Last updated on 2025-10-31 00:51:02 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 5.87 | 128.43 | 134.30 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 4.41 | 97.50 | 101.91 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 15.00 | 236.83 | 251.83 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 12.00 | 245.08 | 257.08 | NOTE | |
| r-devel-windows-x86_64 | 0.1.0 | 9.00 | 190.00 | 199.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 6.96 | 136.46 | 143.42 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 5.88 | 133.03 | 138.91 | OK | |
| r-release-macos-arm64 | 0.1.0 | 3.00 | 83.00 | 86.00 | OK | |
| r-release-macos-x86_64 | 0.1.0 | 5.00 | 78.00 | 83.00 | ERROR | |
| r-release-windows-x86_64 | 0.1.0 | 8.00 | 211.00 | 219.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 3.00 | 78.00 | 81.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.0 | 4.00 | 124.00 | 128.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.0 | 12.00 | 255.00 | 267.00 | OK |
Version: 0.1.0
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Sahir Rai Bhatnagar <sahir.bhatnagar@gmail.com>’
Found the following (possibly) invalid file URI:
URI: CONDUCT.md
From: README.md
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘pander’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘eclust-Ex.R’ failed
The error most likely occurred in:
> ### Name: s_generate_data_mars
> ### Title: Generate non linear response and test and training sets for
> ### non-linear simulation study
> ### Aliases: s_generate_data_mars
>
> ### ** Examples
>
> library(magrittr)
>
> # simulation parameters
> rho = 0.90; p = 500 ;SNR = 1 ; n = 200; n0 = n1 = 100 ; nActive = p*0.10 ; cluster_distance = "tom";
> Ecluster_distance = "difftom"; rhoOther = 0.6; betaMean = 2;
> alphaMean = 1; betaE = 3; distanceMethod = "euclidean"; clustMethod = "hclust";
> cutMethod = "dynamic"; agglomerationMethod = "average"
>
> #in this simulation its blocks 3 and 4 that are important
> #leaveOut: optional specification of modules that should be left out
> #of the simulation, that is their genes will be simulated as unrelated
> #("grey"). This can be useful when simulating several sets, in some which a module
> #is present while in others it is absent.
> d0 <- s_modules(n = n0, p = p, rho = 0, exposed = FALSE,
+ modProportions = c(0.15,0.15,0.15,0.15,0.15,0.25),
+ minCor = 0.01,
+ maxCor = 1,
+ corPower = 1,
+ propNegativeCor = 0.3,
+ backgroundNoise = 0.5,
+ signed = FALSE,
+ leaveOut = 1:4)
simulateDatExpr: simulating 500 genes in 5 modules.
>
> d1 <- s_modules(n = n1, p = p, rho = rho, exposed = TRUE,
+ modProportions = c(0.15,0.15,0.15,0.15,0.15,0.25),
+ minCor = 0.4,
+ maxCor = 1,
+ corPower = 0.3,
+ propNegativeCor = 0.3,
+ backgroundNoise = 0.5,
+ signed = FALSE)
simulateDatExpr: simulating 500 genes in 5 modules.
>
> truemodule1 <- d1$setLabels
>
> X <- rbind(d0$datExpr, d1$datExpr) %>%
+ magrittr::set_colnames(paste0("Gene", 1:p)) %>%
+ magrittr::set_rownames(paste0("Subject",1:n))
>
> betaMainEffect <- vector("double", length = p)
>
> # the first nActive/2 in the 3rd block are active
> betaMainEffect[which(truemodule1 %in% 3)[1:(nActive/2)]] <- runif(
+ nActive/2, betaMean - 0.1, betaMean + 0.1)
>
> # the first nActive/2 in the 4th block are active
> betaMainEffect[which(truemodule1 %in% 4)[1:(nActive/2)]] <- runif(
+ nActive/2, betaMean+2 - 0.1, betaMean+2 + 0.1)
> beta <- c(betaMainEffect, betaE)
>
> result <- s_generate_data_mars(p = p, X = X,
+ beta = beta,
+ binary_outcome = FALSE,
+ truemodule = truemodule1,
+ nActive = nActive,
+ include_interaction = FALSE,
+ cluster_distance = cluster_distance,
+ n = n, n0 = n0,
+ eclust_distance = Ecluster_distance,
+ signal_to_noise_ratio = SNR,
+ distance_method = distanceMethod,
+ cluster_method = clustMethod,
+ cut_method = cutMethod,
+ agglomeration_method = agglomerationMethod,
+ nPC = 1)
Creating data and simulating response for MARS model
Warning in k * error :
Recycling array of length 1 in array-vector arithmetic is deprecated.
Use c() or as.vector() instead.
Calculating similarity matrices
TOM calculation: adjacency..
..will not use multithreading.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
TOM calculation: adjacency..
..will not use multithreading.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
TOM calculation: adjacency..
..will not use multithreading.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
Creating CV folds from training data
Calculating number of clusters based on tom using hclust with average
linkage and the dynamic to determine the number of clusters
..cutHeight not given, setting it to 0.999 ===> 99% of the (truncated) height range in dendro.
..done.
Error in loadNamespace(x) : there is no package called ‘factoextra’
Calls: s_generate_data_mars ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Flavor: r-release-macos-x86_64
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘eclust.Rmd’ using rmarkdown
Quitting from lines 142-168 [unnamed-chunk-6] (eclust.Rmd)
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
there is no package called 'factoextra'
--- failed re-building ‘eclust.Rmd’
SUMMARY: processing the following file failed:
‘eclust.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64