############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:R3CPET.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings R3CPET_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/R3CPET.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘R3CPET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘R3CPET’ version ‘1.24.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘R3CPET’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: data 3.0Mb example 1.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields. * 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 ... NOTE Namespace in Imports field not imported from: 'BiocGenerics' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .GetClusterInfo: no visible binding for global variable 'TxDb.Hsapiens.UCSC.hg19.knownGene' .GetClusterInfo: no visible global function definition for 'toTable' .GetClusterInfo: no visible binding for global variable 'org.Hs.egUCSCKG' .GetClusterInfo: no visible global function definition for 'select' .GetClusterInfo: no visible binding for global variable 'org.Hs.eg.db' .formatDAVIDResult: no visible global function definition for 'formatGeneReportFull' .formatDAVIDResult: no visible global function definition for 'formatGeneReport' .formatDAVIDResult: no visible global function definition for 'formatList' .formatDAVIDResult: no visible global function definition for 'formatGene2Gene' .formatDAVIDResult: no visible global function definition for 'formatAnnotationReport' .get.NetworksGenes: no visible global function definition for 'annotatePeakInBatch' .plot.sota: no visible global function definition for 'legend' .plot.sota: no visible global function definition for 'lines' EnsemblToHGNC: no visible global function definition for 'useMart' EnsemblToHGNC: no visible global function definition for 'useDataset' EnsemblToHGNC: no visible global function definition for 'getBM' EntrezToHGNC: no visible global function definition for 'useMart' EntrezToHGNC: no visible global function definition for 'useDataset' EntrezToHGNC: no visible global function definition for 'getBM' RunHLDA: no visible binding for global variable '_R3CPET_RunHLDA' createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers: no visible global function definition for 'runApp' plot3CPETRes,ChromMaintainers: no visible global function definition for 'plotCurves' plot3CPETRes,ChromMaintainers: no visible global function definition for 'plotAvgCurves' Undefined global functions or variables: TxDb.Hsapiens.UCSC.hg19.knownGene _R3CPET_RunHLDA annotatePeakInBatch formatAnnotationReport formatGene2Gene formatGeneReport formatGeneReportFull formatList getBM legend lines org.Hs.eg.db org.Hs.egUCSCKG plotAvgCurves plotCurves runApp select toTable useDataset useMart Consider adding importFrom("graphics", "legend", "lines") to your NAMESPACE file. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘tests.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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/R3CPET.Rcheck/00check.log’ for details.