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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:pipeComp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings pipeComp_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/pipeComp.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pipeComp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pipeComp’ 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 ‘pipeComp’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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:
  ‘.compileExcludedCells’ ‘.getMM’ ‘.homogenizeDEA’ ‘.runf’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
scrna_describeDatasets: no visible binding for global variable
  ‘cluster’
scrna_describeDatasets: no visible binding for global variable ‘nb’
scrna_describeDatasets : pf: no visible binding for global variable
  ‘.x’
scrna_describeDatasets : rd: no visible binding for global variable ‘y’
scrna_describeDatasets : rd: no visible binding for global variable
  ‘cluster’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘max.lost’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘mean_F1’
scrna_evalPlot_filtering: no visible binding for global variable ‘filt’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘doubletmethod’
scrna_evalPlot_filtering: no visible binding for global variable
  ‘method’
scrna_evalPlot_overall: no visible binding for global variable
  ‘true.nbClusts’
scrna_evalPlot_overall: no visible binding for global variable ‘n_clus’
Undefined global functions or variables:
  .x cluster doubletmethod filt max.lost mean_F1 method n_clus nb
  true.nbClusts y
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'names<-' and siglist 'PipelineDefinition,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Output for data("exampleDEAresults", package = "pipeComp"):
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleDEAresults’
Output for data("exampleResults", package = "pipeComp"):
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
  Warning: namespace ‘rgdal’ is not available and has been replaced
  by .GlobalEnv when processing object ‘exampleResults’
* checking data for non-ASCII characters ... 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
scrna_evalPlot_overall 5.369   0.02   5.397
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/pipeComp.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL pipeComp
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘pipeComp’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pipeComp)