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### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoreGx.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CoreGx_2.0.2.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CoreGx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoreGx' version '2.0.2'
* 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
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.LongTable' '.sensitivityToTRE'
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  subset.immutable
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.checkForIdColumn: no visible binding for global variable 'col_col'
.rebuildInfo: no visible global function definition for 'patterns'
.rebuildInfo: no visible binding for global variable '..keepCols'
.rebuildInfo: no visible binding for global variable 'replicate_id'
.rebuildInfo: no visible binding for global variable 'treatment1id'
.rebuildInfo: no visible binding for global variable 'sampleid'
.rebuildInfo: no visible binding for global variable 'treatmentid'
.rebuildInfo: no visible binding for global variable 'treatment_uid'
.rebuildInfo: no visible binding for global variable '..rowIDcols'
.rebuildInfo: no visible binding for global variable 'sample_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 'sample_uid'
.rebuildProfiles: no visible binding for global variable
  'treatment_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 'sampleid'
.rebuildRaw: no visible binding for global variable 'exp_id'
.rebuildRaw: no visible binding for global variable 'treatment1id'
.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
  '.treatmentCombo'
.rebuildSensNumber: no visible binding for global variable
  '.sampleCombo'
.sensitivityToTRE: no visible binding for global variable 'dose'
.sensitivityToTRE: no visible binding for global variable 'viability'
.sensitivityToTRE: no visible binding for global variable
  'replicate_id'
.sensitivityToTRE: no visible binding for global variable 'rn'
.sensitivityToTRE: no visible binding for global variable 'treatmentid'
.sensitivityToTRE: no visible binding for global variable 'sampleid'
CoreSet: no visible binding for global variable 'cell'
CoreSet: no visible binding for global variable 'drug'
CoreSet: no visible global function definition for '.checkForIdColumns'
cardinality: no visible binding for global variable 'N'
checkColumnCardinality: no visible binding for global variable 'N'
optimizeCoreGx: no visible binding for global variable 'nthread'
optimizeCoreGx: no visible binding for global variable 'total_time'
optimizeCoreGx: no visible binding for global variable 'mem_alloc'
optimizeCoreGx: no visible binding for global variable 'itr/sec'
optimizeCoreGx: no visible binding for global variable 'gc/sec'
optimizeCoreGx: no visible binding for global variable 'median_sec'
optimizeCoreGx: no visible binding for global variable 'N'
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'
reindex,LongTable: no visible binding for global variable '.rowKey'
reindex,LongTable: no visible binding for global variable '.colKey'
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
  'sample_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'
updateObject,LongTable: no visible global function definition for
  'isValid'
Undefined global functions or variables:
  ..colIDcols ..keepCols ..rowIDcols .NATURAL .checkForIdColumns
  .colKey .colnames .feature .rowKey .rownames .sample .sampleCombo
  .treatmentCombo N V1 V2 cell col_col col_id col_ids dose drug exp_id
  funContext gc/sec isValid itr/sec median_sec mem_alloc nthread
  patterns replicate_id rn row_id row_ids sample_uid sampleid
  total_time treatment1id treatment_uid treatmentid 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 ... NOTE
S3 methods shown with full name in documentation object 'setOps-immutable':
  'subset.immutable'

The \usage entries for S3 methods should use the \method markup and not
their full name.
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 8 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
optimizeCoreGx    58.16   2.22   64.72
amcc               2.22   0.05   26.88
gwc                0.75   0.03   12.13
mcc                0.74   0.00   13.84
connectivityScore  0.67   0.05   12.48
cosinePerm         0.69   0.03   12.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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: 5 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/CoreGx.Rcheck/00check.log'
for details.