CRAN Package Check Results for Maintainer ‘Sahir Bhatnagar <sahir.bhatnagar at gmail.com>’

Last updated on 2025-02-16 08:51:40 CET.

Package	ERROR	NOTE	OK
casebase			15
eclust	1	2	12
ggmix			15
manhattanly		5	10

Package casebase

Current CRAN status: OK: 15

Package eclust

Current CRAN status: ERROR: 1, NOTE: 2, OK: 12

Additional issues

noSuggests

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-devel-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-devel-macos-x86_64

Package ggmix

Current CRAN status: OK: 15

Package manhattanly

Current CRAN status: NOTE: 5, OK: 10

Version: 0.3.0
Check: Rd cross-references
Result: NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: manhattanly.Rd: plotly volcanoly.Rd: plotly Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64

Version: 0.3.0
Check: dependencies in R code
Result: NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc