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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpatialDecon_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/SpatialDecon.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 ‘SpatialDecon/DESCRIPTION’ ... OK
* this is package ‘SpatialDecon’ 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 ‘SpatialDecon’ 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
download_profile_matrix: no visible binding for global variable
  ‘profile_matrix’
Undefined global functions or variables:
  profile_matrix
* 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 ... OK
* 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
runCollapseCellTypes-NanoStringGeoMxSet-method 192.345  2.150 194.735
runCollapseCellTypes                           191.338  2.006 193.933
runReverseDecon                                187.847  1.994 190.735
runReverseDecon-NanoStringGeoMxSet-method      186.449  1.997 188.739
runspatialdecon                                 95.851  5.169 101.848
runspatialdecon-Seurat-method                   56.628  3.809  61.411
runspatialdecon-NanoStringGeoMxSet-method       44.689  0.497  45.339
runErrorModel                                   33.432  0.125  33.600
runMergeTumorIntoX                              32.848  0.108  32.994
runMergeTumorIntoX-NanoStringGeoMxSet-method    32.478  0.097  32.624
reverseDecon                                    16.820  0.254  17.094
SpatialDecon-package                             9.496  0.521  10.032
spatialdecon                                     8.171  0.621   8.804
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/SpatialDecon.Rcheck/00check.log’
for details.