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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:STdeconvolve.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings STdeconvolve_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/STdeconvolve.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 ‘STdeconvolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STdeconvolve’ version ‘1.7.0’
* 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 ‘STdeconvolve’ 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
correlationPlot: no visible binding for global variable ‘Var1’
correlationPlot: no visible binding for global variable ‘Var2’
correlationPlot: no visible binding for global variable ‘value’
fitLDA: no visible binding for global variable ‘rareCtsAdj’
fitLDA: no visible binding for global variable ‘K’
fitLDA: no visible binding for global variable ‘perplexAdj’
fitLDA: no visible binding for global variable ‘alphaBool’
perplexityPlot: no visible binding for global variable ‘rareCtsAdj’
perplexityPlot: no visible binding for global variable ‘K’
perplexityPlot: no visible binding for global variable ‘perplexAdj’
perplexityPlot: no visible binding for global variable ‘alphaBool’
vizAllTopics: no visible binding for global variable ‘x’
vizAllTopics: no visible binding for global variable ‘y’
vizAllTopics: no visible binding for global variable ‘Row.names’
vizAllTopics: no visible binding for global variable ‘Pixel.Groups’
vizGeneCounts: no visible binding for global variable ‘x’
vizGeneCounts: no visible binding for global variable ‘y’
vizTopic: no visible binding for global variable ‘x’
vizTopic: no visible binding for global variable ‘y’
Undefined global functions or variables:
  K Pixel.Groups Row.names Var1 Var2 alphaBool perplexAdj rareCtsAdj
  value x y
* 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 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
perplexityPlot  32.052  0.531  38.599
correlationPlot 12.081  0.510  15.611
vizAllTopics    11.428  0.240  13.583
vizTopic         9.506  0.190  11.412
lsatPairs        9.018  0.239  10.988
getCorrMtx       8.663  0.189  10.310
fitLDA           5.434  0.255  24.755
topGenes         5.384  0.227  25.960
getBetaTheta     5.310  0.265  26.455
optimalModel     5.069  0.213  36.612
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc/meat/STdeconvolve.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL STdeconvolve
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘STdeconvolve’ ...
** using staged installation
** R
** data
** 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 (STdeconvolve)

R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(STdeconvolve)
> 
> test_check("STdeconvolve")
A 260x232 simple triplet matrix.
A 260x10 simple triplet matrix.
now fitting LDA model with K = 2 
now fitting LDA model with K = 3 
now fitting LDA model with K = 4 
now fitting LDA model with K = 5 
computing perplexity for LDA model with K = 2 
computing perplexity for LDA model with K = 3 
computing perplexity for LDA model with K = 4 
computing perplexity for LDA model with K = 5 
initial: [1e+02 - 3] [1e+03 - 3] [1e+04 - 2] done
initial: [1e+02 - 3] [1e+03 - 2] [1e+04 - 2] done
initial: [1e+02 - 4] [1e+03 - 4] [1e+04 - 3] done
initial: [1e+02 - 4] [1e+03 - 4] [1e+04 - 4] done
initial: [1e+02 - 4] [1e+03 - 4] [1e+04 - 4] done
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 49.646   1.617  59.816