Closed RachelQueen1 closed 5 years ago
Hi @RachelQueen1
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: Spaniel
Type: Package
Title: Spatial Transcriptomics Analysis
Version: 0.99.0
Author: Rachel Queen <rachel.queen@newcastle.ac.uk>
Maintainer: Rachel Queen <rachel.queen@newcastle.ac.uk>
Description: A collection of tools for analysing Spatial Transcriptomics Data.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0),
Seurat,
SingleCellExperiment,
dplyr
Imports: methods,
ggplot2,
scater,
shiny,
jpeg,
magrittr,
SummarizedExperiment,
utils,
S4Vectors
Suggests:
knitr,
rmarkdown,
testthat,
devtools
VignetteBuilder: knitr
RoxygenNote: 6.1.1.9000
Collate:
'utilities.R'
'addClusterCols.R'
'parseImage.R'
'readData.R'
'removeSpots.R'
'spaniel_plot_internals.R'
'spatialPlot.R'
'shinySpaniel.R'
biocViews: SingleCell, RNASeq, QualityControl,
Preprocessing, Normalization, Visualization, Transcriptomics,
GeneExpression, Sequencing, Software, DataImport,
DataRepresentation, Infrastructure, Coverage, Clustering
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Hi, Just wondered if there is anything I need to do as I haven't had an update for a while? Thanks in advance
Hi @RachelQueen1 ,
I will review your package and post a review in a few days time. You need to set up the build reports for your package, so it can build and check. Please see the comments issued by the bot above.
https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md#adding-a-web-hook
Best,
Nitesh
Great, thank you :)
Rachel
Great, thank you :)
Rachel
Please take a look at the edits in my previous comment.
Thanks, I have added the web hook.
Received a valid push; starting a build. Commits are:
00c23ec Update version
Dear Package contributor,
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push; starting a build. Commits are:
891cdca remove supress messages and update version
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Your package has been built on Linux, Mac, and Windows.
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.
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Received a valid push; starting a build. Commits are:
0da4aab fix typo and update version
Dear Package contributor,
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push; starting a build. Commits are:
a8f8c83 change calculateQCMetrics to addQCPerCell
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: "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.
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Received a valid push; starting a build. Commits are:
a9ecd6d update version
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ok
ok
I cannot get the vignette to run, (Note, there is also an incomplete function call in this.
sce <- scater::addQCPerCell(
sce,
)
The package scater
doesn't have the function addQCPerCell
.
Error: processing vignette 'spaniel-vignette.Rmd' failed with diagnostics:
'addQCPerCell' is not an exported object from 'namespace:scater'
if(removeTmpFile){
}
Please correct these basic issues before a more in depth review.
Received a valid push; starting a build. Commits are:
4de2b51 remove dead code, update description and add versi...
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Received a valid push; starting a build. Commits are:
fd528c1 fix typo
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Received a valid push; starting a build. Commits are:
b709d10 version bump
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Received a valid push; starting a build. Commits are:
7588d1d Version bump
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Received a valid push; starting a build. Commits are:
1569645 remove remove tmp file option from example
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Hi Nitesh,
Thanks for starting the review process. I have now addressed the problem with the Description and removed the dead code. addQCPerCell is exported from the development version of Scater: https://bioconductor.org/packages/devel/bioc/html/scater.html. The function replaces calculateQCMetrics and I was getting a warning message to say that that function would soon be depreciated. Is it the right thing to do to use the development version of scater or should I stick with the current version in Bioconductor?
Thanks in advance,
Rachel
New packages and packages being submitted should use the development version of Bioconductor (and therefore the devel version of packages). So this is the right version to be developing against https://bioconductor.org/packages/devel/bioc/html/scater.html . Cheers.
Variable naming is not consistent. MetaData
vs whichCols
, use
only one type of casing. Use either, "UpperCamelCase" or
"lowerCamelCase"(recommended). Just make sure your variable names
are consistent across.
Add the Bioconductor way of installing the package in the vigneette
BiocManager::install('Spaniel')
.
readSeurat()
and readSCE()
are not very descriptive of
"creating" seurat or SCE objects. The function name should probably be createSeurat
and createSCE()
It would also help if you used markdown formatting features to
annotate your vignette to make it more readable. Function calls can
be functionCall()
, and important points can be marked as
important. This allows greater readability.
Dear Package contributor,
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Received a valid push; starting a build. Commits are:
87fc110 change ST_plot to spanielPlot
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Received a valid push; starting a build. Commits are:
cfaa56d revert to devtools way of installation
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Received a valid push; starting a build. Commits are:
2323a14 revert to devtools way of installation
Dear Package contributor,
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Received a valid push; starting a build. Commits are:
35ef0b5 version bump
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Received a valid push; starting a build. Commits are:
58f4553 change parameter names in removeSpots function
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Received a valid push; starting a build. Commits are:
282152c correct example in removeSpots
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Received a valid push; starting a build. Commits are:
22acc4d fix example for remove spots documentation
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