############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:SGCP.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings SGCP_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/SGCP.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘SGCP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SGCP’ version ‘1.6.0’ * package encoding: UTF-8 * 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 ‘SGCP’ 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) SGCP_clustering.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_clustering.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:81: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_ezSGCP.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) SGCP_semiSupervised.Rd:24: Lost braces 24 | \\item{semiSupervised}{An object of the caret train class representing the semi-supervised classification model.} | ^ checkRd: (-1) SGCP_semiSupervised.Rd:24: Lost braces 24 | \\item{semiSupervised}{An object of the caret train class representing the semi-supervised classification model.} | ^ checkRd: (-1) resFinalGO.Rd:11: Lost braces 11 | \details{code{resFinalGO} is a list containing the following information: | ^ * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/SGCP.Rcheck/00check.log’ for details.