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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoreGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoreGx_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CoreGx.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘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 for sufficient/correct file permissions ... 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 ... 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 ... OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/CoreGx.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoreGx
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CoreGx’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘CoreGx’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘CoreGx’
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoreGx)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> library(testthat)
> library(CoreGx)
Loading required package: BiocGenerics

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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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 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

> 
> test_check("CoreGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 14.384   0.664  15.054