############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:erma.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings erma_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/erma.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'erma/DESCRIPTION' ... OK * this is package 'erma' version '1.14.0' * 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 whether package 'erma' can be installed ... OK * checking installed package size ... NOTE installed size is 199.2Mb sub-directories of 1Mb or more: bed_tabix 161.3Mb data 37.1Mb * 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 geneTxRange: no visible global function definition for 'select' genemodelOLD: no visible binding for global variable 'exonsBy' stateProfile: no visible binding for global variable 'states_25' stateProfile: no visible binding for global variable 'short_celltype' stateProfile: no visible binding for global variable 'name' statesByRange: no visible binding for global variable 'mod' statesByRange: no visible binding for global variable 'upstream' statesByRange: no visible binding for global variable 'downstream' statesByRange : : no visible binding for global variable 'tss' statesByRange: no visible binding for global variable 'states_25' Undefined global functions or variables: downstream exonsBy mod name select short_celltype states_25 tss upstream * 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed erma-package 7.63 0.32 27.34 stateProfile 3.14 0.14 20.98 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.16-bioc/meat/erma.Rcheck/00check.log' for details.