############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings PharmacoGx_3.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PharmacoGx.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 ‘PharmacoGx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PharmacoGx’ version ‘3.10.0’ * 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 ‘PharmacoGx’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... OK * 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 ... NOTE Namespace in Imports field not imported from: ‘BiocGenerics’ All declared Imports should be used. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.Hill’ ‘.summarizeSensitivityNumbers’ ‘partialCorQUICKSTOP’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .computeZIPdelta: no visible binding for global variable ‘EC50_proj_1_to_2’ .computeZIPdelta: no visible binding for global variable ‘EC50_proj_2_to_1’ .computeZIPdelta: no visible binding for global variable ‘HS_proj_1_to_2’ .computeZIPdelta: no visible binding for global variable ‘HS_proj_2_to_1’ .computeZIPdelta: no visible binding for global variable ‘E_inf_proj_2_to_1’ .computeZIPdelta: no visible binding for global variable ‘E_inf_proj_1_to_2’ .computeZIPdelta: no visible binding for global variable ‘Rsqr_1_to_2’ .computeZIPdelta: no visible binding for global variable ‘Rsqr_2_to_1’ .plotProjHill: no visible binding for global variable ‘treatment1id’ .plotProjHill: no visible binding for global variable ‘treatment2id’ .plotProjHill: no visible binding for global variable ‘treatment2dose’ .plotProjHill: no visible binding for global variable ‘EC50_proj_2_to_1’ .plotProjHill: no visible binding for global variable ‘HS_proj_2_to_1’ .plotProjHill: no visible binding for global variable ‘EC50_2’ .plotProjHill: no visible binding for global variable ‘E_inf_2’ .plotProjHill: no visible binding for global variable ‘E_inf_proj_2_to_1’ .plotProjHill: no visible binding for global variable ‘HS_2’ .plotProjHill: no visible binding for global variable ‘treatment1dose’ .plotProjHill: no visible binding for global variable ‘combo_viability’ .plotProjHill: no visible binding for global variable ‘x’ .plotProjHill: no visible binding for global variable ‘EC50_proj_1_to_2’ .plotProjHill: no visible binding for global variable ‘HS_proj_1_to_2’ .plotProjHill: no visible binding for global variable ‘EC50_1’ .plotProjHill: no visible binding for global variable ‘HS_1’ .plotProjHill: no visible binding for global variable ‘E_inf_1’ .plotProjHill: no visible binding for global variable ‘E_inf_proj_1_to_2’ PharmacoSet2: no visible global function definition for ‘MultiAssayExperiment’ fitTwowayZIP: no visible binding for global variable ‘treatment1dose’ fitTwowayZIP: no visible binding for global variable ‘combo_viability’ fitTwowayZIP: no visible binding for global variable ‘treatment2dose’ fitTwowayZIP: no visible binding for global variable ‘EC50_2’ fitTwowayZIP: no visible binding for global variable ‘HS_2’ fitTwowayZIP: no visible binding for global variable ‘E_inf_2’ fitTwowayZIP: no visible binding for global variable ‘EC50_1’ fitTwowayZIP: no visible binding for global variable ‘HS_1’ fitTwowayZIP: no visible binding for global variable ‘E_inf_1’ mergePSets: no visible global function definition for ‘checkPSetStructure’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘ZIP’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘EC50_proj_1_to_2’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘EC50_proj_2_to_1’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘EC50_1’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘EC50_2’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘HS_proj_1_to_2’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘HS_proj_2_to_1’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘HS_1’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘HS_2’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘E_inf_1’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘E_inf_2’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘E_inf_proj_2_to_1’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘E_inf_proj_1_to_2’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘treatment1dose’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘treatment2dose’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘Rsqr_1_to_2’ computeZIPdelta,TreatmentResponseExperiment: no visible binding for global variable ‘Rsqr_2_to_1’ Undefined global functions or variables: EC50_1 EC50_2 EC50_proj_1_to_2 EC50_proj_2_to_1 E_inf_1 E_inf_2 E_inf_proj_1_to_2 E_inf_proj_2_to_1 HS_1 HS_2 HS_proj_1_to_2 HS_proj_2_to_1 MultiAssayExperiment Rsqr_1_to_2 Rsqr_2_to_1 ZIP checkPSetStructure combo_viability treatment1dose treatment1id treatment2dose treatment2id x * 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 ... NOTE Note: found 2251 marked UTF-8 strings * 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 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/PharmacoGx.Rcheck/00check.log’ for details.