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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:STdeconvolve.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings STdeconvolve_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/STdeconvolve.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘STdeconvolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STdeconvolve’ version ‘1.3.0’
* 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 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 loading without being on the library search path ... WARNING
Error in library(STdeconvolve, lib.loc = "/home/biocbuild/bbs-3.17-bioc/R/library") : 
  there is no package called ‘STdeconvolve’
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* 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 ... SKIPPED
* 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 ...
  ‘vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/STdeconvolve.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL STdeconvolve
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* installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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 
 46.234   0.884  52.132