############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOSim.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOSim_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MOSim/DESCRIPTION’ ... OK * this is package ‘MOSim’ version ‘2.2.0’ * 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 ‘MOSim’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘dplyr::count’ by ‘matrixStats::count’ when loading ‘MOSim’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... NOTE installed size is 6.7Mb sub-directories of 1Mb or more: data 5.8Mb * 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 whether startup messages can be suppressed ... 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 make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq.a’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq.ao’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘cluster’ make_association_dataframe : keep_remaining: no visible binding for global variable ‘Freq’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq.a’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq.ao’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘cluster’ make_association_dataframe : keep_remaining2: no visible binding for global variable ‘Freq’ make_association_dataframe: no visible binding for global variable ‘Peak_ID’ make_association_dataframe: no visible binding for global variable ‘Gene_ID’ Undefined global functions or variables: Freq Freq.a Freq.ao Gene_ID Peak_ID cluster * checking Rd files ... NOTE checkRd: (-1) TF_human.Rd:12: Lost braces; missing escapes or markup? 12 | @source {https://tflink.net/} | ^ checkRd: (-1) associationList.Rd:14: Lost braces; missing escapes or markup? 14 | @source {Created in-house to serve as an example} | ^ checkRd: (-1) sc_mosim.Rd:94: Lost braces; missing escapes or markup? 94 | {https://tflink.net/}} | ^ checkRd: (-1) scatac.Rd:14-15: Lost braces 14 | @source {https://github.com/satijalab/seurat-data, we took 11 cells | ^ checkRd: (-1) scrna.Rd:14-15: Lost braces 14 | @source {https://github.com/satijalab/seurat-data, we took 11 cells | ^ checkRd: (-1) scrna.Rd:23-28: Lost braces 23 | for (cell_type in unique_cell_types) { | ^ * 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 discretize 154.085 6.020 165.596 omicSettings 143.198 5.725 159.034 omicSim 138.003 6.609 150.978 plotProfile 132.513 6.642 146.135 omicResults 107.891 5.039 119.761 experimentalDesign 107.732 4.702 115.488 mosim 104.778 5.157 114.282 sc_mosim 58.307 1.000 61.827 sc_omicSettings 47.844 0.634 57.252 sc_omicResults 47.261 0.507 49.751 make_cluster_patterns 37.953 0.277 42.429 omicData 6.721 0.074 7.137 * 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: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00check.log’ for details.