############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cellmig.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cellmig_0.99.16.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmig.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘cellmig/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cellmig’ version ‘0.99.16’ * 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 ‘cellmig’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 76.6Mb sub-directories of 1Mb or more: extdata 3.2Mb libs 72.9Mb * 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘base’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE gen_partial: no visible binding for global variable ‘delta’ get_dose_response_profile: no visible binding for global variable ‘isTip’ get_dose_response_profile: no visible binding for global variable ‘label’ get_dose_response_profile: no visible binding for global variable ‘dose’ get_dose_response_profile: no visible binding for global variable ‘X2.5.’ get_dose_response_profile: no visible binding for global variable ‘X97.5.’ get_pairs: no visible binding for global variable ‘group_x’ get_pairs: no visible binding for global variable ‘group_y’ get_pairs: no visible binding for global variable ‘rho_M’ get_pairs: no visible binding for global variable ‘rho_M_exp’ get_ppc_means: no visible binding for global variable ‘v’ get_ppc_means: no visible binding for global variable ‘X2.5.’ get_ppc_means: no visible binding for global variable ‘X97.5.’ get_ppc_violins: no visible binding for global variable ‘dose’ get_ppc_violins: no visible binding for global variable ‘v’ get_ppc_violins: no visible binding for global variable ‘well’ get_ppc_violins: no visible binding for global variable ‘yhat’ get_treatment_profile: no visible binding for global variable ‘isTip’ get_treatment_profile: no visible binding for global variable ‘label’ get_violins: no visible binding for global variable ‘dose’ get_violins: no visible binding for global variable ‘rho’ Undefined global functions or variables: X2.5. X97.5. delta dose group_x group_y isTip label rho rho_M rho_M_exp v well yhat * checking Rd files ... OK * 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 shell scripts ... 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 ... INFO GNU make is a SystemRequirements. * 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 cellmig-package 156.539 1.724 107.784 cellmig 112.735 2.250 79.459 get_dose_response_profile 102.652 1.573 71.444 get_treatment_profile 101.319 1.868 69.455 ppc_violin 30.145 0.913 23.741 ppc_means 25.601 1.203 19.381 get_violins 24.470 1.252 18.403 get_groups 24.185 1.407 18.427 get_pairs 24.594 0.933 18.498 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmig.Rcheck/00check.log’ for details.