CRAN Package Check Results for Maintainer ‘Karl Broman <broman at wisc.edu>’

Last updated on 2024-11-13 11:49:52 CET.

Package	ERROR	NOTE	OK
aRxiv			13
broman			13
chromer			13
lineup			13
lineup2			13
mbmixture			13
mmconvert			13
negenes			13
qtl		6	7
qtl2		6	7
qtl2convert			13
qtl2fst	2		11
qtlbook			13
qtlcharts			13
regress			13
simcross			13
xoi			13

Package aRxiv

Current CRAN status: OK: 13

Package broman

Current CRAN status: OK: 13

Package chromer

Current CRAN status: OK: 13

Package lineup

Current CRAN status: OK: 13

Package lineup2

Current CRAN status: OK: 13

Package mbmixture

Current CRAN status: OK: 13

Package mmconvert

Current CRAN status: OK: 13

Package negenes

Current CRAN status: OK: 13

Package qtl

Current CRAN status: NOTE: 6, OK: 7

Version: 1.70
Check: installed package size
Result: NOTE installed size is 11.5Mb sub-directories of 1Mb or more: R 2.0Mb contrib 3.7Mb doc 3.0Mb libs 1.3Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package qtl2

Current CRAN status: NOTE: 6, OK: 7

Version: 0.36
Check: installed package size
Result: NOTE installed size is 44.5Mb sub-directories of 1Mb or more: extdata 3.3Mb libs 39.9Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Package qtl2convert

Current CRAN status: OK: 13

Package qtl2fst

Current CRAN status: ERROR: 2, OK: 11

Version: 0.28
Check: examples
Result: ERROR Running examples in 'qtl2fst-Ex.R' failed The error most likely occurred in: > ### Name: replace_path > ### Title: Replace the path used in fst_genoprob object > ### Aliases: replace_path > > ### ** Examples > > library(qtl2) > grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2")) > probs <- calc_genoprob(grav2, error_prob=0.002) > dir <- tempdir() > fprobs <- fst_genoprob(probs, "grav2", dir, overwrite=TRUE) writing D:\temp\2024_11_12_11_12_08_24475\Rtmpq2uy2Q/grav2_1.fst writing D:\temp\2024_11_12_11_12_08_24475\Rtmpq2uy2Q/grav2_2.fst writing D:\temp\2024_11_12_11_12_08_24475\Rtmpq2uy2Q/grav2_3.fst writing D:\temp\2024_11_12_11_12_08_24475\Rtmpq2uy2Q/grav2_4.fst writing D:\temp\2024_11_12_11_12_08_24475\Rtmpq2uy2Q/grav2_5.fst > > # move the probabilities into a different directory > new_dir <- file.path(tempdir(), "subdir") > if(!dir.exists(new_dir)) dir.create(new_dir) > for(file in fst_files(fprobs)) { + file.rename(file, file.path(new_dir, basename(file))) + } > > # revise the path in fprobs > new_path <- sub(dir, new_dir, fst_path(fprobs)) Warning in sub(dir, new_dir, fst_path(fprobs)) : TRE pattern compilation error 'Invalid back reference' Error in sub(dir, new_dir, fst_path(fprobs)) : invalid regular expression 'D:\temp\2024_11_12_11_12_08_24475\Rtmpq2uy2Q', reason 'Invalid back reference' Execution halted Flavor: r-release-windows-x86_64

Version: 0.28
Check: examples
Result: ERROR Running examples in 'qtl2fst-Ex.R' failed The error most likely occurred in: > ### Name: replace_path > ### Title: Replace the path used in fst_genoprob object > ### Aliases: replace_path > > ### ** Examples > > library(qtl2) > grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2")) > probs <- calc_genoprob(grav2, error_prob=0.002) > dir <- tempdir() > fprobs <- fst_genoprob(probs, "grav2", dir, overwrite=TRUE) writing D:\temp\2024_11_11_17_15_36_10152\Rtmp84jAAc/grav2_1.fst writing D:\temp\2024_11_11_17_15_36_10152\Rtmp84jAAc/grav2_2.fst writing D:\temp\2024_11_11_17_15_36_10152\Rtmp84jAAc/grav2_3.fst writing D:\temp\2024_11_11_17_15_36_10152\Rtmp84jAAc/grav2_4.fst writing D:\temp\2024_11_11_17_15_36_10152\Rtmp84jAAc/grav2_5.fst > > # move the probabilities into a different directory > new_dir <- file.path(tempdir(), "subdir") > if(!dir.exists(new_dir)) dir.create(new_dir) > for(file in fst_files(fprobs)) { + file.rename(file, file.path(new_dir, basename(file))) + } > > # revise the path in fprobs > new_path <- sub(dir, new_dir, fst_path(fprobs)) Warning in sub(dir, new_dir, fst_path(fprobs)) : TRE pattern compilation error 'Invalid back reference' Error in sub(dir, new_dir, fst_path(fprobs)) : invalid regular expression 'D:\temp\2024_11_11_17_15_36_10152\Rtmp84jAAc', reason 'Invalid back reference' Execution halted Flavor: r-oldrel-windows-x86_64

Package qtlbook

Current CRAN status: OK: 13

Package qtlcharts

Current CRAN status: OK: 13

Package regress

Current CRAN status: OK: 13

Package simcross

Current CRAN status: OK: 13

Package xoi

Current CRAN status: OK: 13