############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Guitar.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Guitar_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Guitar.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘Guitar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Guitar’ version ‘2.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'GenomicFeatures', 'rtracklayer', 'AnnotationDbi', 'GenomicRanges', 'magrittr', 'ggplot2', 'knitr', 'dplyr' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘Guitar’ can be installed ... OK * checking installed package size ... NOTE installed size is 15.9Mb sub-directories of 1Mb or more: extdata 15.7Mb * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘knitr’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘GenomicRanges:::get_out_of_bound_index’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .extractComponent: no visible binding for global variable ‘gene_id’ .generate_guitar_coordinates: no visible global function definition for ‘makeGuitarCoordsFromTxDb’ .generate_guitar_coordinates: no visible binding for global variable ‘noBins’ Undefined global functions or variables: gene_id makeGuitarCoordsFromTxDb noBins * checking Rd files ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GuitarPlot 28.474 0.423 28.899 GRangesListmapToTranscripts 13.549 0.420 13.973 samplePoints 12.012 0.104 12.116 makeGuitarTxdb 11.661 0.123 11.786 normalize 11.561 0.036 11.597 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Guitar-Overview.Rnw’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/Guitar.Rcheck/00check.log’ for details.