Last updated on 2025-12-20 05:49:49 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.5 | 2.86 | 36.13 | 38.99 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.0.5 | 2.11 | 23.37 | 25.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.5 | 50.47 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.5 | 46.95 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.5 | 4.00 | 113.00 | 117.00 | OK | |
| r-patched-linux-x86_64 | 1.0.5 | 2.91 | 32.84 | 35.75 | OK | |
| r-release-linux-x86_64 | 1.0.5 | 2.86 | 32.65 | 35.51 | OK | |
| r-release-macos-arm64 | 1.0.5 | OK | ||||
| r-release-macos-x86_64 | 1.0.5 | 2.00 | 32.00 | 34.00 | OK | |
| r-release-windows-x86_64 | 1.0.5 | 4.00 | 52.00 | 56.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.5 | OK | ||||
| r-oldrel-macos-x86_64 | 1.0.5 | 2.00 | 30.00 | 32.00 | OK | |
| r-oldrel-windows-x86_64 | 1.0.5 | 6.00 | 61.00 | 67.00 | NOTE |
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:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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-linux-x86_64-debian-gcc
Version: 1.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/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-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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.5
Check: tests
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.5
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'doMC'
Flavor: r-oldrel-windows-x86_64