Closed asiort closed 6 months ago
Hi @asiort
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: ClustAll
Type: Package
Title: ClustAll: Data driven strategy to find groups
of patients within complex diseases
Version: 0.99.0
Authors@R: c(person("Asier", "Ortega-Legarreta", role = c("aut","cre"),
email = "aortegal@navarra.es",
comment = c(ORCID = "0009-0000-3563-5362")),
person("Sara", "Palomino-Echeverria", role = c("aut"),
email = "spalomie@navarra.es"))
Imports: FactoMineR, bigstatsr, clValid, clusteval, doSNOW,
parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3,
methods, ComplexHeatmap, RColorBrewer, circlize, ggplot2, grid,
stats, utils
Suggests: knitr
Description: Data driven strategy to find hidden groups of patients with complex
diseases using clinical data. ClustAll facilitates the unsupervised
identification of multiple robust stratifications. ClustAll, is able to
overcome the most common limitations found when dealing with clinical
data (missing values, correlated data, mixed data types).
Depends: R (>= 4.2.0)
License: GPL-2
Encoding: UTF-8
biocViews: Software, StatisticalMethod, Clustering, DimensionReduction,
PrincipalComponent
RoxygenNote: 7.2.3
VignetteBuilder: knitr
git_url: https://github.com/TranslationalBioinformaticsUnit/ClustAll
NeedsCompilation: no
Packaged: 2023-08-10 12:55:36 UTC; asier.ortega
All package dependencies must be active on CRAN or Bioconductor. clusteval was removed from CRAN in June of 2021. See https://cran.r-project.org/web/packages/clusteval/index.html . You must not use this package as a dependency or reach out to the clusteval maintainers to reinstate on CRAN.
I have fixed the dependencies problem and updated my GitHub repository. But when I push to git@git.bioconductor.org:packages/ClustAll I have problems with the credentials.
I am following the tutorial 21.5.1 New package workflow but when doing "git fetch --all" I get the following error: """ $ git fetch --all Fetching origin Fetching upstream git@git.bioconductor.org: Permission denied (publickey). fatal: Could not read from remote repository.
Please make sure you have the correct access rights and the repository exists. error: could not fetch upstream """ How could I fix it?
Thanks in advance.
I will put this through to getting on our git and getting our build reports but when I ran this locally there were many ERROR and Warnings that need to be cleaned up before a reviewer will be assigned for in depth review.
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
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A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
I have evaluated the package and identified some improvements which are needed.
for
loops mustn't be used. Use lapply or vapply instead, in accordance with the Developer's Guide.
createEmptyArrays <- function(nvariables, data_use) {
summary_matrices <- vector("list", nvariables)
for(i in seq_len(nvariables)) {
summary_matrices[[i]] <- as_FBM(matrix(0,nrow(data_use),nrow(data_use)))
}
ClustAllObject
has no show
method. It floods my R console when printed out. Also, there are no accessors.
> obj_noNA
... ...
560 0.096530 0.2112 0.08732
561 0.104800 0.2250 0.08321
562 0.000000 0.1566 0.05905
563 0.235600 0.4089 0.14090
564 0.254200 0.2929 0.09873
565 0.221600 0.2060 0.07115
566 0.162800 0.2572 0.06637
567 0.141800 0.2218 0.07820
568 0.265000 0.4087 0.12400
569 0.000000 0.2871 0.07039
Slot "dataImputed": NULL
Slot "dataValidation": [1] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 1 2 1 1 1 1 1 2 2 1 2 2 1 1 1 1 2 1 2 2 1 1 1 1 2 1 2 2 1 2 1 2 2 1 1 [82] 1 2 2 1 2 2 2 1 1 1 2 1 1 2 2 1 1 1 2 2 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 2 2 2 1 2 2 1 1 1 2 2 1 2 1 2 2 1 2 2 1 1 2 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 [163] 2 1 2 1 1 2 2 1 1 2 2 1 1 1 1 2 1 1 2 2 2 1 2 1 2 1 1 1 2 1 1 2 2 1 2 2 2 2 1 2 2 2 1 2 1 2 1 1 2 1 2 2 2 2 1 1 2 2 1 1 1 2 1 1 1 1 1 2 2 1 1 2 1 1 2 2 1 2 1 1 1 [244] 1 2 1 1 1 1 1 2 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 2 1 2 1 1 2 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 2 1 2 [325] 1 1 1 1 2 2 2 1 1 1 1 2 1 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 2 2 1 1 1 1 1 1 1 1 1 1 1 2 2 1 2 2 2 1 2 2 1 1 1 1 1 2 1 1 1 1 1 2 1 1 1 2 1 1 2 2 1 1 1 1 1 1 2 1 1 1 1 [406] 1 1 1 2 1 1 1 1 1 2 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 2 1 2 2 1 2 1 1 1 1 1 2 1 1 2 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 2 2 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 [487] 1 2 1 2 1 1 2 1 1 1 1 1 2 2 1 2 1 2 1 1 1 1 1 2 1 1 2 1 2 1 2 2 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 2 1 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 [568] 2 1
Slot "nImputation": [1] 0
Slot "processed": [1] FALSE
Slot "summary_clusters": NULL
Slot "JACCARD_DISTANCE_F": NULL
- Vignette needs work. The breast cancer example consists of a bunch of headings and code blocks with no interpretation of output. Also, the first part is just a list of arguments and definitions from the functions. Don't duplicate such information.
- There is only one unit test and it simply creates an S4 object. Needs non-trivial testing for correctness of calculations.
@DarioS Thanks for evaluating the package. I will implement your suggestions as soon as possible :)
Received a valid push on git.bioconductor.org; starting a build for commit id: 0bb53604a63e2a45c59e66fa0ccd62ec3098d419
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The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): ClustAll_0.99.11.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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@DarioS I have implemented the changes you suggested:
I modify the inefficient for loop using apply. You will find those implementations in the following functions: From ClustAll_runClustAll_internal.R file: createEmptyArrays (line 7), cstats.table_hclust (line 113). From ClustAll_ClustAllObject_Methods.R file: resStratification (lines 205 and 207), plotSANKEY (line 380) From ClustAll_ClustAllObject_Methods_internal.R file: chooseClusters (line 80)
Implemented show and accessors (with the exception of the accessor to access data slot to not overwrite the utils::data() function. Instead I have generated the method showData). Now look like this:
> obj_noNA1
ClustAllObject
Data: Number of variables: 30. Number of patients: 569
Imputation: NO.
Number of imputations: 0
Processed: TRUE
Number of stratifications: 72
Thanks for your time!
The issues have been partially addressed. I still think that the vignette and code both have room for improvement.
# This part of the code is commented out as it exceeds the R CMD check time on the macOS 12.7.1 Monterey.
That's actually fine, so please uncomment this. It is a known issue and the timeout for that machine is fine to have happening.checkEquals
).for
loops. For example,
paint_names <- c()
for (i in seq_len(length(res))) {
paint_names <- c(paint_names, res[[i]][[1]][1])
paint_names <- c(paint_names, res[[i]][[length(res[[i]])]][1])
}
This has the exact define-and-grow format which the developer's guide requires us not to do. 27 for
loops remain. Some of them look necessary but all of the ones that are indexed from one to the length of a vector are very likely not necessary.
fig.height
or hide the labels.
Also, one minor observation. The package is called ClustAll but, in the vignette, it varies between ClustALL and ClustAll. ALL makes me think of Acute Lymphoblastic Leukemia, so perhaps it is best to use ClustAll consistently.
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Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): ClustAll_0.99.12.tar.gz
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Received a valid push on git.bioconductor.org; starting a build for commit id: e0657fb225942262b870d89f1b04a2923da1a3e2
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): ClustAll_0.99.13.tar.gz
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Remember: if you submitted your package after July 7th, 2020,
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Hi @DarioS I've implemented the new suggestions:
Regarding the tests:
Regarding the Vignette:
Regarding the for loops:
Find here the for loops that I modified into applys:
Here are the for loops that I consider necessary:
Please let me know if any other improvements would be necessary to implement or discuss. Thanks again for your time.
Thank you.
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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