##############################################################################
##############################################################################
###
### 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_3.12.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PharmacoGx.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PharmacoGx’ version ‘3.12.0’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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                  <NA>
17-AAG                                17-AAG          Tanespimycin
AEW541                                AEW541                  <NA>
Nilotinib                          Nilotinib               Tasigna
PHA-665752                        PHA-665752                  <NA>
lapatinib                          Lapatinib                Tykerb
Nutlin-3                            Nutlin-3                  <NA>
AZD0530                              AZD0530           Saracatinib
Crizotinib                        PF-2341066            Crizotinib
L-685458                            L-685458                  <NA>
Vandetanib                        Vandetanib               Zactima
Panobinostat                    Panobinostat              Faridak 
Sorafenib                          Sorafenib               Nexavar
Irinotecan                        Irinotecan         Camptosar\xa0
Topotecan                          Topotecan              Hycamtin
LBW242                                LBW242                  <NA>
PD-0332991                        PD-0332991                  <NA>
paclitaxel                        Paclitaxel                 Taxol
AZD6244                              AZD6244           Selumetinib
PLX4720                              PLX4720                  <NA>
RAF265                                RAF265                  <NA>
TAE684                                TAE684                  <NA>
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: <Anonymous> -> 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.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PharmacoGx
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘PharmacoGx’ ...
** this is package ‘PharmacoGx’ version ‘3.12.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c metaPermC.c -o metaPermC.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rCPP_bridge.cpp -o rCPP_bridge.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PharmacoGx.so RcppExports.o metaPermC.o rCPP_bridge.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-PharmacoGx/00new/PharmacoGx/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PharmacoGx)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.unsetenv("R_TESTS")
> 
> library(testthat)
> library(PharmacoGx)
Loading required package: CoreGx
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'PharmacoGx'

The following objects are masked from 'package:CoreGx':

    .parseToRoxygen, amcc, connectivityScore, cosinePerm, gwc, mcc

> 
> test_check("PharmacoGx")
   Dataset Name             Date Created         PSet Name      version
1          GDSC 2021-12-16T19:58:28.388Z GDSC_2020(v2-8.2) 2020(v2-8.2)
2          FIMM 2020-06-24T14:39:26.588Z         FIMM_2016         2016
3         Tavor 2021-03-05T17:05:08.535Z        Tavor_2020         2020
4         NCI60 2021-08-18T16:28:45.207Z        NCI60_2021         2021
5     UHNBreast 2020-06-24T14:39:26.588Z    UHNBreast_2019         2019
6          GDSC 2021-12-16T19:10:35.091Z GDSC_2020(v1-8.2) 2020(v1-8.2)
7         PRISM 2021-08-18T16:28:45.207Z        PRISM_2020         2020
8       BeatAML 2021-03-05T16:55:27.968Z      BeatAML_2018         2018
9          gCSI 2021-06-11T21:58:16.390Z         gCSI_2019         2019
10       CTRPv2 2020-06-24T14:39:26.588Z       CTRPv2_2015         2015
11         GRAY 2021-02-23T14:39:26.588Z         GRAY_2017         2017
12         CCLE 2020-06-24T14:39:26.588Z         CCLE_2015         2015
13         PDTX 2022-01-07T00:00:00.000Z         PDTX_2019         2019
14          GBM 2022-01-07T00:00:00.000Z          GBM_scr2         2021
15          GBM 2022-01-07T00:00:00.000Z          GBM_scr3         2021
16   NCISarcoma                     <NA>   NCISarcoma_2015         2015
17        TCL38 2024-11-20T14:46:07.030Z             TCL38         2015
          type  publication                     DOI
1  sensitivity c("Yang,....  10.5281/zenodo.5787145
2  sensitivity Mpindi, ....  10.5281/zenodo.7823755
3  sensitivity Sigal Ta....  10.5281/zenodo.5979590
4  sensitivity Shoemake....  10.5281/zenodo.7893032
5         both Mammolit....  10.5281/zenodo.7826860
6  sensitivity c("Yang,....  10.5281/zenodo.7829915
7  sensitivity Corsello....  10.5281/zenodo.7826864
8  sensitivity Tyner, J....  10.5281/zenodo.7829853
9         <NA> Petr Smi....  10.5281/zenodo.7829857
10 sensitivity c("Rees,....  10.5281/zenodo.7826870
11 sensitivity Hafner, ....  10.5281/zenodo.7826847
12 sensitivity Barretin....  10.5281/zenodo.3905461
13        <NA> Bruna, A....  10.5281/zenodo.7826875
14        <NA>               10.5281/zenodo.7829873
15        <NA>               10.5281/zenodo.7829873
16        <NA> Bruna, A....                        
17        <NA>           ,  10.5281/zenodo.14733210
                                                                 Download
1           https://zenodo.org/records/5787145/files/GDSC2.rds?download=1
2        https://zenodo.org/record/7823755/files/PSet_FIMM.rds?download=1
3            https://zenodo.org/record/5979590/files/Tavor.rds?download=1
4       https://zenodo.org/record/7893032/files/PSet_NCI60.rds?download=1
5   https://zenodo.org/record/7826860/files/PSet_UHNBreast.rds?download=1
6    https://zenodo.org/record/7829915/files/PSet_GDSC2020.rds?download=1
7       https://zenodo.org/record/7826864/files/PSet_PRISM.rds?download=1
8     https://zenodo.org/record/7829853/files/PSet_BeatAML.rds?download=1
9    https://zenodo.org/record/7829857/files/PSet_gCSI2019.rds?download=1
10     https://zenodo.org/record/7826870/files/PSet_CTRPv2.rds?download=1
11   https://zenodo.org/record/7826847/files/PSet_GRAY2017.rds?download=1
12            https://zenodo.org/record/3905462/files/CCLE.rds?download=1
13 https://zenodo.org/record/7826875/files/PSet_PDTXBreast.rds?download=1
14   https://zenodo.org/record/7829873/files/PSet_GBM_scr2.rds?download=1
15   https://zenodo.org/record/7829873/files/PSet_GBM_scr3.rds?download=1
16                                                                       
17    https://zenodo.org/records/14733210/files/TCL38_PSet.RDS?download=1

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[1]  1  1 -1
[1] 0
[1] 0
             [,1] [,2] [,3]
lower_bounds    0    0    0
upper_bounds    1    1   -1

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[ FAIL 0 | WARN 3 | SKIP 1 | PASS 132 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_PharmacoSet_utils.R:28:1'

[ FAIL 0 | WARN 3 | SKIP 1 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
 21.753   0.336  23.293