* using log directory 'd:/Rcompile/CRANpkg/local/3.6/hlaR.Rcheck' * using R version 3.6.3 (2020-02-29) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'hlaR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'hlaR' version '0.1.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'hlaR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [12s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'hlaR-Ex.R' failed The error most likely occurred in: > ### Name: EvalAlleleMism > ### Title: Evaluate mismatched alleles > ### Aliases: EvalAlleleMism > > ### ** Examples > > dat <- read.csv(system.file("extdata/example", "HLA_Clean_test.csv", package = "hlaR")) > re <- EvalAlleleMism(dat$donor_a1, dat$donor_a2, dat$recipient_a1, dat$recipient_a2, hmz_cnt = 2) Error: Problem with `mutate()` column `mism_cnt`. i `mism_cnt = ifelse(...)`. x level sets of factors are different Backtrace: x 1. +-hlaR::EvalAlleleMism(...) 2. | \-`%>%`(...) 3. +-dplyr::select(., -c(mism_1, mism_2, cnt)) 4. +-dplyr::mutate(...) 5. +-dplyr:::mutate.data.frame(...) 6. | \-dplyr:::mutate_cols(.data, ..., caller_env = caller_env()) 7. | +-base::withCallingHandlers(...) 8. | \-mask$eval_all_mutate(quo) 9. +-base::ifelse(...) 10. +-base::Ops.factor(don_1_clean, don_2_clean) 11. | \-base::stop("level sets of factors are different") 12. \-base::.handleSimpleError(...) 13. \-dplyr:::h(simpleError(msg, call)) Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [272s] WARNING Error(s) in re-building vignettes: --- re-building 'allele-haplotype.Rmd' using rmarkdown -- Attaching packages --------------------------------------- tidyverse 1.3.1 -- v ggplot2 3.3.3 v dplyr 1.0.6 v tibble 3.1.1 v stringr 1.4.0 v tidyr 1.1.3 v forcats 0.5.1 v purrr 0.3.4 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag() --- finished re-building 'allele-haplotype.Rmd' --- re-building 'eplet-mm.Rmd' using rmarkdown -- Attaching packages --------------------------------------- tidyverse 1.3.1 -- v ggplot2 3.3.3 v purrr 0.3.4 v tibble 3.1.1 v dplyr 1.0.6 v tidyr 1.1.3 v stringr 1.4.0 v readr 1.4.0 v forcats 0.5.1 -- Conflicts ------------------------------------------ tidyverse_conflicts() -- x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag() Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) 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Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Unknown Type: promise (5) Quitting from lines 71-88 (eplet-mm.Rmd) Error: processing vignette 'eplet-mm.Rmd' failed with diagnostics: invalid number of 'breaks' --- failed re-building 'eplet-mm.Rmd' SUMMARY: processing the following file failed: 'eplet-mm.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING