• using R Under development (unstable) (2023-11-30 r85651)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-13 (Debian 13.2.0-5) 13.2.0     GNU Fortran (Debian 13.2.0-5) 13.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘RAINBOWR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘RAINBOWR’ version ‘0.1.33’
• 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 ‘RAINBOWR’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-13 (Debian 13.2.0-5) 13.2.0’
• 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 R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [3s/6s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/5s] OK
• checking whether the package can be unloaded cleanly ... [3s/6s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/5s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/5s] OK
• checking loading without being on the library search path ... [3s/5s] 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 ... [59s/90s] OK
• checking Rd files ... [1s/2s] NOTE checkRd: (-1) RGWAS.epistasis.Rd:46: Lost braces; missing escapes or markup?     46 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.epistasis.Rd:46: Lost braces; missing escapes or markup?     46 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.multisnp.Rd:59: Lost braces; missing escapes or markup?     59 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.multisnp.Rd:59: Lost braces; missing escapes or markup?     59 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.multisnp.interaction.Rd:62: Lost braces; missing escapes or markup?     62 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.multisnp.interaction.Rd:62: Lost braces; missing escapes or markup?     62 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.normal.Rd:47: Lost braces; missing escapes or markup?     47 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.normal.Rd:47: Lost braces; missing escapes or markup?     47 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.normal.interaction.Rd:55: Lost braces; missing escapes or markup?     55 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.normal.interaction.Rd:55: Lost braces; missing escapes or markup?     55 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.twostep.Rd:71: Lost braces; missing escapes or markup?     71 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.twostep.Rd:71: Lost braces; missing escapes or markup?     71 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.twostep.epi.Rd:63: Lost braces; missing escapes or markup?     63 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) RGWAS.twostep.epi.Rd:63: Lost braces; missing escapes or markup?     63 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) Rice_geno_score.Rd:17: Lost braces; missing escapes or markup?     17 | A dataset containing the information of marker genotype (scored with {-1, 0, 1})        | ^ checkRd: (-1) SS_gwas.Rd:28: Lost braces; missing escapes or markup?     28 | \item{x}{A N (lines) x M (markers) marker genotype data (matrix), coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) SS_gwas.Rd:28: Lost braces; missing escapes or markup?     28 | \item{x}{A N (lines) x M (markers) marker genotype data (matrix), coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) estNetwork.Rd:86: Lost braces; missing escapes or markup?     86 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) estNetwork.Rd:86: Lost braces; missing escapes or markup?     86 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) estNetwork.Rd:139: Lost braces; missing escapes or markup?    139 | complemented haplotype will consist of only homozygous sites ({-1, 1}).        | ^ checkRd: (-1) estNetwork.Rd:140: Lost braces; missing escapes or markup?    140 | If FALSE, complemented haplotype will consist of both homozygous & heterozygous sites ({-1, 0, 1}).}        | ^ checkRd: (-1) estPhylo.Rd:78: Lost braces; missing escapes or markup?     78 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^ checkRd: (-1) estPhylo.Rd:78: Lost braces; missing escapes or markup?     78 | Columns 4 and higher contain the marker scores for each line, coded as {-1, 0, 1} = {aa, Aa, AA}.}        | ^
• 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... 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 ... [16s/24s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking re-building of vignette outputs ... [16s/26s] OK
• checking PDF version of manual ... [9s/18s] OK
• checking HTML version of manual ... [6s/12s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 NOTE