* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/rNeighborGWAS.Rcheck’
* using R Under development (unstable) (2024-04-05 r86344)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘rNeighborGWAS/DESCRIPTION’ ... OK
* this is package ‘rNeighborGWAS’ version ‘1.2.4’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rNeighborGWAS’ can be installed ... [12s/16s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/rNeighborGWAS-00install.html' for details.
* 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 code 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 ... [17s/23s] OK
* checking Rd files ... NOTE
checkRd: (-1) calc_PVEnei.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calc_PVEnei.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calc_PVEnei.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calc_PVEnei.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gaston2neiGWAS.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gaston2neiGWAS.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gaston2neiGWAS.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) neiGWAS.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) neiGWAS.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) neiGWAS.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lm.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lm.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lm.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lm.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lmm.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lmm.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lmm.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) nei_lmm.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qtl_pheno_simu.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [122s/156s] OK
  Running ‘testthat.R’ [122s/156s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [46s/58s] OK
* checking PDF version of manual ... [7s/11s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE