Closed s-aibar closed 7 years ago
Hi @s-aibar
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: AUCell
Type: Package
Title: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g.
identify cells with specific gene signatures)
Version: 0.7.3
Date: 2017-03-14
Author: Sara Aibar, Stein Aerts. Laboratory of Computational Biology. VIB-KU
Leuven Center for Brain & Disease Research. Leuven, Belgium
Maintainer: Sara Aibar <sara.aibar@kuleuven.vib.be>
Description: AUCell allows to identify cells with active gene sets (e.g.
signatures, gene modules...) in single-cell RNA-seq data.
URL: http://scenic.aertslab.org
Imports:
data.table,
mixtools,
BiocGenerics
Enhances: doMC, doRNG
Suggests:
Biobase,
GEOquery,
DT,
NMF,
plotly,
BiocStyle,
knitr,
rmarkdown,
testthat
License: file LICENSE
biocViews: SingleCell, GeneSetEnrichment, Transcriptomics, Transcription, GeneExpression
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 5.0.1
Your package has been approved for building. Your package is now submitted to our queue.
IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.
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Received a valid push; starting a build. Commits are:
aca8d67 Update version to 0.99.0
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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:
77bf72f 0.99.1: Do not load doMC on vignette. It is not av...
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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:
df97f42 0.99.1: Do not load doMC on vignette. It is not av... c4696a0 Merge branch 'master' of https://github.com/aertsl...
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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:
bf939c1 Update DESCRIPTION
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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:
3fa68eb Update DESCRIPTION
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Your package has been built on Linux, Mac, and Windows.
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DESCRIPTION
Provide a more extensive Description:, analogous to a paper abstract where the method being implemented is described in sufficient detail to help the user decide whether the package is appropriate for them.
LICENSE: The license appears to be non-standard, and 'academic use' only. Generally, such academic-only licenses are not appropriate for Bioconductor packages.
vignette
R
The use of '.' in function names is discouraged, use snake_case or camelCase instead.
To facilitate interoperability with other Bioconductor packages and work flows, use the GSEABase package to input, output, and represent gene sets.
Vectorize where appropriate, e.g.,
tmp <- unname(sapply(readLines(fileName), function(x) strsplit(as.character(x),"\t")))
is tmp <- strsplit(readLines(fileName), "\t"))
E.g., 01_buildRankings.R:35 paste()
is not usually required inside warning()
and friends.
Consider using BiocParallel for parallel evaluation, so that Bioconductor users experience a more consistent interface.
avoid 1:length(x)
in favor of seq_along(x)
(more robust when length(x) == 0) or seq_len()
Consider wrapping code and documentation lines to 80 character width, to increase readability. Indent consistently, e.g., in priv_auc.assignmnetThreshold_v5.R:25
Also, format if()
statements so that clauses are on distnict lines, e.g., write (03_AUCell.exploreThresholds.R:81
if(verbose) message(paste("Using", getDoParWorkers(), "cores."))
as
if (verbose)
message("Using ", getDoParWorkers(), " cores.")
for tryCatch()
e.g., priv_auc.assignmnetThreshold_v5.R:56
, avoid
excessive indentation by using a form like
result <- tryCatch({
....
}, error = function(e) {
...
})
Do NOT manipulate the random number generator set.seed()
inside function.
Use the SummarizedExperiment class instead of matrixWrapper
so that Bioconductor users do not need to learn how to use yet another class. E.g., SummarizedExperiment(list(AUC=..., ranking=...)
The deadline for addition of packages to the next Bioconductor release is this Friday. If you'd like your package to be considered, please update your package and provide a written response to the review comments above.
Hello,
Thank you for reviewing the package and the heads-up about the deadline. We are working on the points mentioned on the review, but we are not expecting to be included in the next release of Bioc. We will push the new version to Github when it is ready -probably within a few weeks-.
Thank you, Sara Aibar
Received a valid push; starting a build. Commits are:
2689603 Update to version 0.99.3: - Improved selection of ... f762bd9 Merge branch 'master' of https://github.com/aertsl...
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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.
Please see the following build report for more details:
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It looks like development on this package has stalled. I will close the issue. Feel free to re-open it when you are ready to continue.
Received a valid push; starting a build. Commits are:
7ad1130 v 0.99.6
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Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, WARNINGS, 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:
b304c9f v 0.99.7
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: "skipped, ERROR, 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 following build report for more details:
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Received a valid push; starting a build. Commits are:
f0f64f0 v 0.99.8
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 following build report for more details:
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Dear @mtmorgan ,
I have submitted a new version which addresses your comments. (Thank you for the suggestions, some of them were very useful!)
R CMD check and BiocCheck also run without error or warnings, except this one (which I'm not sure how to address):
Warning: replacing previous import SummarizedExperiment::shift by data.table::shift when loading AUCell
Thank you, Sara Aibar
PS: I think I cannot re-open the issue...
In the NAMESPACE, instead of importing the entire package import(data.table)
import only the things that you want importFrom(data.table, foo, bar)
or import(data.table, except=shift)
.
Received a valid push; starting a build. Commits are:
be899b2 v 0.99.9 (Remove R CMD check warning)
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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:
f6193fc v 0.99.10 (small vignette fixex)
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Received a valid push; starting a build. Commits are:
5e7729c v0.99.11 (Code cleaning)
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Received a valid push; starting a build. Commits are:
f8efc7c v0.99.12
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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:
35f3038 v0.99.12 732619e Merge branch 'master' of https://github.com/aertsl...
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: "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:
568aa71 (version bump)
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Thanks very much for your revisions, which are mostly in line with the original comments. Unfortunately...
DESCRIPTION
Received a valid push; starting a build. Commits are:
dfb7304 v0.99.15: Change lisence & minor changes
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Received a valid push; starting a build. Commits are:
ebdf893 v 0.99.16 eed8066 Merge branch 'master' of https://github.com/aertsl...
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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:
ebf08d8 v 0.99.17
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This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
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Received a valid push; starting a build. Commits are:
db434ef 0.99.18
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Hello,
We have changed the License to GPL-3 (plus a couple minor improvements). Please, let me know if everything is in order now.
Regards, Sara Aibar
Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.
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