############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genomation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genomation_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/genomation.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘genomation/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘genomation’ version ‘1.36.0’ * package encoding: latin1 * 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 ‘genomation’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’ See ‘/Users/biocbuild/bbs-3.19-bioc/meat/genomation.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * 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: in ScoreMatrixBin() function. Cannot process chunk/lines: NEW FUNCTIONS AND FEATURES Cannot process chunk/lines: The character vectors will label the x-axis of heatmaps. Examples: xcoords=c("-2kb","0","2kb") Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. Cannot process chunk/lines: Implemented by Bozena Mika-Gospodorz. * checking code 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 Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ 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 ScoreMatrixBin,RleList-GRangesList: no visible binding for global variable ‘id’ ScoreMatrixBin,RleList-GRangesList: no visible global function definition for ‘:=’ Undefined global functions or variables: := id * checking Rd files ... NOTE checkRd: (-1) plotMeta.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotMeta.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotMeta.Rd:59-60: Lost braces in \itemize; meant \describe ? * 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 compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed enrichmentMatrix-ScoreMatrixList-method 4.995 1.844 12.527 enrichmentMatrix-ScoreMatrixList-ScoreMatrix-method 4.934 0.776 10.396 enrichmentMatrix-ScoreMatrix-method 3.828 0.246 5.288 ScoreMatrix-methods 3.888 0.067 6.033 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘genomation_unit_tests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/genomation.Rcheck/00check.log’ for details.