############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:microbiomeDataSets.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings microbiomeDataSets_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/microbiomeDataSets.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘microbiomeDataSets/DESCRIPTION’ ... OK * this is package ‘microbiomeDataSets’ version ‘1.15.0’ * 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 ‘microbiomeDataSets’ 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) GrieneisenTSData.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:39: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:41: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:42: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:43: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:46: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:47: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) GrieneisenTSData.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) availableDataSets.Rd:12: Lost braces in \itemize; \value handles \item{}{} directly * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: GrieneisenTSData.Rd: TreeSummarizedExperiment-class LahtiMLData.Rd: MultiAssayExperiment-class, TreeSummarizedExperiment-class, SummarizedExperiment-class OKeefeDSData.Rd: TreeSummarizedExperiment-class SilvermanAGutData.Rd: TreeSummarizedExperiment-class SongQAData.Rd: TreeSummarizedExperiment-class SprockettTHData.Rd: TreeSummarizedExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed LahtiMLData 7.638 0.638 9.066 GrieneisenTSData 6.350 0.456 7.414 SilvermanAGutData 6.393 0.376 7.266 SprockettTHData 5.514 0.359 6.377 SongQAData 5.247 0.415 6.106 OKeefeDSData 4.809 0.248 5.422 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/microbiomeDataSets.Rcheck/00check.log’ for details.