############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhenStat.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PhenStat/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PhenStat’ version ‘2.42.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 for sufficient/correct file permissions ... OK * checking whether package ‘PhenStat’ 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 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘SmoothWin’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) plot.PhenList.Rd:49-53: Lost braces 49 | \item boxplotSexGenotype. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:54-58: Lost braces 54 | \item boxplotSexGenotypeBatchAdjusted. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:59-63: Lost braces 59 | \item boxplotSexGenotypeWeightBatchAdjusted. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:64-68: Lost braces 64 | \item scatterplotSexGenotypeBatch. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:69-73: Lost braces 69 | \item scatterplotGenotypeWeight. See documentations for { | ^ checkRd: (-1) plot.PhenList.Rd:74-78: Lost braces 74 | \item boxplotSexGenotypeBatch. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:41-45: Lost braces 41 | \item boxplotSexGenotypeResult. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:46-50: Lost braces 46 | \item scatterplotSexGenotypeBatchResult. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:51-55: Lost braces 51 | \item scatterplotGenotypeWeightResult. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:56-60: Lost braces 56 | \item plotResidualPredicted. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:61-65: Lost braces 61 | \item qqplotRandomEffects. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:66-70: Lost braces 66 | \item boxplotResidualBatch. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:71-75: Lost braces 71 | \item qqplotRotatedResiduals. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:76-80: Lost braces 76 | \item qqplotGenotype. See documentations for { | ^ checkRd: (-1) plot.PhenTestResult.Rd:81-85: Lost braces 81 | \item categoricalBarplot. See documentations for { | ^ checkRd: (-1) qqplotRotatedResiduals.Rd:18: Lost braces 18 | Houseman, E. A., Ryan, L. M., Coull, B. A. (2004): Cholesky residuals for assessing normal errors in a linear model with correlated outcomes. \emph{Journal of the American Statistical Association} \bold{99}{466}: pg 383-394. Doi 10.1198 | ^ * 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 ... NOTE Documented arguments not in \usage in Rd file 'printLROutput.Rd': ‘effectValues’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'plot.PhenList.Rd': ‘\dots’ Argument items with no description in Rd file 'plot.PhenTestResult.Rd': ‘\dots’ * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... 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 ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhenStat.Rcheck/00check.log’ for details.