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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SCATE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SCATE_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SCATE/DESCRIPTION’ ... OK
* this is package ‘SCATE’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'parallel', 'preprocessCore', 'splines', 'splines2', 'xgboost',
  'SCATEData', 'Rtsne', 'mclust'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘SCATE’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'SCATEData' is deprecated and will be removed from Bioconductor
  Warning: Package 'SCATE' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck/00install.out’ for details.
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘SCATEData’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SCATE : SCATEsingle: no visible global function definition for
  ‘IRanges’
cellcluster : <anonymous>: no visible global function definition for
  ‘IRanges’
extractfeature: no visible global function definition for ‘IRanges’
makedatabase: no visible global function definition for ‘IRanges’
makedatabase: no visible global function definition for ‘seqlevels’
peakcall: no visible global function definition for ‘IRanges’
Undefined global functions or variables:
  IRanges seqlevels
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
SCATE         162.507  7.276 192.664
SCATEpipeline 159.329  6.209 198.485
peakcall      141.495  4.757 159.280
cellcluster    26.037  1.889  31.759
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/SCATE.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SCATE
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘SCATE’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'SCATEData' is deprecated and will be removed from Bioconductor
  version 3.19 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'SCATEData' is deprecated and will be removed from Bioconductor
  version 3.19
Warning: Package 'SCATE' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'SCATEData' is deprecated and will be removed from Bioconductor
  version 3.19
Warning: Package 'SCATE' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (SCATE)