• using R Under development (unstable) (2024-11-15 r87338)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• 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 serialization versions ... OK
• checking whether package ‘rNeighborGWAS’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] 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 ... [9s/12s] OK
• checking Rd files ... [0s/0s] 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   gaston2neiGWAS.Rd: gaston, bed.matrix 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 ... 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 ... [3s/3s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [48s/61s] OK   Running ‘testthat.R’ [48s/60s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [17s/21s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 NOTEs