* using log directory ‘/srv/hornik/tmp/CRAN/GiANT.Rcheck’ * using R Under development (unstable) (2023-10-24 r85407) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (15) GNU Fortran (Debian 13.2.0-4) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GiANT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GiANT’ version ‘1.3.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/3s] NOTE Maintainer: ‘Hans Kestler ’ New submission Package was archived on CRAN CRAN repository db overrides: X-CRAN-Comment: Archived on 2021-03-24 as check problems were not corrected in time. BioC package 'GlobalAncova' not used conditionally. * 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 ‘GiANT’ can be installed ... [2s/2s] OK * 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) GiANT-package.Rd:25-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) GiANT-package.Rd:29-31: Lost braces in \itemize; meant \describe ? checkRd: (-1) GiANT-package.Rd:33-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) GiANT-package.Rd:37-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) evaluateGeneSetUncertainty.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:66-82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) evaluateGeneSetUncertainty.Rd:86-88: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) globalAnalysis.Rd:52-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) globalAnalysis.Rd:56-58: Lost braces in \itemize; meant \describe ? checkRd: (-1) globalAnalysis.Rd:60-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) gls.Rd:71-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) gls.Rd:76-78: Lost braces in \itemize; meant \describe ? checkRd: (-1) gls.Rd:81-83: Lost braces in \itemize; meant \describe ? checkRd: (-1) gls.Rd:86-88: Lost braces in \itemize; meant \describe ? checkRd: (-1) gls.Rd:91-93: Lost braces in \itemize; meant \describe ? checkRd: (-1) gls.Rd:96-98: Lost braces in \itemize; meant \describe ? checkRd: (-1) gsAnalysis.Rd:68-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) gsAnalysis.Rd:72-74: Lost braces in \itemize; meant \describe ? checkRd: (-1) gsAnalysis.Rd:77-79: Lost braces in \itemize; meant \describe ? checkRd: (-1) gsAnalysis.Rd:82-84: Lost braces in \itemize; meant \describe ? checkRd: (-1) gsAnalysis.Rd:87-89: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:68-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:73-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:78-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:83-85: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:88-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:93-95: Lost braces in \itemize; meant \describe ? checkRd: (-1) gss.Rd:98-100: Lost braces in \itemize; meant \describe ? checkRd: (-1) predefinedAnalyses.Rd:31-32: Lost braces in \itemize; meant \describe ? checkRd: (-1) predefinedAnalyses.Rd:34-35: Lost braces in \itemize; meant \describe ? checkRd: (-1) predefinedAnalyses.Rd:37-38: Lost braces in \itemize; meant \describe ? checkRd: (-1) predefinedAnalyses.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) predefinedAnalyses.Rd:43-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) predefinedAnalyses.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) predefinedAnalyses.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) significance.Rd:69-71: Lost braces in \itemize; meant \describe ? checkRd: (-1) significance.Rd:74-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) significance.Rd:79-81: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformation.Rd:63-65: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformation.Rd:68-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformation.Rd:73-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformation.Rd:78-80: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformation.Rd:83-85: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformation.Rd:88-90: Lost braces in \itemize; meant \describe ? checkRd: (-1) transformation.Rd:93-94: Lost braces in \itemize; meant \describe ? * 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/0s] OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [8s/8s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 NOTEs