perf plsda error: "object 'test.keepX' not found"

Issue #157 new
Former user created an issue

Hello, Not sure if this has to do with using parallel (as this error doesn't occur when I don't use cpus)?

plsda.perf <- perf(plsda.res, validation = "Mfold", folds = 10, dist = "mahalanobis.dist", progressBar = FALSE, auc = F, nrepeat = 5, cpus = 2) Error in get(name, envir = envir) : object 'test.keepX' not found In addition: Warning messages: 1: In checkCluster(cl) : closing unused connection 4 (<-localhost:11750) 2: In checkCluster(cl) : closing unused connection 3 (<-localhost:11750)

Thanks!

PS:Some more info below.

str(plsda.res) List of 19 $ call : language plsda(X = smok$beta, Y = Y, ncomp = 10) $ X : num [1:359, 1:185466] -0.66 -0.943 2.496 -0.909 -0.53 ... ..- attr(, "dimnames")=List of 2 .. ..$ : chr [1:359] "35" "45" "50" "73" ... .. ..$ : chr [1:185466] "cg00000029" "cg00000109" "cg00000236" "cg00000289" ... ..- attr(, "scaled:center")= Named num [1:185466] 0.327 0.748 0.648 0.272 0.569 ... .. ..- attr(, "names")= chr [1:185466] "cg00000029" "cg00000109" "cg00000236" "cg00000289" ... ..- attr(, "scaled:scale")= num [1:185466] 0.1116 0.071 0.0783 0.0518 0.0925 ... $ Y : Factor w/ 4 levels "0","1","2","3": 3 1 1 1 1 1 1 1 1 1 ... $ ind.mat : num [1:359, 1:4] -1.618 0.616 0.616 0.616 0.616 ... ..- attr(, "levels")= chr [1:4] "0" "1" "2" "3" ..- attr(, "dimnames")=List of 2 .. ..$ : chr [1:359] "35" "45" "50" "73" ... .. ..$ : chr [1:4] "0" "1" "2" "3" ..- attr(, "scaled:center")= Named num [1:4] 0.7242 0.117 0.1142 0.0446 .. ..- attr(, "names")= chr [1:4] "0" "1" "2" "3" ..- attr(, "scaled:scale")= num [1:4] 0.448 0.322 0.319 0.207 $ ncomp : num 10 $ mode : chr "regression" $ variates :List of 2 ..$ X: num [1:359, 1:10] -14.65 -122.74 -3.44 -101.58 15.86 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr [1:359] "35" "45" "50" "73" ... .. .. ..$ : chr [1:10] "comp 1" "comp 2" "comp 3" "comp 4" ... ..$ Y: num [1:359, 1:10] 1.381 -0.786 -0.786 -0.786 -0.786 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr [1:359] "35" "45" "50" "73" ... .. .. ..$ : chr [1:10] "comp 1" "comp 2" "comp 3" "comp 4" ... $ loadings :List of 2 ..$ X: num [1:185466, 1:10] 4.73e-03 -1.28e-05 1.14e-03 5.13e-03 -1.70e-03 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr [1:185466] "cg00000029" "cg00000109" "cg00000236" "cg00000289" ... .. .. ..$ : chr [1:10] "comp 1" "comp 2" "comp 3" "comp 4" ... ..$ Y: num [1:4, 1:10] -0.704 0.645 0.189 0.23 -0.733 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr [1:4] "0" "1" "2" "3" .. .. ..$ : chr [1:10] "comp 1" "comp 2" "comp 3" "comp 4" ... $ loadings.star :List of 2 ..$ : num [1:185466, 1:10] 4.73e-03 -1.28e-05 1.14e-03 5.13e-03 -1.70e-03 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr [1:185466] "cg00000029" "cg00000109" "cg00000236" "cg00000289" ... .. .. ..$ : NULL ..$ : num [1:4, 1:10] -0.704 0.645 0.189 0.23 -0.733 ... .. ..- attr(, "dimnames")=List of 2 .. .. ..$ : chr [1:4] "0" "1" "2" "3" .. .. ..$ : NULL $ names :List of 3 ..$ sample : chr [1:359] "35" "45" "50" "73" ... ..$ colnames:List of 2 .. ..$ X: chr [1:185466] "cg00000029" "cg00000109" "cg00000236" "cg00000289" ... .. ..$ Y: chr [1:4] "0" "1" "2" "3" ..$ blocks : chr [1:2] "X" "Y" $ tol : num 1e-06 $ iter : num [1:10] 1 1 1 1 1 1 1 1 1 1 $ max.iter : num 100 $ nzv : NULL $ scale : logi TRUE $ logratio : chr "none" $ explained_variance:List of 2 ..$ X: Named num [1:10] 0.06021 0.03085 0.01619 0.00732 0.00576 ... .. ..- attr(, "names")= chr [1:10] "comp 1" "comp 2" "comp 3" "comp 4" ... ..$ Y: Named num [1:10] 0.441 0.373 0.244 0.288 0.265 ... .. ..- attr(, "names")= chr [1:10] "comp 1" "comp 2" "comp 3" "comp 4" ... $ input.X : num [1:359, 1:185466] 0.254 0.222 0.606 0.226 0.268 ... ..- attr(, "dimnames")=List of 2 .. ..$ : chr [1:359] "35" "45" "50" "73" ... .. ..$ : chr [1:185466] "cg00000029" "cg00000109" "cg00000236" "cg00000289" ... $ mat.c : num [1:185466, 1:10] 0.008212 -0.000431 0.003374 0.006941 -0.001705 ... ..- attr(, "dimnames")=List of 2 .. ..$ : chr [1:185466] "cg00000029" "cg00000109" "cg00000236" "cg00000289" ... .. ..$ : NULL - attr(, "class")= chr [1:3] "mixo_plsda" "mixo_pls" "DA" sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/2018 .3.222/compilers_and_libr_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp 64.so

locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] snow_0.4-3 mixOmics_6.7.1 ggplot2_3.1.0 lattice_0.20-35 [5] MASS_7.3-50

loaded via a namespace (and not attached): [1] Rcpp_1.0.0 RSpectra_0.13-1 pillar_1.3.1 compiler_3.5.1 [5] RColorBrewer_1.1-2 plyr_1.8.4 bindr_0.1.1 tools_3.5.1 [9] tibble_2.0.1 gtable_0.2.0 pkgconfig_2.0.2 rlang_0.3.1 [13] Matrix_1.2-14 igraph_1.2.3 parallel_3.5.1 bindrcpp_0.2.2 [17] gridExtra_2.3 withr_2.1.2 dplyr_0.7.8 stringr_1.4.0 [21] grid_3.5.1 tidyselect_0.2.5 glue_1.3.0 ellipse_0.4.1 [25] R6_2.3.0 rARPACK_0.11-0 purrr_0.3.0 tidyr_0.8.2 [29] reshape2_1.4.3 corpcor_1.6.9 magrittr_1.5 scales_1.0.0 [33] matrixStats_0.54.0 assertthat_0.2.0 colorspace_1.4-0 stringi_1.2.4 [37] lazyeval_0.2.1 munsell_0.5.0 crayon_1.3.4

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