck.
Currently, our visualization methods support SingleCellExperiment
, SpatialExperiment
, and Seurat
objects.
For the note you mentioned, we can't do anything about it because it is an issue with the Seurat package.
> asNamespace(ns="Seurat")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
<environment: namespace:Seurat>
Received a valid push on git.bioconductor.org; starting a build for commit id: df532be6e619e75c686a29b68510161c5f528086
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.6.tar.gz macOS 12.6.5 Monterey: ggsc_0.99.6.tar.gz
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@lshep We have fixed all the issues to satisfy BiocCheck.
Currently, our visualization methods support
SingleCellExperiment
,SpatialExperiment
, andSeurat
objects.For the note you mentioned, we can't do anything about it because it is an issue with the Seurat package.
> asNamespace(ns="Seurat") The legacy packages maptools, rgdal, and rgeos, underpinning the sp package, which was just loaded, will retire in October 2023. Please refer to R-spatial evolution reports for details, especially https://r-spatial.org/r/2023/05/15/evolution4.html. It may be desirable to make the sf package available; package maintainers should consider adding sf to Suggests:. The sp package is now running under evolution status 2 (status 2 uses the sf package in place of rgdal) <environment: namespace:Seurat>
The issue will be fixed in the next release of Seurat. Currently, we can ignore this note.
general
docs
?ggsc
they get an
overview or pointer how to get started.vignette
[ ] Please include an intro that explains why it is being included in Bioconductor and any comparisons to similar packages. See vignette. There also is no textual context to what the code in the vignette is doing. Why are the plots significant, important, different from what is already provided in Bioconductor or by default.
[ ] You have some commented out code in the vignette coding sections. do not include code that is not part of the example. Similarly in the R code if there are commented unused code chunks please remove.
[ ] Why is the transformation from a dgTMatrix to dgCMatrix necessary?
The Makefile
is not just the helper file for a single developer, it is useful for developers to build
or check
... on the local computer since it can save time by collecting.
the ggsc
man and vignette
will be updated as quickly as possible.
Yes, it is not necessary to convert dgTMatrix
to dgCMatrix
.
Please remember to push updates to git.bioconductor.org to trigger a new build and comment back here with the updates when you are ready for a re-review.
Received a valid push on git.bioconductor.org; starting a build for commit id: bb4f73dba906bcf7b7aa79cdde5a971064513631
Received a valid push on git.bioconductor.org; starting a build for commit id: bc386f1d94f9f747757845a015382150c3158bb0
Makefile
is for maintaining the package and it is added in the .Rbuildignore
. We have this file in several BioC packages (e.g., clusterProfiler and ggtree) and I think it is fine to have it.dgTMatrix
instead of dgCMatrix
Dear Package contributor,
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.7.tar.gz macOS 12.6.5 Monterey: ggsc_0.99.7.tar.gz
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The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: ggsc_0.99.8.tar.gz Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.8.tar.gz
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Received a valid push on git.bioconductor.org; starting a build for commit id: 30b74d9695f1282865af6e66480717d4dba9bc62
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.9.tar.gz macOS 12.6.5 Monterey: ggsc_0.99.9.tar.gz
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- WARNING: Empty or missing \value sections found in man pages.
@lshep The warning reported by BiocCheck
is weird. All the man pages of exported functions have \value
session.
We can check the .Rd
files in the man folder and all files contain value
session except the ggsc-package.Rd
and reexports.Rd
.
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.10.tar.gz macOS 12.6.5 Monterey: ggsc_0.99.10.tar.gz
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@lshep By adding \value
session in reexports.Rd
, all issues have been solved.
Thank you. everything looks good now. I am happy to accept.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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