* using log directory 'd:/RCompile/CRANincoming/R-devel/gpcp.Rcheck'
* using R Under development (unstable) (2025-07-30 r88476 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'gpcp/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gpcp' version '0.1.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Christine Nyaga <cmn92@cornell.edu>'

Possibly misspelled words in DESCRIPTION:
  gpcp (11:18)
* 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 serialization versions ... OK
* checking whether package 'gpcp' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 14.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'CRAN-SUBMISSION' 'cran-comments.md'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [12s] OK
* checking whether the package can be loaded with stated dependencies ... [14s] 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 ... [13s] OK
* checking loading without being on the library search path ... [11s] 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 ... [47s] OK
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated name 'runGPCP':
  'gpcp.Rd' 'runGPCP.Rd'
Rd files with duplicated alias 'runGPCP':
  'gpcp.Rd' 'runGPCP.Rd'
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gpcp.Rd: sommer, dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'gpcp.Rd':
runGPCP
  Code: function(phenotypeFile, genotypeFile = NA, genotypeData = NA,
                 genotypes, traits, weights = NA, userSexes = "",
                 userFixed = NA, userRandom = NA, Ploidy = NA, NCrosses
                 = NA)
  Docs: function(phenotypeFile, genotypeFile, genotypes, traits,
                 weights = NA, userSexes = "", userFixed = NA,
                 userRandom = NA, Ploidy = NA, NCrosses = NA)
  Argument names in code not in docs:
    genotypeData
  Mismatches in argument names (first 3):
    Position: 3 Code: genotypeData Docs: genotypes
    Position: 4 Code: genotypes Docs: traits
    Position: 5 Code: traits Docs: weights
  Mismatches in argument default values:
    Name: 'genotypeFile' Code: NA Docs: 

* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'gpcp-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: runGPCP
> ### Title: Genomic Prediction of Cross Performance
> ### Aliases: runGPCP
> ### Keywords: genomic prediction cross performance
> 
> ### ** Examples
> 
> # Load phenotype data from CSV
> phenotypeFile <- read.csv("~/Documents/GCPC_input_files/2020_TDr_PHENO (1).csv")
Warning in file(file, "rt") :
  cannot open file 'C:\Users\CRAN\Documents/Documents/GCPC_input_files/2020_TDr_PHENO (1).csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 3 NOTEs