CRAN Package Check Results for Maintainer ‘Scott Ritchie <sritchie73 at gmail.com>’

Last updated on 2025-12-28 03:52:18 CET.

Package	ERROR	NOTE	OK
BootstrapQTL	1	3	9
NetRep		2	11
ukbnmr	1		12

Package BootstrapQTL

Current CRAN status: ERROR: 1, NOTE: 3, OK: 9

Version: 1.0.5
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Scott Ritchie <sritchie73@gmail.com>’ No Authors@R field in DESCRIPTION. Please add one, modifying Authors@R: c(person(given = c("Qin", "Qin"), family = "Huang", role = "aut"), person(given = "Scott", family = "Ritchie", role = c("aut", "cre"), email = "sritchie73@gmail.com")) as necessary. Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.0.5
Check: examples
Result: 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 Flavor: r-devel-windows-x86_64

Version: 1.0.5
Check: tests
Result: ERROR Running 'testthat.R' [2s] 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 Flavor: r-devel-windows-x86_64

Version: 1.0.5
Check: package dependencies
Result: NOTE Package suggested but not available for checking: 'doMC' Flavor: r-oldrel-windows-x86_64

Package NetRep

Current CRAN status: NOTE: 2, OK: 11

Version: 1.2.9
Check: installed package size
Result: NOTE installed size is 8.7Mb sub-directories of 1Mb or more: doc 1.7Mb libs 5.9Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package ukbnmr

Current CRAN status: ERROR: 1, OK: 12

Version: 3.3.1
Check: examples
Result: ERROR Running examples in 'ukbnmr-Ex.R' failed The error most likely occurred in: > ### Name: remove_technical_variation > ### Title: Remove technical variation from NMR biomarker data in UK > ### Biobank. > ### Aliases: remove_technical_variation > > ### ** Examples > > ukb_data <- ukbnmr::test_data # Toy example dataset for testing package > processed <- remove_technical_variation(ukb_data) Checking for revelant UKB fields... Extracting and pre-processing data... Checking for required sample processing fields needed for QC procedure... Processing sample processing fields for QC procedure... Error in `[.data.table`(sinfo, , `:=`(Spectrometer.Date.Bin, bin_dates(Plate.Measured.Date, : attempt access index 17/17 in VECTOR_ELT Calls: remove_technical_variation -> [ -> [.data.table Execution halted Flavor: r-devel-windows-x86_64

Version: 3.3.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'ukbnmr.Rmd' using rmarkdown Quitting from ukbnmr.Rmd:115-121 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 17/17 in VECTOR_ELT --- Backtrace: ▆ 1. └─ukbnmr::remove_technical_variation(exported) 2. ├─...[] 3. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ukbnmr.Rmd' failed with diagnostics: attempt access index 17/17 in VECTOR_ELT --- failed re-building 'ukbnmr.Rmd' SUMMARY: processing the following file failed: 'ukbnmr.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64