############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PharmacoGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PharmacoGx_3.11.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PharmacoGx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PharmacoGx’ version ‘3.11.1’ * 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: computeZIPdelta-TreatmentResponseExperiment-method.Rd: TreatmentResponseExperiment fitTwowayZIP.Rd: data.table Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ... ERROR Running examples in ‘PharmacoGx-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: PharmacoSet-accessors > ### Title: Accessing and modifying information in a 'PharmacoSet' > ### Aliases: PharmacoSet-accessors drugInfo > ### treatmentInfo,PharmacoSet-method treatmentInfo drugInfo<- > ### treatmentInfo<-,PharmacoSet,data.frame-method treatmentInfo<- > ### drugNames treatmentNames,PharmacoSet-method treatmentNames > ### drugNames<- treatmentNames<-,PharmacoSet,character-method > ### treatmentNames<- annotation,PharmacoSet-method annotation > ### annotation<-,PharmacoSet,list-method annotation<- > ### dateCreated,PharmacoSet-method dateCreated > ### dateCreated<-,PharmacoSet,character-method > ### dateCreated<-,PharmacoSet-method dateCreated<- > ### name,PharmacoSet-method name name<-,PharmacoSet-method > ### name<-,PharmacoSet,character-method name<- > ### sampleInfo,PharmacoSet-method sampleInfo cellInfo,PharmacoSet-method > ### cellInfo sampleInfo<-,PharmacoSet,data.frame-method sampleInfo<- > ### cellInfo<-,PharmacoSet,data.frame-method cellInfo<- > ### sampleNames,PharmacoSet-method sampleName,PharmacoSet-method > ### sampleNames cellName,PharmacoSet-method cellNames > ### sampleNames<-,PharmacoSet,character-method > ### sampleNames<-,PharmacoSet,list-method sampleNames<- > ### cellNames<-,PharmacoSet,list-method cellNames<- > ### curation,PharmacoSet-method curation > ### curation<-,PharmacoSet,list-method curation<- > ### datasetType,PharmacoSet-method datasetType > ### datasetType<-,PharmacoSet,character-method datasetType<- > ### molecularProfiles,PharmacoSet-method molecularProfiles > ### molecularProfiles<-,PharmacoSet,character,character,matrix-method > ### molecularProfiles<-,PharmacoSet,character,missing,matrix-method > ### molecularProfiles<-,PharmacoSet,missing,missing,list-method > ### molecularProfiles<-,PharmacoSet,missing,missing,MutliAssayExperiment-method > ### molecularProfiles<- featureInfo,PharmacoSet-method featureInfo > ### featureInfo<-,PharmacoSet,character,data.frame-method > ### featureInfo<-,PharmacoSet,character,DataFrame-method featureInfo<- > ### phenoInfo,PharmacoSet,character-method phenoInfo > ### phenoInfo<-,PharmacoSet,character,data.frame-method > ### phenoInfo<-,PharmacoSet,character,DataFrame-method phenoInfo<- > ### fNames,PharmacoSet,character-method fNames > ### fNames<-,PharmacoSet,character,character-method fNames<- > ### mDataNames,PharmacoSet-method mDataNames > ### mDataNames<-,PharmacoSet-method mDataNames<-,PharmacoSet,ANY-method > ### mDataNames<- molecularProfilesSlot,PharmacoSet-method > ### moleculerProfilesSlot,PharmacoSet-method molecularProfilesSlot > ### molecularProfilesSlot<-,PharmacoSet,list_OR_MAE-method > ### molecularProfilesSlot<-,PharmacoSet,list-method > ### molecularProfilesSlot<-PharmacoSet,MultiAssayExperiment-method > ### molecularProfilesSlot<- sensitivityInfo,PharmacoSet-method > ### sensitivityInfo,PharmacoSet,missing-method > ### sensitivityInfo,PharmacoSet,character-method > ### sensitivityInfo<-,PharmacoSet,data.frame-method > ### sensitivityInfo<-,PharmacoSet,missing,data.frame-method > ### sensitvityInfo<-,PharmacoSet,character,data.frame-method > ### sensitivityMeasures,PharmacoSet-method > ### sensitivityMeasures<-,PharmacoSet,character-method > ### sensitivityProfiles,PharmacoSet-method > ### sensitivityProfiles<-,PharmacoSet,data.frame-method > ### sensitivityRaw,PharmacoSet-method > ### sensitivityRaw<-,PharmacoSet,array-method > ### treatmentResponse,PharmacoSet-method treatmentResponse > ### sensitivitySlot > ### treatmentResponse<-,PharmacoSet,list_OR_LongTable-method > ### treatmentResponse<- treamentResponse<-,PharmacoSet,list-method > ### treatmentResponse<-,PharmacoSet,LongTable-method sensitivitySlot<- > ### sensNumber,PharmacoSet-method sensNumber > ### sensNumber<-,PharmacoSet,matrix-method sensNumber<- > ### pertNumber,PharmacoSet-method pertNumber > ### pertNumber<-,PharmacoSet,array-method pertNumber<- > > ### ** Examples > > data(CCLEsmall) > treatmentInfo(CCLEsmall) Compound..code.or.generic.name. Compound..brand.name. PD-0325901 PD-0325901 17-AAG 17-AAG Tanespimycin AEW541 AEW541 Nilotinib Nilotinib Tasigna PHA-665752 PHA-665752 lapatinib Lapatinib Tykerb Nutlin-3 Nutlin-3 AZD0530 AZD0530 Saracatinib Crizotinib PF-2341066 Crizotinib L-685458 L-685458 Vandetanib Vandetanib Zactima Panobinostat Panobinostat Faridak Sorafenib Sorafenib Nexavar Irinotecan Irinotecan Camptosar\xa0 Topotecan Topotecan Hycamtin LBW242 LBW242 PD-0332991 PD-0332991 paclitaxel Paclitaxel Taxol AZD6244 AZD6244 Selumetinib PLX4720 PLX4720 RAF265 RAF265 TAE684 TAE684 TKI258 TKI258 Dovitinib Erlotinib Erlotinib Tarceva Target.s. PD-0325901 MEK 17-AAG HSP90 AEW541 IGF-1R Nilotinib Abl/Bcr-Abl PHA-665752 c-MET lapatinib EGFR, HER2 Nutlin-3 MDM2 AZD0530 Src, Abl/Bcr-Abl, EGFR Crizotinib c-MET, ALK L-685458 Gamma Secretase Vandetanib Abl, EGFR, Flt3, C-KIT, RET, VEGFR-1, KDR, FLT4 Panobinostat HDAC Sorafenib Flt3, C-KIT, PDGFRbeta, RET, Raf kinase B, Raf kinase C, VEGFR-1, KDR, FLT4 Irinotecan Topoisomerase I Topotecan Topoisomerase I LBW242 IAP PD-0332991 CDK4/6 paclitaxel beta-tubulin AZD6244 MEK PLX4720 RAF RAF265 Raf kinase B, KDR TAE684 ALK TKI258 EGFR, FGFR1, PDGFRbeta, VEGFR-1, KDR Erlotinib EGFR Mechanism.of.action PD-0325901 MEK1 and MEK2 Inhibitor 17-AAG Heat Shock Protein 90 (hsp90) Inhibitor AEW541 IGF-1R Inhibitor Nilotinib Abl Inhibitor PHA-665752 c-MET Inhibitor lapatinib EGFR and HER2 Inhibitor Nutlin-3 MDM2 Inhibitor AZD0530 Src and Abl inhibitor Crizotinib c-MET and ALK Inhibitor L-685458 gamma-Secretase Inhibitor Vandetanib Multi-kinase inhibitor Panobinostat Histone Deacetylase (HDAC) Inhibitor Sorafenib Multi-kinase inhibitor Irinotecan DNA Topoisomerase I Inhibitor Topotecan DNA Topoisomerase I Inhibitor LBW242 Inhibitor of Apoptosis Proteins (IAP) Inhibitor PD-0332991 CDK4/6 Inhibitor paclitaxel Microtubule-Stabilizing Agents AZD6244 MEK1 and MEK2 Inhibitor PLX4720 Raf kinase B Inhibitor RAF265 Raf kinase B and KDR Inhibitor TAE684 ALK Inhibitor TKI258 Multi-kinase inhibitor Erlotinib EGFR Inhibitor Class Highest.Phase Organization PD-0325901 Kinase inhibitor Discontinued Pfizer 17-AAG Other targeted therapies Phase III Bristol-Myers Squibb AEW541 Kinase inhibitor Preclinical Novartis Nilotinib Kinase inhibitor Launched-2007 Novartis PHA-665752 Kinase inhibitor Preclinical Pfizer lapatinib Kinase inhibitor Launched-2007 GlaxoSmithKline Nutlin-3 Other targeted therapies Preclinical Roche AZD0530 Kinase inhibitor Phase II AstraZeneca Crizotinib Kinase inhibitor Launched-2011 Pfizer L-685458 Other targeted therapies Preclinical Merck Sharp & Dohme Vandetanib Kinase inhibitor Launched-2011 AstraZeneca Panobinostat Other targeted therapies Pre-Registered Novartis Sorafenib Kinase inhibitor Launched-2005 Bayer Irinotecan Cytotoxic Launched-1994 Pfizer Topotecan Cytotoxic Launched-1996 GlaxoSmithKline LBW242 Other targeted therapies Preclinical Novartis PD-0332991 Kinase inhibitor Phase II Pfizer paclitaxel Cytotoxic Launched-1993 Bristol-Myers Squibb AZD6244 Kinase inhibitor Phase II AstraZeneca PLX4720 Kinase inhibitor Preclinical Plexxikon RAF265 Kinase inhibitor Phase I Novartis TAE684 Kinase inhibitor Preclinical Novartis TKI258 Kinase inhibitor Phase III Novartis Erlotinib Kinase inhibitor Launched-2004 Genentech treatmentid drug.name PD-0325901 PD-0325901 PD-0325901 17-AAG 17-AAG 17-AAG AEW541 AEW541 AEW541 Nilotinib Nilotinib Nilotinib PHA-665752 PHA-665752 PHA-665752 lapatinib lapatinib Lapatinib Nutlin-3 Nutlin-3 Nutlin-3 AZD0530 AZD0530 AZD0530 Crizotinib Crizotinib PF-2341066 L-685458 L-685458 L-685458 Vandetanib Vandetanib Vandetanib Panobinostat Panobinostat Panobinostat Sorafenib Sorafenib Sorafenib Irinotecan Irinotecan Irinotecan Topotecan Topotecan Topotecan LBW242 LBW242 LBW242 PD-0332991 PD-0332991 PD-0332991 paclitaxel paclitaxel Paclitaxel AZD6244 AZD6244 AZD6244 PLX4720 PLX4720 PLX4720 RAF265 RAF265 RAF265 TAE684 TAE684 TAE684 TKI258 TKI258 TKI258 Erlotinib Erlotinib Erlotinib > > treatmentInfo(CCLEsmall) <- treatmentInfo(CCLEsmall) > > treatmentNames(CCLEsmall) [1] "PD-0325901" "17-AAG" "AEW541" "Nilotinib" "PHA-665752" [6] "lapatinib" "Nutlin-3" "AZD0530" "Crizotinib" "L-685458" [11] "Vandetanib" "Panobinostat" "Sorafenib" "Irinotecan" "Topotecan" [16] "LBW242" "PD-0332991" "paclitaxel" "AZD6244" "PLX4720" [21] "RAF265" "TAE684" "TKI258" "Erlotinib" > > treatmentNames(CCLEsmall) <- treatmentNames(CCLEsmall) > > > ## @annotation > > annotation(CCLEsmall) $name [1] "CCLE" $dateCreated [1] "Fri Nov 6 14:00:53 2015" $sessionInfo R version 3.1.1 (2014-07-10) Platform: x86_64-apple-darwin13.1.0 (64-bit) Matrix products: Error in if (nzchar(LAver <- x$LA_version)) { : argument is of length zero Calls: -> print.sessionInfo Execution halted * 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 ERROR, 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck/00check.log’ for details.