############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MOSim.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MOSim_2.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 ... 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 7.2Mb 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) associationList.Rd:14: Lost braces; missing escapes or markup? 14 | @source {Created in-house to serve as an example} | ^ 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 57.335 1.184 58.520 omicSettings 51.048 0.544 51.592 plotProfile 49.122 0.192 49.314 omicSim 49.013 0.256 49.270 scMOSim 38.919 0.280 39.200 omicResults 36.651 0.247 36.900 mosim 35.593 0.351 35.945 experimentalDesign 35.482 0.411 35.895 scOmicSettings 35.200 0.092 35.292 scOmicResults 34.968 0.208 35.175 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00check.log’ for details.