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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:iSEEu.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings iSEEu_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/iSEEu.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iSEEu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iSEEu’ version ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘iSEEu’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: '.setOrganism' is deprecated.
  Warning: '.setIdentifierType' is deprecated.
  Warning: 'GeneSetTable' is deprecated.
  Warning: 'setPValuePattern' is deprecated.
  Warning: 'setPValuePattern' is deprecated.
  Warning: '.setIdentifierType' is deprecated.
  Warning: '.getIdentifierType' is deprecated.
  Warning: '.setOrganism' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
  Warning: '.getIdentifierType' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.getOrganism' is deprecated.
  Warning: '.setGeneSetCommands' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
  Warning: '.getGeneSetCommands' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
AggregatedDotPlot                 25.022  1.449  27.983
modeReducedDim                    21.162  0.243  22.389
FeatureSetTable-class             17.674  0.376  19.570
DynamicMarkerTable-class          16.687  0.299  18.103
GeneSetTable-class                16.511  0.313  18.483
ReducedDimensionHexPlot-class     15.914  0.235  17.161
DynamicReducedDimensionPlot-class 15.520  0.288  16.788
registerFeatureSetCollections     15.200  0.263  17.017
modeGating                        12.564  0.212  13.848
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/iSEEu.Rcheck/00check.log’
for details.