Closed kevinwang09 closed 5 years ago
Hi @kevinwang09
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: scMerge
Type: Package
Title: scMerge: Merging multiple batches of scRNA-seq data
Version: 0.99.0
Authors@R: c(
person("Kevin", "Wang", email = "kevin.wang@sydney.edu.au", role = c("aut", "cre")
),
person("Yingxin", "Lin", email = "yingxin.lin@sydney.edu.au", role = c("aut")
),
person("Sydney Bioinformatics and Biometrics Group", email = "bioinformatics@maths.usyd.edu.au", role = c("fnd"))
)
Maintainer: Kevin Wang <kevin.wang@sydney.edu.au>
Description: Remove batch effect and unwanted variations for single-cell RNA-seq expression matrix.
The method includes the function of identification of stably expressed genes (SEG) from single-cell data, and also creating pseudo-replicates from the data.
License: GPL-3
Encoding: UTF-8
LazyData: false
Depends:
R (>= 3.5)
Imports:
BiocParallel,
distr,
doSNOW,
foreach,
igraph,
irlba,
iterators,
kBET,
matrixStats,
M3Drop,
parallel,
pdist,
proxy,
Rcpp (>= 0.12.18),
RcppEigen (>= 0.3.3.4.0),
rsvd,
ruv,
S4Vectors,
SingleCellExperiment,
SummarizedExperiment
LinkingTo:
Rcpp (>= 0.12.18),
RcppEigen,
testthat
RoxygenNote: 6.1.1
Suggests:
BiocStyle,
knitr,
rmarkdown,
scater,
testthat
VignetteBuilder: knitr
biocViews: BatchEffect, GeneExpression, Normalization, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
URL: https://github.com/SydneyBioX/scMerge
BugReports: https://github.com/SydneyBioX/scMerge/issues
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Received a valid push; starting a build. Commits are:
59e68ec V0.99.1 rm kBET from import to comply with BioC
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3b8beae resolve scater add_ticks issue
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9c50e01 V0.99.3: upd to be compatible with M3DropV1.9.4
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Received a valid push; starting a build. Commits are:
112c3c1 V0.99.4 version no bump
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Received a valid push; starting a build. Commits are:
c0c32bf V0.99.5 rm redundant files, version bump
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Received a valid push; starting a build. Commits are:
13d4b14 rm redu test files
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Received a valid push; starting a build. Commits are:
404d203 upd travis and R version to 3.6
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Hi, the only warning at this point is that we exceeded 5 minutes when running R CMD check… (Somehow Windows and Mac took much longer to run than Linux). We are also not sure why "BUILD BIN" was skipped on Linux. Any help would be appreciated. Thanks!
Received a valid push; starting a build. Commits are:
f8f4a32 V0.99.8 try to resolve check time limit
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Received a valid push; starting a build. Commits are:
684110c V0.99.9 reduced data size again
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Received a valid push; starting a build. Commits are:
ae71dd3 V0.99.10 recommit due to time stamp issue
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Received a valid push; starting a build. Commits are:
046f02c V0.99.11 upd example_data
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No need to use Maintainer
and Authors@R
. Just Authors@R is
enough.
Description needs to be like a paper abstract. Enough information needs to be provided
Include a package installation step as
well. BiocManager::install("scMerge")
.
The title of the vignette doesn't load. Please check your vignette.
What are the other Rmd files in the vignettes folder,
Breast_Data
CellBench_Data
ESC_Data
Mouse_Liver_Data
Neuronal_Data
Pancreas4_Data
mESC_Data
These are not linked to the vignettes, because when the user does `browseVignettes('scMerge') these sources don't show up. It's likely because they need to be in the vignettes parent folder and not sub folders. Please check this.
The CSS styling gets displayed when the vignette is run using,
R CMD Stangle scMerge.Rmd
R -e "source('vignettes/scMerge.R', max=Inf, echo=TRUE)"
.....
> source("vignettes/scMerge.R", max=Inf, echo=TRUE)
> ## ----style, echo = FALSE, results = 'asis'-------------------------------
> BiocStyle::markdown()
<script type="text/javascript">
document.addEventListener("DOMContentLoaded", function() {
document.querySelector("h1").className = "title";
});
</script>
<script type="text/javascript">
document.addEventListener("DOMContentLoaded", function() {
var links = document.links;
for (var i = 0, linksLength = links.length; i < linksLength; i++)
if (links[i].hostname != window.location.hostname)
links[i].target = '_blank';
});
</script>
<style type="text/css" scoped>
body {
margin: 0px auto;
max-width: 1134px;
font-family: sans-serif;
font-size: 10pt;
}
utils::news()
the tests you have for your package are not sufficient. Consider writing test cases for the R code, per function. Tests need to be robust, and have code coverage.
One good way to write test cases is break up your functions into smaller testable units.
eg:
main <- function(a, b) {
res <- add_two(a,b)
message("result of addition: ", res)
res1 <- complex_integrated_function(res, a, b)
res * res1
}
add_two <- function(a, b) { a + b }
test case:
test_add_two <- function() {
a <- 5
b <- 5
expect_equal(a + b, 10)
}
Do this through out your code base. Break them up into testable small units.
Don't use "print" as an end user message in your code.
End-User messages
message() communicates diagnostic messages (e.g., progress during lengthy computations) during code evaluation.
warning() communicates unusual situations handled by your code.
stop() indicates an error condition.
cat() or print() are used only when displaying an object to the user, e.g., in a show method.
http://bioconductor.org/developers/how-to/coding-style/
You don't need a loop for this,
cell_type <- apply(M, 1, function(x) which(x == 1))
eg:
which(diag(11) == 1)
You need to better indent your code. Please follow formatting used in formatR.
Use <-
when defining functions.
calculateSil = function(x, fast_svd, cell_type, batch)
Remove commented out code.
Received a valid push; starting a build. Commits are:
1dd0524 v0.99.12 added tests and fix vignettes
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9c7aecf 0.9913: fixed examples
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d639c0c 0.99.14 fix doc warning, commit before major updat...
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7e8ffc4 V0.99.15: major upd on scReplicate
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Received a valid push; starting a build. Commits are:
d2f0346 V0.99.16 fixed namespace for utils::head
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Received a valid push; starting a build. Commits are:
d69041e V0.99.18: added verbose, added tests, simplified s...
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Received a valid push; starting a build. Commits are:
3b35730 V0.99.19: Fixed man and tests
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f5391c2 V0.99.20: upd vignette and man
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Received a valid push; starting a build. Commits are:
bb6c7ac V0.99.21:covr at 85%, fixed logo
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Received a valid push; starting a build. Commits are:
a4b1f77 V0.99.22 fixed namespace issue
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@nturaga
Thank you for your review comments. We have updated the scMerge
package to Version 0.99.22. A summary of the updates:
The package description, news, namespace, installation instruction and the manuals were updated based on your comments. We hope this is sufficient to give the end-users a concise summary of the package and each implemented functions.
With regard to the vignette. We have fixed the title issue and it should now load with vignette(“scMerge”)
.
Files like Breast_Data.Rmd
are included purely for the construction of our pkgdown
-GitHub webpage (https://sydneybiox.github.io/scMerge/). These files should be ignored. The only vignette file we intend for our package is vignette/scMerge.Rmd
. The pkgdown
package automatically creates a “docs” folder, which, to the best of our understanding, does not install to user’s computer.
With regards to the print methods, we have implemented your suggestion. We have consolidated all diagnostic print outs under a verbose option.
With regards to testing scripts, thank you for this comment. We have included these scripts now and the code coverage at this point is 85%.
With regards to computational speed-ups, we have done another check of our codes to make sure vectorisation is used wherever possible.
With regards to code styling, we have used the formatR
package with some manual editing at places where it fails to correct for line-character length.
Thank you, Best wishes, Kevin Wang on behalf of all authors
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