• using R version 4.5.1 Patched (2025-07-24 r88462)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
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• this is package ‘GRAB’ version ‘0.2.2’
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[5s/6s] ERROR Running examples in ‘GRAB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GRAB.POLMM > ### Title: POLMM method in GRAB package > ### Aliases: GRAB.POLMM > > ### ** Examples > > ### First, Read Data and Convert Phenotype to a Factor > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’:     filter, lag The following objects are masked from ‘package:base’:     intersect, setdiff, setequal, union > PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB") > PhenoData <- data.table::fread(PhenoFile, header = TRUE) > PhenoData <- PhenoData %>% mutate(OrdinalPheno = factor(OrdinalPheno, + levels = c(0, 1, 2) + )) > > ### Step 1: Fit a null model > # If a sparse GRM is used in model fitting, SparseGRMFile is required. > # If SparseGRMFile isn't provided, GRAB.NullModel() will calculate dense GRM from GenoFile. > > SparseGRMFile <- system.file("SparseGRM", "SparseGRM.txt", package = "GRAB") > GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB") > obj.POLMM <- GRAB.NullModel( + formula = OrdinalPheno ~ AGE + GENDER, + data = PhenoData, + subjData = PhenoData$IID, + method = "POLMM", + traitType = "ordinal", + GenoFile = GenoFile, + SparseGRMFile = SparseGRMFile, + control = list( + showInfo = FALSE, + LOCO = FALSE, + tolTau = 0.2, + tolBeta = 0.1 + ) + ) Number of subjects in 'formula': 1000 Reading bim file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.bim Reading fam file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam setting PLINK object in CPP.... Reading bim file.... Reading fam file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.fam m_N: 1000 Setting position of samples in PLINK files.... posSampleInPlink: 501 510 600 SampleInModel: Subj-1 Subj-10 Subj-100 SampleInPlink: f1_1 f1_2 f1_3 Number of samples: 1000 Based on the 'GenoFile' and 'GenoFileIndex',PLINKformat is used for genotype data. Sparse GRM is used when fitting a null model. The below are the list of control parameters used in null model fitting. 2-1301000.10.20.21001e-061001e-100.10.1200.0025auto10.010.1FALSEFALSEFALSE gIndex: 1016 gIndex: 678 gIndex: 128 gIndex: 929 gIndex: 470 gIndex: 298 gIndex: 269 gIndex: 596 gIndex: 329 gIndex: 36 gIndex: 728 gIndex: 877 gIndex: 484 gIndex: 873 gIndex: 381 gIndex: 974 gIndex: 800 gIndex: 851 gIndex: 930 gIndex: 325 gIndex: 1091 gIndex: 553 gIndex: 110 gIndex: 531 gIndex: 555 gIndex: 888 gIndex: 342 gIndex: 581 gIndex: 39 gIndex: 536 gIndex: 374 gIndex: 247 gIndex: 377 gIndex: 38 gIndex: 434 gIndex: 809 gIndex: 525 gIndex: 641 gIndex: 21 gIndex: 192 gIndex: 498 gIndex: 982 gIndex: 842 gIndex: 464 gIndex: 995 gIndex: 83 gIndex: 1052 gIndex: 251 gIndex: 732 gIndex: 619 gIndex: 556 gIndex: 286 gIndex: 613 gIndex: 328 gIndex: 486 gIndex: 854 gIndex: 850 gIndex: 857 gIndex: 618 gIndex: 575 gIndex: 989 gIndex: 1022 gIndex: 315 gIndex: 1051 gIndex: 649 gIndex: 1097 gIndex: 810 gIndex: 954 gIndex: 281 gIndex: 284 gIndex: 500 gIndex: 510 gIndex: 535 gIndex: 692 gIndex: 987 gIndex: 736 gIndex: 338 gIndex: 345 gIndex: 674 gIndex: 42 gIndex: 0 gIndex: 28 gIndex: 589 gIndex: 917 gIndex: 837 gIndex: 795 gIndex: 627 gIndex: 232 gIndex: 292 gIndex: 572 gIndex: 941 gIndex: 368 gIndex: 450 gIndex: 85 gIndex: 482 gIndex: 326 gIndex: 621 gIndex: 354 gIndex: 818 gIndex: 811 gIndex: 48 gIndex: 360 gIndex: 1037 gIndex: 241 gIndex: 439 gIndex: 757 gIndex: 816 gIndex: 817 gIndex: 246 gIndex: 750 gIndex: 218 gIndex: 134 It took 0.003357 seconds (0.003355 CPU seconds) to calculate 30 genKinbVec(). Start iteration ..... d2eps: -1.3071e+02 d1eps: 2.7770 deps: 0.0212 iter: 0 m_eps: 0    0.9821 eps0: 0    0.9609 m_tolEps: 1e-10 d2eps: -1.2536e+02 d1eps: 0.0574 deps: 0.0005 iter: 1 m_eps: 0    0.9826 eps0: 0    0.9821 m_tolEps: 1e-10 d2eps: -1.2525e+02 d1eps: 2.5614e-05 deps: 2.0451e-07 iter: 2 m_eps: 0    0.9826 eps0: 0    0.9826 m_tolEps: 1e-10 d2eps: -1.2525e+02 d1eps: 5.0837e-12 deps: 4.0590e-14 iter: 3 m_eps: 0    0.9826 eps0: 0    0.9826 m_tolEps: 1e-10 UpdateEps iter: 3 eps:         0    0.9826 beta:   -37.5557     0.5975     0.3791 diffBeta: 0.00275036 Start updating tau... iter: 0 beta:   -37.5557     0.5975     0.3791 tau: 0.0293943 d2eps: -1.2360e+02 d1eps: -2.2300 deps: -0.0180 iter: 0 m_eps: 0    0.9646 eps0: 0    0.9826 m_tolEps: 1e-10 d2eps: -1.2811e+02 d1eps: 0.0403 deps: 0.0003 iter: 1 m_eps: 0    0.9649 eps0: 0    0.9646 m_tolEps: 1e-10 d2eps: -1.2803e+02 d1eps: 1.2656e-05 deps: 9.8853e-08 iter: 2 m_eps: 0    0.9649 eps0: 0    0.9649 m_tolEps: 1e-10 d2eps: -1.2803e+02 d1eps: 1.2440e-12 deps: 9.7169e-15 iter: 3 m_eps: 0    0.9649 eps0: 0    0.9649 m_tolEps: 1e-10 UpdateEps iter: 3 eps:         0    0.9649 beta:   -37.5479     0.5974     0.3811 diffBeta: 0.00231347 Start updating tau... iter: 1 beta:   -37.5479     0.5974     0.3811 tau: 0.0136161 It took 0.084108 seconds (0.072103 CPU seconds) to fit the null POLMM.. Start estimating variance ratio.... nSNPs for CV: 20 CV: 5.84339e-06 Complete the null model fitting in package GRAB: Complete Time: 2025-07-30 05:31:57.92245 > > objPOLMMFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB") > save(obj.POLMM, file = objPOLMMFile) Warning in gzfile(file, "wb") :   cannot open compressed file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/GRAB/results/objPOLMMFile.RData', probable reason 'Read-only file system' Error in gzfile(file, "wb") : cannot open the connection Calls: save -> gzfile Execution halted
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• DONE

Status: 1 ERROR