############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMitoMut.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMitoMut_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMitoMut.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scMitoMut/DESCRIPTION’ ... OK * this is package ‘scMitoMut’ version ‘1.1.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘scMitoMut’ can be installed ... WARNING Found the following significant warnings: Warning: scMitoMut.Rd:3: docType ‘_PACKAGE’ is unrecognized See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMitoMut.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * 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 ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE export_dt: no visible binding for global variable ‘af’ export_dt: no visible binding for global variable ‘fwd_depth’ export_dt: no visible binding for global variable ‘rev_depth’ export_dt: no visible binding for global variable ‘coverage’ export_dt: no visible binding for global variable ‘alt_count’ export_dt: no visible binding for global variable ‘alt_depth’ export_dt: no visible binding for global variable ‘mut_status’ export_dt: no visible binding for global variable ‘cell_barcode’ export_dt: no visible binding for global variable ‘n’ export_dt: no visible binding for global variable ‘loc’ filter_loc: no visible binding for global variable ‘mut_cell_n’ plot_locus: no visible binding for global variable ‘alt_depth’ plot_locus: no visible binding for global variable ‘depth’ plot_locus: no visible binding for global variable ‘af’ plot_locus: no visible binding for global variable ‘highlight’ process_locus_bb: no visible binding for global variable ‘alt_depth’ process_locus_bb: no visible binding for global variable ‘fwd_depth’ process_locus_bb: no visible binding for global variable ‘rev_depth’ process_locus_bm: no visible binding for global variable ‘alt_depth’ process_locus_bm: no visible binding for global variable ‘fwd_depth’ process_locus_bm: no visible binding for global variable ‘rev_depth’ process_locus_summary: no visible binding for global variable ‘alt_depth’ process_locus_summary: no visible binding for global variable ‘fwd_depth’ process_locus_summary: no visible binding for global variable ‘rev_depth’ read_locus: no visible binding for global variable ‘cell_barcode’ read_locus: no visible binding for global variable ‘fwd_depth’ read_locus: no visible binding for global variable ‘rev_depth’ read_locus: no visible binding for global variable ‘coverage’ read_locus: no visible binding for global variable ‘alt’ read_locus: no visible binding for global variable ‘af’ read_mgatk: no visible binding for global variable ‘fwd_depth’ read_mgatk: no visible binding for global variable ‘rev_depth’ Undefined global functions or variables: af alt alt_count alt_depth cell_barcode coverage depth fwd_depth highlight loc mut_cell_n mut_status n rev_depth * checking Rd files ... WARNING prepare_Rd: scMitoMut.Rd:3: docType ‘_PACKAGE’ is unrecognized * 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 ... WARNING Undocumented arguments in Rd file 'rm_mtmutObj.Rd' ‘envir’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed export_dt 5.869 1.736 6.626 plot_heatmap 5.715 0.960 5.888 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 3 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMitoMut.Rcheck/00check.log’ for details.