############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BaseSpaceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BaseSpaceR_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BaseSpaceR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * 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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BaseSpaceR/DESCRIPTION’ ... OK * this is package ‘BaseSpaceR’ version ‘1.44.0’ * 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 ‘BaseSpaceR’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: BUG FIXES Cannot process chunk/lines: Changed Access token and projects ID used in the vignette to reflect changes in Cannot process chunk/lines: the permission enforcements performed by BaseSpace * 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 startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘Rsamtools’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE asBamFile: no visible global function definition for ‘BamFile’ GET,ServiceURI: no visible global function definition for ‘basicHeaderGatherer’ GET,ServiceURI: no visible global function definition for ‘basicTextGatherer’ GET,ServiceURI: no visible global function definition for ‘getForm’ GET,ServiceURI: no visible global function definition for ‘curlOptions’ POST,ServiceURI: no visible global function definition for ‘basicHeaderGatherer’ POST,ServiceURI: no visible global function definition for ‘basicTextGatherer’ POST,ServiceURI: no visible global function definition for ‘curlPerform’ POSTForm,ServiceURI: no visible global function definition for ‘basicHeaderGatherer’ POSTForm,ServiceURI: no visible global function definition for ‘basicTextGatherer’ POSTForm,ServiceURI: no visible global function definition for ‘postForm’ POSTForm,ServiceURI: no visible global function definition for ‘curlOptions’ getBAMs,AppResults: no visible binding for global variable ‘BamFileList’ getFiles,AppAuth : .toDisk: no visible global function definition for ‘CFILE’ getFiles,AppAuth : .toDisk: no visible global function definition for ‘curlPerform’ getFiles,AppAuth : .toMem: no visible global function definition for ‘getURLContent’ getFiles,AppAuth : .toMem: no visible binding for global variable ‘dsize’ Undefined global functions or variables: BamFile BamFileList CFILE basicHeaderGatherer basicTextGatherer curlOptions curlPerform dsize getForm getURLContent postForm * checking Rd files ... WARNING checkRd: (5) Genomes-class.Rd:49-52: \item in \describe must have non-empty label checkRd: (5) Genomes-class.Rd:53-58: \item in \describe must have non-empty label checkRd: (5) Genomes-class.Rd:59-62: \item in \describe must have non-empty label checkRd: (5) Projects-class.Rd:55-58: \item in \describe must have non-empty label checkRd: (5) Projects-class.Rd:59-64: \item in \describe must have non-empty label checkRd: (5) Projects-class.Rd:65-68: \item in \describe must have non-empty label checkRd: (5) Runs-class.Rd:55-58: \item in \describe must have non-empty label checkRd: (5) Runs-class.Rd:59-64: \item in \describe must have non-empty label checkRd: (5) Runs-class.Rd:65-68: \item in \describe must have non-empty label checkRd: (5) Samples-class.Rd:63-66: \item in \describe must have non-empty label checkRd: (5) Samples-class.Rd:67-72: \item in \describe must have non-empty label checkRd: (5) Samples-class.Rd:73-76: \item in \describe must have non-empty label checkRd: (5) Users-class.Rd:33-36: \item in \describe must have non-empty label checkRd: (5) Users-class.Rd:37-41: \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 data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed Runs-class 0.162 0.012 5.579 * 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 ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BaseSpaceR.Rcheck/00check.log’ for details.