############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicRanges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicRanges_1.52.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicRanges.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicRanges/DESCRIPTION’ ... OK * this is package ‘GenomicRanges’ version ‘1.52.1’ * 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 ‘GenomicRanges’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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: SIGNIFICANT USER-VISIBLE CHANGES Cannot process chunk/lines: DEPRECATED AND DEFUNCT * 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 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) GRanges-class.Rd:115-165: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:173-176: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:177-182: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:183-187: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:188-191: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:192-195: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:196-199: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:200-204: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:205-208: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:209-218: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:219-223: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:224-228: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:229-238: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:239-245: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:246-251: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:252-257: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:258-263: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:264-267: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:268-276: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:284-299: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:300-307: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:308-322: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:323-332: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:333-342: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:343-349: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:356-361: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:368-371: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:372-376: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:377-380: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:381-394: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:409-415: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:421-427: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:433-445: \item in \describe must have non-empty label checkRd: (5) GRanges-class.Rd:453-466: \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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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 genomicvars 76.293 8.718 107.593 GPos-class 58.629 3.398 79.880 setops-methods 6.985 0.070 8.907 inter-range-methods 4.918 0.274 6.538 findOverlaps-methods 3.960 0.040 5.077 makeGRangesFromDataFrame 1.413 0.225 9.235 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ 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 ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc/meat/GenomicRanges.Rcheck/00check.log’ for details.