############################################################################## ############################################################################## ### ### 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_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MOSim/DESCRIPTION’ ... OK * this is package ‘MOSim’ version ‘2.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 15.0.0 (clang-1500.1.0.2.5)’ * 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 omicSettings 18.726 2.751 21.477 omicSim 17.197 2.892 20.094 discretize 18.660 1.213 19.873 plotProfile 17.116 2.753 19.871 sc_mosim 16.103 0.284 16.388 omicResults 13.390 2.372 15.770 mosim 13.226 1.986 15.215 experimentalDesign 13.046 0.689 13.734 sc_omicResults 13.513 0.125 13.638 sc_omicSettings 13.199 0.191 13.394 * 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.