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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:STdeconvolve.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings STdeconvolve_1.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/STdeconvolve.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘STdeconvolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STdeconvolve’ version ‘1.9.0’
* 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 code 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 loading without being on the library search path ... 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  17.069  0.208  17.275
correlationPlot  6.269  0.174   6.443
vizAllTopics     5.901  0.250   6.151
vizTopic         5.232  0.256   5.488
fitLDA           3.218  0.254  11.416
getBetaTheta     3.117  0.234  11.250
topGenes         3.060  0.146  11.246
optimalModel     2.872  0.118  16.547
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/STdeconvolve.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL STdeconvolve
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 28.206   0.645  28.842