• using R Under development (unstable) (2025-07-15 r88411)
• 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
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘GRAB/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘GRAB’ version ‘0.2.1’
• package encoding: UTF-8
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• checking whether package ‘GRAB’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
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• checking examples ... [1s/1s] ERROR Running examples in ‘GRAB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GRAB.Marker > ### Title: Conduct marker-level genetic association testing > ### Aliases: GRAB.Marker > > ### ** Examples > > objNullFile <- system.file("results", "objPOLMMFile.RData", package = "GRAB") > load(objNullFile) > class(obj.POLMM) # "POLMM_NULL_Model", that indicates an object from POLMM method. [1] "POLMM_NULL_Model" > > OutputDir <- system.file("results", package = "GRAB") > OutputFile <- paste0(OutputDir, "/simuOUTPUT.txt") > GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB") > > ## make sure the output files does not exist at first > if (file.exists(OutputFile)) file.remove(OutputFile) > if (file.exists(paste0(OutputFile, ".index"))) file.remove(paste0(OutputFile, ".index")) > > GRAB.Marker(obj.POLMM, + GenoFile = GenoFile, + OutputFile = OutputFile + ) The below is the list of control parameters used in marker-level genetic association analysis. 2c("beta", "seBeta")mean0.150.00120100003 Reading bim file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/extdata/simuPLINK.bim Reading fam file: /home/hornik/tmp/R.check/r-devel-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-devel-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. Number of all markers to test: 1100 Number of markers in each chunk: 10000 Number of chunks for all markers: 1 The current control$nMarkersEachChunk is 10000. (2025-07-26 13:19:20.964078) ---- Analyzing Chunk 1/1: chrom 1 ---- Completed 0/1100 markers in the chunk. Completed 1000/1100 markers in the chunk. Warning in file(file, ifelse(append, "a", "w")) :   cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/GRAB/results/simuOUTPUT.txt': Read-only file system Error in file(file, ifelse(append, "a", "w")) :   cannot open the connection Calls: GRAB.Marker -> writeOutputFile -> write.table -> file Execution halted
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• DONE

Status: 1 ERROR