############################################################################## ############################################################################## ### ### 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_2.2.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking installed package size ... NOTE installed size is 7.3Mb 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 ... 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 47.677 1.095 51.107 omicSettings 39.252 0.485 41.673 sc_mosim 38.344 0.131 42.694 omicSim 35.620 0.169 37.000 plotProfile 34.827 0.093 36.227 sc_omicResults 33.908 0.028 36.239 sc_omicSettings 33.835 0.021 35.393 experimentalDesign 29.832 0.188 31.922 omicResults 27.558 0.142 28.949 mosim 26.525 0.098 27.900 make_cluster_patterns 9.828 0.000 10.485 * 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, 4 NOTEs See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/MOSim.Rcheck/00check.log’ for details.