############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocOncoTK_1.22.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocOncoTK.Rcheck’ * using R version 4.3.3 (2024-02-29) * 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 Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocOncoTK/DESCRIPTION’ ... OK * this is package ‘BiocOncoTK’ version ‘1.22.2’ * 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 ... NOTE Found the following hidden files and directories: .dockstore.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BiocOncoTK’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: data 2.3Mb pamphlets 4.5Mb * 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 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 ... NOTE ggscat_av: warning in png(file = tempfile()): partial argument match of 'file' to 'filename' .flexbi: no visible binding for global variable ‘v1’ .flexbi: no visible binding for global variable ‘v2’ .rainfall.bq.df: no visible global function definition for ‘seqlengths’ .rainfall.maeGRL.df: no visible global function definition for ‘genome’ .rainfall.maeGRL.df: no visible global function definition for ‘seqlengths’ acronym_to_system: no visible binding for global variable ‘map_tcga_ncit’ add_sym: no visible global function definition for ‘mapIds’ bipg_tests: no visible global function definition for ‘new’ checkCache_patel: no visible global function definition for ‘BiocFileCache’ chrbounds_basic: no visible global function definition for ‘seqlengths’ ggFeatDens : : no visible binding for global variable ‘Consequence’ ggFeatDens: no visible binding for global variable ‘tfstart’ ggFeatureSegs: no visible binding for global variable ‘symbol’ ggMutDens : : no visible binding for global variable ‘Consequence’ ggMutDens: no visible binding for global variable ‘project_short_name’ ggbox: no visible binding for global variable ‘acronym’ ggbox: no visible binding for global variable ‘symbol’ ggbox: no visible binding for global variable ‘log2ex’ ggbox: no visible binding for global variable ‘msicode’ ggscat: no visible binding for global variable ‘acronym’ ggscat: no visible binding for global variable ‘symbol’ ggscat: no visible binding for global variable ‘msival’ ggscat: no visible binding for global variable ‘log2ex’ ggscat_av: no visible binding for global variable ‘acronym’ ggscat_av: no visible binding for global variable ‘symbol’ ggscat_av: no visible binding for global variable ‘msival’ ggscat_av: no visible binding for global variable ‘tmsi’ ggscat_av: no visible binding for global variable ‘log2exa’ mc3toGR : : no visible binding for global variable ‘Consequence’ multiviz: no visible binding for global variable ‘acronym’ multiviz: no visible binding for global variable ‘msival’ prc: no visible binding for global variable ‘acronym’ prc: no visible global function definition for ‘right_join’ rainfall: no visible global function definition for ‘genome’ tumNorSet : : no visible global function definition for ‘pancan_SE’ Undefined global functions or variables: BiocFileCache Consequence acronym genome log2ex log2exa mapIds map_tcga_ncit msicode msival new pancan_SE project_short_name right_join seqlengths symbol tfstart tmsi v1 v2 Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 46 marked UTF-8 strings * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/BiocOncoTK.Rcheck/00check.log’ for details.