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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RadioGx.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings RadioGx_2.3.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/RadioGx.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RadioGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RadioGx' version '2.3.0'
* 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 whether package 'RadioGx' can be installed ... OK
* 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 R 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 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
RadioSet: no visible binding for global variable 'treatment'
RadioSet: no visible binding for global variable 'curationTreatment'
RadioSet: no visible binding for global variable 'curationSample'
Undefined global functions or variables:
curationSample curationTreatment treatment
* 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 ... WARNING
Undocumented arguments in documentation object 'RadioSet'
'name' 'molecularProfiles' 'cell' 'radiation' 'sensitivityInfo'
'sensitivityRaw' 'sensitivityProfiles' 'sensitivityN' 'perturbationN'
'curationCell' 'curationTissue' 'datasetType' 'verify'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 14 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'RadioGx-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RadioSet-accessors
> ### Title: Accessing and modifying information in a 'RadioSet'
> ### Aliases: RadioSet-accessors radiationInfo treatmentInfo,RadioSet-method
> ### treatmentInfo radiationInfo<-
> ### treatmentInfo<-,RadioSet,data.frame-method treatmentInfo<-
> ### radiationTypes treatmentNames,RadioSet-method treatmentNames
> ### radiationTypes<- treatmentNames<-,RadioSet,character-method
> ### treatmentNames<- annotation,RadioSet-method annotation
> ### annotation<-,RadioSet,list-method annotation<-
> ### dateCreated,RadioSet-method dateCreated
> ### dateCreated<-,RadioSet,character-method dateCreated<-,RadioSet-method
> ### dateCreated<- name,RadioSet-method name name<-,RadioSet-method
> ### name<-,RadioSet,character-method name<- sampleInfo,RadioSet-method
> ### sampleInfo cellInfo,RadioSet-method cellInfo
> ### sampleInfo<-,RadioSet,data.frame-method sampleInfo<-
> ### cellInfo<-,RadioSet,data.frame-method cellInfo<-
> ### sampleNames,RadioSet-method sampleName,RadioSet-method sampleNames
> ### cellName,RadioSet-method cellNames
> ### sampleNames<-,RadioSet,character-method
> ### sampleNames<-,RadioSet,list-method sampleNames<-
> ### cellNames<-,RadioSet,list-method cellNames<- curation,RadioSet-method
> ### curation curation<-,RadioSet,list-method curation<-
> ### datasetType,RadioSet-method datasetType
> ### datasetType<-,RadioSet,character-method datasetType<-
> ### molecularProfiles,RadioSet-method molecularProfiles
> ### molecularProfiles<-,RadioSet,character,character,matrix-method
> ### molecularProfiles<-,RadioSet,character,missing,matrix-method
> ### molecularProfiles<-,RadioSet,missing,missing,list-method
> ### molecularProfiles<-,RadioSet,missing,missing,MutliAssayExperiment-method
> ### molecularProfiles<- featureInfo,RadioSet-method featureInfo
> ### featureInfo<-,RadioSet,character,data.frame-method
> ### featureInfo<-,RadioSet,character,DataFrame-method featureInfo<-
> ### phenoInfo,RadioSet,character-method phenoInfo
> ### phenoInfo<-,RadioSet,character,data.frame-method
> ### phenoInfo<-,RadioSet,character,DataFrame-method phenoInfo<-
> ### fNames,RadioSet,character-method fNames
> ### fNames<-,RadioSet,character,character-method fNames<-
> ### mDataNames,RadioSet-method mDataNames mDataNames<-,RadioSet-method
> ### mDataNames<-,RadioSet,ANY-method mDataNames<-
> ### molecularProfilesSlot,RadioSet-method
> ### moleculerProfilesSlot,RadioSet-method molecularProfilesSlot
> ### molecularProfilesSlot<-,RadioSet,list_OR_MAE-method
> ### molecularProfilesSlot<-,RadioSet,list-method
> ### molecularProfilesSlot<-RadioSet,MultiAssayExperiment-method
> ### molecularProfilesSlot<- sensitivityInfo,RadioSet-method
> ### sensitivityInfo,RadioSet,missing-method
> ### sensitivityInfo,RadioSet,character-method
> ### sensitivityInfo<-,RadioSet,data.frame-method
> ### sensitivityInfo<-,RadioSet,missing,data.frame-method
> ### sensitvityInfo<-,RadioSet,character,data.frame-method
> ### sensitivityMeasures,RadioSet-method
> ### sensitivityMeasures<-,RadioSet,character-method
> ### sensitivityProfiles,RadioSet-method
> ### sensitivityProfiles<-,RadioSet,data.frame-method
> ### sensitivityRaw,RadioSet-method sensitivityRaw<-,RadioSet,array-method
> ### treatmentResponse,RadioSet-method treatmentResponse sensitivitySlot
> ### treatmentResponse<-,RadioSet,list_OR_LongTable-method
> ### treatmentResponse<- treamentResponse<-,RadioSet,list-method
> ### treatmentResponse<-,RadioSet,LongTable-method sensitivitySlot<-
> ### sensNumber,RadioSet-method sensNumber
> ### sensNumber<-,RadioSet,matrix-method sensNumber<-
> ### pertNumber,RadioSet-method pertNumber
> ### pertNumber<-,RadioSet,array-method pertNumber<-
>
> ### ** Examples
>
> data(clevelandSmall)
> treatmentInfo(clevelandSmall)
treatmentid
radiation radiation
>
> treatmentInfo(clevelandSmall) <- treatmentInfo(clevelandSmall)
>
> treatmentNames(clevelandSmall)
[1] "radiation"
>
> treatmentNames(clevelandSmall) <- treatmentNames(clevelandSmall)
>
>
> ## @annotation
>
> annotation(clevelandSmall)
$name
[1] "Cleveland"
$dateCreated
[1] "Wed Oct 25 17:38:42 2017"
$sessionInfo
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylibError in grepl(LAver, lapack, fixed = TRUE) : invalid 'pattern' argument
Calls: <Anonymous> -> print.sessionInfo -> grepl
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 1 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/RadioGx.Rcheck/00check.log'
for details.