############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FoldGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FoldGO_1.21.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FoldGO.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FoldGO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FoldGO’ version ‘1.21.1’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘FoldGO’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'FoldGO' is deprecated and will be removed from Bioconductor See ‘/Users/biocbuild/bbs-3.19-bioc/meat/FoldGO.Rcheck/00install.out’ for details. * 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 R 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 ... 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 ... WARNING checkRd: (5) fagroupstopgo_class.Rd:16: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:17: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:18-19: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:20-21: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:22: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:23: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:25: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:26-27: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:28-29: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:30-31: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:32-33: \item in \describe must have non-empty label checkRd: (5) fagroupstopgo_class.Rd:42: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:21: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:22: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:23: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:24-25: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:26-27: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:35: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:36: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:37: \item in \describe must have non-empty label checkRd: (5) foldspectest_class.Rd:38: \item in \describe must have non-empty label checkRd: (5) gafreader_class.Rd:19: \item in \describe must have non-empty label checkRd: (5) gafreader_class.Rd:20: \item in \describe must have non-empty label checkRd: (5) gafreader_class.Rd:28: \item in \describe must have non-empty label checkRd: (5) gafreader_class.Rd:29: \item in \describe must have non-empty label checkRd: (5) gafreader_class.Rd:37-38: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:24-25: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:26: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:27: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:35-36: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:37-38: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:39: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:40: \item in \describe must have non-empty label checkRd: (5) genegroups_class.Rd:41: \item in \describe must have non-empty label * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot-FoldSpecTest-ANY-method 12.711 0.143 15.567 fagroupstopgo_class 10.474 0.457 12.668 gafreader_class 5.418 1.931 8.743 foldspectest_class 6.794 0.103 7.919 getWholeIntName 5.697 0.104 7.045 * 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: 2 WARNINGs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/FoldGO.Rcheck/00check.log’ for details.