• using R Under development (unstable) (2025-12-19 r89206)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘BootstrapQTL/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘BootstrapQTL’ version ‘1.0.5’
• package encoding: UTF-8
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• checking whether package ‘BootstrapQTL’ can be installed ... OK See the install log for details.
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• checking for unstated dependencies in examples ... OK
• checking examples ... ERROR Running examples in ‘BootstrapQTL-Ex.R’ failed The error most likely occurred in: > ### Name: BootstrapQTL > ### Title: Bootstrap QTL analysis for accurate effect size estimation > ### Aliases: BootstrapQTL > > ### ** Examples > > # Locations for example data from the MatrixEQTL package > base.dir = find.package('MatrixEQTL'); > SNP_file_name = paste(base.dir, "/data/SNP.txt", sep=""); > snps_location_file_name = paste(base.dir, "/data/snpsloc.txt", sep=""); > expression_file_name = paste(base.dir, "/data/GE.txt", sep=""); > gene_location_file_name = paste(base.dir, "/data/geneloc.txt", sep=""); > covariates_file_name = paste(base.dir, "/data/Covariates.txt", sep=""); > > # Load the SNP data > snps = SlicedData$new(); > snps$fileDelimiter = "\t"; # the TAB character > snps$fileOmitCharacters = "NA"; # denote missing values; > snps$fileSkipRows = 1; # one row of column labels > snps$fileSkipColumns = 1; # one column of row labels > snps$fileSliceSize = 2000; # read file in slices of 2,000 rows > snps$LoadFile(SNP_file_name); Rows read: 15 done. > > # Load the data detailing the position of each SNP > snpspos = read.table(snps_location_file_name, header = TRUE, stringsAsFactors = FALSE); > > # Load the gene expression data > gene = SlicedData$new(); > gene$fileDelimiter = "\t"; # the TAB character > gene$fileOmitCharacters = "NA"; # denote missing values; > gene$fileSkipRows = 1; # one row of column labels > gene$fileSkipColumns = 1; # one column of row labels > gene$fileSliceSize = 2000; # read file in slices of 2,000 rows > gene$LoadFile(expression_file_name); Rows read: 10 done. > > # Load the data detailing the position of each gene > genepos = read.table(gene_location_file_name, header = TRUE, stringsAsFactors = FALSE); > > # Load the covariates data > cvrt = SlicedData$new(); > cvrt$fileDelimiter = "\t"; # the TAB character > cvrt$fileOmitCharacters = "NA"; # denote missing values; > cvrt$fileSkipRows = 1; # one row of column labels > cvrt$fileSkipColumns = 1; # one column of row labels > if(length(covariates_file_name)>0) { + cvrt$LoadFile(covariates_file_name); + } Rows read: 2 done. > > # Run the BootstrapQTL analysis > eQTLs <- BootstrapQTL(snps, gene, snpspos, genepos, cvrt, n_bootstraps=10, n_cores=2) Registering 2 cores for bootstrap procedure. Mapping QTLs and obtaining nominal effect size estimates... 10 of 10 genes matched 15 of 15 SNPs matched 100.00% done, 100 cis-eQTLs Error in `[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue, :   attempt access index 6/6 in VECTOR_ELT Calls: BootstrapQTL -> hierarchical_correction -> [ -> [.data.table Restoring global environment... Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... ERROR   Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(BootstrapQTL)   Loading required package: MatrixEQTL   >   > test_check("BootstrapQTL")   Mapping QTLs and obtaining nominal effect size estimates...   Saving _problems/test-50.R   Restoring global environment...   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test.R:48:5'): Run BootstrapQTL ─────────────────────────────────────   Error in ``[.data.table`(cis_assocs, , `:=`(local_pval, adjust_p(pvalue, method = local)), by = gene)`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. ├─base::tryCatch(...) at test.R:47:3    2. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)    3. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])    4. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)    5. └─BootstrapQTL::BootstrapQTL(...) at test.R:48:5    6. └─BootstrapQTL:::hierarchical_correction(...)    7. ├─...[]    8. └─data.table:::`[.data.table`(...)      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [6s/10s] OK
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• DONE

Status: 2 ERRORs