Closed ChristopherEeles closed 4 years ago
Hi @ChristopherEeles
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: RadioGx
Type: Package
Title: Analysis of Large-Scale Radio-Genomic Data
Version: 0.99.3
Date: 2020-03-30
Authors@R: c(
person("Venkata","Manem", email = "mail2mvskumar@gmail.com",
role = c("aut")),
person("Petr","Smirnov", email = "petr.smirnov@uhnresearch.ca",
role = c("aut")),
person("Ian","Smith", email = "ianc.smith@mail.utoronto.ca",
role = c("aut")),
person("Meghan","Lambie", email = "megan.lambie@mail.utoronto.ca",
role = c("aut")),
person("Christopher","Eeles", email = "christopher.eeles@uhnresearch.ca",
role = c("aut")),
person("Scott", "Bratman", email = "scott.bratman@rmp.uhn.ca",
role = c("aut")),
person("Benjamin","Haibe-Kains", email = "benjamin.haibe.kains@utoronto.ca",
role = c("aut","cre"))
)
Description: Computational tool box for radio-genomic analysis which integrates
radio-response data, radio-biological modelling and comprehensive cell line
annotations for hundreds of cancer cell lines. The 'RadioSet' class enables
creation and manipulation of standardized datasets including information
about cancer cells lines, radio-response assays and dose-response indicators.
Included methods allow fitting and plotting dose-response data using
established radio-biological models along with quality control to validate
results. Additional functions related to fitting and plotting dose response
curves, quantifying statistical correlation and calculating area under the
curve (AUC) or survival fraction (SF) are included. For more details please
see the included documentation, references, as well as:
Manem, V. et al (2018) <doi:10.1101/449793>.
License: GPL-3
VignetteBuilder: knitr
VignetteEngine: knitr::rmarkdown
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0), CoreGx
Imports:
SummarizedExperiment,
S4Vectors,
Biobase,
parallel,
BiocParallel,
RColorBrewer,
caTools,
magicaxis,
methods,
reshape2,
scales,
grDevices,
graphics,
stats,
utils,
assertthat,
matrixStats
Suggests:
rmarkdown,
BiocStyle,
knitr,
pander
biocViews: Software, Pharmacogenetics, QualityControl, Survival
RoxygenNote: 7.1.0
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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.
ok
ok
ok
ok
Ok.
It seems there will be more details added to the vignette to make it more complete.
Replace
##FIXME:: Why write as character and convert to numeric?
D <- as.numeric(c("0","1","2","3","4","5","6","8","10"))
with
D <- c(0:6,8,10)
You can check with class(D)
and it'll show you it's numeric
.
As I mentioned in the review for PharmacoGx
as well, there is a
real formatting inconsistency in your codebase. This makes it very
hard for a reviewer to follow. Specifically, consider the 2 space
indent vs 4
space. http://bioconductor.org/developers/how-to/coding-style/
There are multiple NOTES in your build report (NOTE count: 8 ). The build report acts as a way for you to correct the NOTES before the reviewer takes a look. I will point out some of them below. I'm particular about the sapply() issue, please rectify that. The other ones, i'm less particular about, but consider fixing those as well.
* NOTE: Avoid sapply(); use vapply()
Found in files:
computeSensitivity.R (line 94, column 12)
computeSensitivity.R (line 95, column 11)
doseResponseCurve.R (line 287, column 18)
geneDrugSensitivity.R (line 36, column 27)
plotCurve.R (line 96, column 13)
radSensitivitySig.R (line 195, column 24)
radSensitivitySig.R (line 214, column 17)
radSensitivitySig.R (line 220, column 14)
rankGeneDrugSensitivity.R (line 104, column 24)
rankGeneDrugSensitivity.R (line 107, column 25)
rankGeneDrugSensitivity.R (line 121, column 26)
There are also no test cases for such an extensive codebase in
this package. testthat
makes it very easy to write test cases.
Please consider writing some test cases.
As I mentioned about the formatting, the build report throws the same as a NOTE,
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 345 lines (6%) are > 80 characters
long.
First 6 lines:
R/computeAUC.R:82 CoreGx::.sanitizeInput(pars = pars, # Added this ...
R/computeAUC.R:107 return(pars[[1]] / 2 * (lower ^ 2 - upper ^ 2)...
R/computeAUC.R:113 return((exp(-pars[[1]] * lower) - exp(-par...
R/computeSensitivity.R:1 ## This function computes pars/AUC/SF2/D10 for...
R/computeSensitivity.R:28 pars <- lapply(names(AUC), function(exp, ...
R/computeSensitivity.R:29 if(length(grep("///", raw.sensitivity[e...
* NOTE: Consider 4 spaces instead of tabs; 32 lines (1%) contain
tabs.
First 6 lines:
R/RadioSetClass.R:1269 exps <- adArgs[["exps"]]
R/RadioSetClass.R:1270 if(is(exps,"data.frame")){
R/RadioSetClass.R:1271 exps2 <- exps[[name(object)]]
R/RadioSetClass.R:1272 names(exps2) <- rownames(exps)
R/RadioSetClass.R:1273 exps <- exps2
R/RadioSetClass.R:1274 } else{
* NOTE: Consider multiples of 4 spaces for line indents, 1399
lines(23%) are not.
First 6 lines:
R/computeAUC.R:38 SF_as_log = FALSE,
R/computeAUC.R:39 area.type = c("Fitted", "Actua...
R/computeAUC.R:40 verbose = TRUE)
R/computeAUC.R:41 {
R/computeAUC.R:42 area.type <- match.arg(area.type)
R/computeAUC.R:44 if (!missing(SF)) {
See http://bioconductor.org/developers/how-to/coding-style/
See FormatR package:
https://cran.r-project.org/web/packages/formatR/index.html
Based on your previous response, (during the CoreGx package review, and I asked to uniformly fix them across all the packages). It seems like some of these issues which I raised in my last review still persist. You spoke of an upcoming "refractor". Any idea when this is going to happen? Please keep in mind, when you have such a massive code refractor to improve the codebase , why not do it before the review and make it easier for the reviewer as well?
Coding style: I realize that some of our functions are hard to
read, we are in the process of refactoring all four packages
(CoreGx, PharmacoGx, RadioGx, ToxicoGx) and plan to get the
codebase in shape within a month or two. Until then please let me
know if there are any style issues I should address immediately
There are still some slots in your object being accessed with the
'@' function. eg: object@curation
I highly recommend you break up the file RadioSetClass.R, the file has over 1700 lines of code which are complex. Break it up into multiple files if needed, the functions can be made easier too by writing a few helper functions. This will also help you be able to debug in case something goes wrong in your code, since there are no test cases.
Since you are aiming to get this in for the conference, please make as many updates as you can and leave a reply on each point detailing what is possible and what isn't at the moment. That way we can move forward to package acceptance in a faster way.
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.
Received a valid push; starting a build. Commits are:
a14eb57 Update: Version bump to trigger build
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.
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.
Vignette
Replace
Formatting inconsistency
Notes
Tests
Refactor
@ Access
RadioSet
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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