* using log directory 'd:/Rcompile/CRANpkg/local/4.0/statgenMPP.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'statgenMPP/DESCRIPTION' ... OK
* this is package 'statgenMPP' version '1.0.0'
* 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 'statgenMPP' 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 ... [8s] 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [22s] ERROR
Running examples in 'statgenMPP-Ex.R' failed
The error most likely occurred in:

> ### Name: selQTLMPP
> ### Title: Multi round genome scans for QTL detection
> ### Aliases: selQTLMPP
> 
> ### ** Examples
> 
> ## Read phenotypic data.
> pheno <- read.delim(system.file("extdata/multipop", "AxBxCpheno.txt",
+                                package = "statgenMPP"))
> ## Rename first column to genotype.
> colnames(pheno)[1] <- "genotype"
> 
> 
> ## Compute IBD probabilities for simulated population - AxB, AxC.
> ABC <- calcIBDMPP(crossNames = c("AxB", "AxC"),
+                   markerFiles = c(system.file("extdata/multipop", "AxB.txt",
+                                               package = "statgenMPP"),
+                                   system.file("extdata/multipop", "AxC.txt",
+                                               package = "statgenMPP")),
+                   pheno = pheno,
+                   popType = "F4DH",
+                   mapFile = system.file("extdata/multipop", "mapfile.txt",
+                                         package = "statgenMPP"),
+                   evalDist = 5)
> 
> ## Single-QTL Mapping.
> ABC_SQM <- selQTLMPP(ABC, trait = "pheno", maxCofactors = 0)
Error in FUN(array(newX[, i], d.call, dn.call), ...) : 
  unused argument (simplify = FALSE)
Calls: selQTLMPP -> do.call -> apply
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [17s] ERROR
  Running 'tinytest.R' [16s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("statgenMPP")
  + }
  Loading required package: statgenGWAS
  
  test_calcIBDmpp.R.............    0 tests    
  test_calcIBDmpp.R.............    0 tests    
  test_calcIBDmpp.R.............    0 tests    
  test_calcIBDmpp.R.............    0 tests    
  test_calcIBDmpp.R.............    1 tests OK 
  test_calcIBDmpp.R.............    2 tests OK 
  test_calcIBDmpp.R.............    3 tests OK 
  test_calcIBDmpp.R.............    4 tests OK 
  test_calcIBDmpp.R.............    5 tests OK 
  test_calcIBDmpp.R.............    6 tests OK 
  test_calcIBDmpp.R.............    7 tests OK 
  test_calcIBDmpp.R.............    8 tests OK 
  test_calcIBDmpp.R.............    9 tests OK 
  test_calcIBDmpp.R.............   10 tests OK 
  test_calcIBDmpp.R.............   11 tests OK 
  test_calcIBDmpp.R.............   12 tests OK 
  test_calcIBDmpp.R.............   13 tests OK 
  test_calcIBDmpp.R.............   14 tests OK 
  test_calcIBDmpp.R.............   15 tests OK 
  test_calcIBDmpp.R.............   16 tests OK 
  test_calcIBDmpp.R.............   17 tests OK 
  test_calcIBDmpp.R.............   18 tests OK 
  test_calcIBDmpp.R.............   19 tests OK 
  test_calcIBDmpp.R.............   20 tests OK 
  test_calcIBDmpp.R.............   21 tests OK 
  test_calcIBDmpp.R.............   22 tests OK 
  test_calcIBDmpp.R.............   23 tests OK 
  test_calcIBDmpp.R.............   24 tests OK 
  test_calcIBDmpp.R.............   25 tests OK 
  test_calcIBDmpp.R.............   25 tests OK 
  test_calcIBDmpp.R.............   26 tests OK 
  test_calcIBDmpp.R.............   27 tests OK 
  test_calcIBDmpp.R.............   28 tests OK 
  test_calcIBDmpp.R.............   28 tests OK 
  test_calcIBDmpp.R.............   29 tests OK 5.1s
  
  test_createGDataMPP.R.........    0 tests    
  test_createGDataMPP.R.........    0 tests    
  test_createGDataMPP.R.........    0 tests    
  test_createGDataMPP.R.........    0 tests    
  test_createGDataMPP.R.........    0 tests    
  test_createGDataMPP.R.........    1 tests OK 
  test_createGDataMPP.R.........    2 tests OK 
  test_createGDataMPP.R.........    2 tests OK 
  test_createGDataMPP.R.........    3 tests OK 
  test_createGDataMPP.R.........    4 tests OK 
  test_createGDataMPP.R.........    5 tests OK 
  test_createGDataMPP.R.........    6 tests OK 
  test_createGDataMPP.R.........    7 tests OK 
  test_createGDataMPP.R.........    8 tests OK 
  test_createGDataMPP.R.........    9 tests OK 
  test_createGDataMPP.R.........   10 tests OK 
  test_createGDataMPP.R.........   11 tests OK 
  test_createGDataMPP.R.........   11 tests OK 
  test_createGDataMPP.R.........   12 tests OK 
  test_createGDataMPP.R.........   13 tests OK 
  test_createGDataMPP.R.........   14 tests OK 
  test_createGDataMPP.R.........   15 tests OK 8.9s
  
  test_createQTLmpp.R...........    0 tests    
  test_createQTLmpp.R...........    0 tests    
  test_createQTLmpp.R...........    0 tests    
  test_createQTLmpp.R...........    0 tests    Error in FUN(array(newX[, i], d.call, dn.call), ...) : 
    unused argument (simplify = FALSE)
  Calls: <Anonymous> ... FUN -> eval -> eval -> selQTLMPP -> do.call -> apply
  In addition: Warning messages:
  1: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 3@30' in 'mbcsToSbcs': dot substituted for <e2>
  2: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 3@30' in 'mbcsToSbcs': dot substituted for <86>
  3: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 3@30' in 'mbcsToSbcs': dot substituted for <90>
  4: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 3@30' in 'mbcsToSbcs': dot substituted for <e2>
  5: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 3@30' in 'mbcsToSbcs': dot substituted for <86>
  6: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 3@30' in 'mbcsToSbcs': dot substituted for <90>
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [11s] WARNING
Error(s) in re-building vignettes:
--- re-building 'QTLMapping_in_MultiParentPopulations.Rmd' using rmarkdown
Quitting from lines 139-143 (QTLMapping_in_MultiParentPopulations.Rmd) 
Error: processing vignette 'QTLMapping_in_MultiParentPopulations.Rmd' failed with diagnostics:
unused argument (simplify = FALSE)
--- failed re-building 'QTLMapping_in_MultiParentPopulations.Rmd'

SUMMARY: processing the following file failed:
  'QTLMapping_in_MultiParentPopulations.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING