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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoreGx.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CoreGx_1.6.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CoreGx.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoreGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoreGx' version '1.6.0'
* 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 'CoreGx' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.paste_slashes: no visible binding for global variable '..'
.rebuildInfo: no visible global function definition for 'patterns'
.rebuildInfo: no visible binding for global variable '..keepCols'
.rebuildInfo: no visible binding for global variable 'drugid'
.rebuildInfo: no visible binding for global variable 'drug1id'
.rebuildInfo: no visible binding for global variable 'drug_uid'
.rebuildInfo: no visible binding for global variable '..rowIDcols'
.rebuildInfo: no visible binding for global variable 'cell_uid'
.rebuildInfo: no visible binding for global variable '..colIDcols'
.rebuildInfo: no visible binding for global variable 'exp_id'
.rebuildProfiles: no visible binding for global variable 'cell_uid'
.rebuildProfiles: no visible binding for global variable 'drug_uid'
.rebuildProfiles: no visible binding for global variable 'exp_id'
.rebuildRaw: no visible binding for global variable '.NATURAL'
.rebuildRaw: no visible binding for global variable 'cellid'
.rebuildRaw: no visible binding for global variable 'exp_id'
.rebuildRaw: no visible binding for global variable 'drug1id'
.rebuildRaw: no visible binding for global variable 'row_ids'
.rebuildRaw: no visible binding for global variable 'col_ids'
.rebuildRaw: no visible binding for global variable 'dose'
.rebuildRaw: no visible global function definition for 'patterns'
.rebuildSensNumber: no visible global function definition for
  'patterns'
.rebuildSensNumber: no visible binding for global variable '.drugCombo'
.rebuildSensNumber: no visible binding for global variable '.cellCombo'
.sensitivityToLongTable: no visible binding for global variable 'dose'
.sensitivityToLongTable: no visible binding for global variable
  'viability'
.sensitivityToLongTable: no visible binding for global variable
  'replicate_id'
.summarizePerturbationNumbers: no visible global function definition
  for 'drugInfo'
.summarizeSensitivityNumbers: no visible global function definition for
  'drugInfo'
assay<-,LongTable-character: no visible binding for global variable
  '..missingRowCols'
assay<-,LongTable-character: no visible binding for global variable
  '..missingColCols'
coerce,SummarizedExperiment-data.table: no visible binding for global
  variable '.sample'
coerce,SummarizedExperiment-data.table: no visible binding for global
  variable '.feature'
colData<-,LongTable-ANY: no visible binding for global variable
  '.NATURAL'
colData<-,LongTable-ANY: no visible binding for global variable
  '.colnames'
metaConstruct,LongTableDataMapper: no visible binding for global
  variable '..rowIDs'
metaConstruct,LongTableDataMapper: no visible binding for global
  variable '..colIDs'
rowData<-,LongTable: no visible binding for global variable '.NATURAL'
rowData<-,LongTable: no visible binding for global variable '.rownames'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  'V2'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  'V1'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  'cell_uid'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  'rn'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  'row_id'
sensitivityRaw<-,CoreSet-array: no visible binding for global variable
  'col_id'
sensitivitySlot<-,CoreSet-list_or_LongTable: no visible binding for
  global variable 'funContext'
updateObject,CoreSet: no visible global function definition for
  'isValid'
Undefined global functions or variables:
  .. ..colIDcols ..colIDs ..keepCols ..missingColCols ..missingRowCols
  ..rowIDcols ..rowIDs .NATURAL .cellCombo .colnames .drugCombo
  .feature .rownames .sample V1 V2 cell_uid cellid col_id col_ids dose
  drug1id drugInfo drug_uid drugid exp_id funContext isValid patterns
  replicate_id rn row_id row_ids viability
* 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 8 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
amcc              1.70   0.02   23.01
cosinePerm        0.69   0.02   10.67
gwc               0.65   0.00   12.19
connectivityScore 0.60   0.00   10.67
mcc               0.57   0.00   12.80
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
amcc              2.50   0.04   26.11
cosinePerm        0.80   0.00   13.10
gwc               0.79   0.01   13.41
mcc               0.76   0.00   13.45
connectivityScore 0.67   0.02   12.06
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CoreGx.Rcheck/00check.log'
for details.