Closed ellispatrick closed 4 years ago
Hi @ellispatrick
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: spicyR
Type: Package
Title: Spatial analysis of in situ cytometry data
Version: 0.99.1
Author: Nicolas Canete and Ellis Patrick
Maintainer: Ellis Patrick <ellis.patrick@sydney.edu.au>
Description: spicyR provides a series of functions to aid in the analysis of both
immunofluorescence and mass cytometry imaging data as well as other assays that
can deeply phenotype individual cells and their spatial location.
License: GPL (>=2)
biocViews:
SingleCell, CellBasedAssays
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Imports: ggplot2, class, concaveman, grid, BiocParallel, spatstat, lmerTest, BiocGenerics, S4Vectors, lme4, methods, mgcv, pheatmap,
purrr, rlang, grDevices, IRanges
Suggests: BiocStyle, knitr, rmarkdown
Depends: R (>= 4.0.0)
RoxygenNote: 7.0.2
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Received a valid push; starting a build. Commits are:
d25f173 version bump
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Received a valid push; starting a build. Commits are:
2013791 Shortened examples
Received a valid push; starting a build. Commits are:
1b38732 Shortened examples.
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Received a valid push; starting a build. Commits are:
bd8267a Version bump. Updated examples to make things quic...
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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.
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Received a valid push; starting a build. Commits are:
fd76938 Added R dependency 3.5
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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.
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Received a valid push; starting a build. Commits are:
d1a7ea7 version bump with R v4 dependency
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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.
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Hi @LiNk-NY there seems to be some conflicting advice on slack with how to deal with the R dependency warning.
Hi Ellis, @ellispatrick
Thank you for your submission to Bioconductor. I have taken a look at your package. Please see the short review below. If you have any questions, feel free to respond on this thread.
WRT the R dependency warning, please remove R (>= 4.0.0)
from the DESCRIPTION
file.
We have R version limits to each release of Bioconductor already set in place so this is
redundant.
Best regards, Marcel
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 2.6Mb
extdata 2.7Mb
* checking R code for possible problems ... NOTE
signifPlot: warning in pheatmap(pVal, col = pal, breaks = breaks,
cluster_rows = FALSE, cluster_cols = FALSE): partial argument match
of 'col' to 'color'
.show_spicy: no visible binding for global variable ‘p.adjust’
hatchingPlot: no visible binding for global variable ‘x’
hatchingPlot: no visible binding for global variable ‘y’
makeWindow : <anonymous>: no visible global function definition for
‘rnorm’
signifPlot: no visible global function definition for ‘p.adjust’
spatialLM: no visible global function definition for ‘predict’
spatialLM: no visible global function definition for ‘lm’
spatialMEM: no visible global function definition for ‘predict’
top,spicy: no visible global function definition for ‘p.adjust’
top,spicy: no visible global function definition for ‘Which’
Undefined global functions or variables:
Which lm p.adjust predict rnorm x y
Consider adding
importFrom("stats", "lm", "p.adjust", "predict", "rnorm")
to your NAMESPACE file.
Authors@R
field instead of the Author
&
Maintainer
combo.LazyData: true
if you have small datasets that don't take a long time
to load.BugReports:
field in the DESCRIPTION
with a link to the
GitHub reposessionInfo()
sectionspicy
? A list
seems too simple.setReplaceMethod
instead of
location<-
for readability and easier identification@
. There should be methods for data extraction, otherwise
you can create accessor functions for those dataas.data.frame
for your class don't create an S4
generic. Preferably, create an as(x, "data.frame")
coercion method.cat
and use message
instead. Use cat
only for show
methodsplot.segmentedCells
. Should there only be one?cellData
, why not use those as the default
argumetns for the rest of the function segmentedCells
and avoid creating new
columns?grepl
instead of length(grep(...)) == 0
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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.
Received a valid push; starting a build. Commits are:
4a2a7f0 Make some lines shorter
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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.
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Received a valid push; starting a build. Commits are:
8f8df26 Reverted vignette to fix evals error
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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.
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Hi @LiNk-NY Thanks for all of suggestions. They were helpful. I believe we have address nearly all of them.
R CMD check [x] The data should be small in order to demonstrate functionality
[x] Make sure all variables are accounted for
I get a size warning when I do this. I've skipped it.
[x] Include a BugReports: field in the DESCRIPTION with a link to the GitHub repo NAMESPACE [x] (Optional) Bioconductor convention has a class names's first letter capitalized Some names seem pretty general / vague: top, location
I have changed top to topPairs, change location to cellSummary, intensity to cellMarks, morphology to cellMorph and pheno to imagePheno to make them sound less vague
vignettes/ [x] For readability and easy maintenance, keep an 80 column width limit to text.
It is still not a strict 80 but much closer
[x] Include an installation and sessionInfo() section [x] It's good to have broken up topics by vignette 👍
R [x] Given the number of Bioconductor classes available, is there a class that could accommodate the needs of spicy? A list seems too simple.
I haven't been able to find any as we want to store the pairwise comparisons. I have renamed the class SpicyResults for more clarity.
[x] Although it's the same, you could use setReplaceMethod instead of location<- for readability and easier identification
[x] Avoid the use of @. There should be methods for data extraction, otherwise you can create accessor functions for those data
Replaced @listData with slot(x,"listData")
[x] Register an S3 method as.data.frame for your class don't create an S4 generic. Preferably, create an as(x, "data.frame") coercion method.
[x] Avoid using cat and use message instead. Use cat only for show methods
[x] Where possible, use name-based subsetting instead of index-based for robustness
[x] There are two plot.segmentedCells. Should there only be one? If you have default names in cellData, why not use those as the default argumetns for the rest of the function segmentedCells and avoid creating new columns? [x] Minor: You can use grepl instead of length(grep(...)) == 0
Hi Ellis, @ellispatrick Thanks for making those changes.
as.data.frame.SegmentedCells
method so that it be available to users. Depends:
field in the DESCRIPTION
file with R (>= 4.0.0)
due to
having serialized data in the package. listData
say something like:
.getData <- function(x)
getElement(x, "listData")
to make the code a bit more clean.
It's looking good!
Received a valid push; starting a build. Commits are:
3c4af8d Exported as.data.frame S3 Added a .putData() funct... 0ac7784 Merge branch 'master' of https://github.com/ellisp...
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Thanks again @LiNk-NY
I can definetely see how all of these things are going to help me in the future, onwards and upwards :)
I exported as.data.frame and added back in the R dependency. I also wrote .putData() function to write to listData
@ellispatrick Thanks for making those changes!
It's almost good to go.
Make sure you are updating your documentation as you make changes. Ensure that you have the latest version of roxygen2 (>= 7.1.0)
and that your file names match the capitalization of the class.
For example, segmentedCells-class.R
should be SegmentedCells-class.R
for consistency.
Received a valid push; starting a build. Commits are:
b2259c5 Updated Roxygen to 7.1.0 Fixed name of plot-Segmen...
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Thanks @LiNk-NY !
Done :)
Hi Ellis, @ellispatrick
The file names issue is not major. Thank you for your contribution!
Your package has been accepted.
Best regards, Marcel
Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.
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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("spicyR")
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