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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Sconify_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Sconify.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 ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.19.0’
* 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 ‘Sconify’ 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 ... OK
* 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
SconeValues   17.844  0.100  17.944
ImputeTesting  5.446  0.032   5.478
* 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 ...
  ‘DataQuality.Rmd’ using ‘UTF-8’... OK
  ‘FindingIdealK.Rmd’ using ‘UTF-8’... OK
  ‘Step1.PreProcessing.Rmd’ using ‘UTF-8’... OK
  ‘Step2.TheSconeWorkflow.Rmd’ using ‘UTF-8’... OK
  ‘Step3.PostProcessing.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Sconify
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Sconify’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '/' 
Note: wrong number of arguments to 'asinh' 
** 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 (Sconify)

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(Sconify)
> 
> test_check("Sconify")
Read the 100 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.967600)!
Learning embedding...
Iteration 50: error is 50.887375 (50 iterations in 0.02 seconds)
Iteration 100: error is 49.601587 (50 iterations in 0.02 seconds)
Iteration 150: error is 51.872885 (50 iterations in 0.02 seconds)
Iteration 200: error is 51.967749 (50 iterations in 0.02 seconds)
Iteration 250: error is 51.511668 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.363598 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.545730 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.223780 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.186069 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.175093 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.154929 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.148359 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.144842 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.143067 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.143082 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.143338 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.143245 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.143553 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.144148 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.142821 (50 iterations in 0.01 seconds)
Fitting performed in 0.27 seconds.
Read the 1000 x 27 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.18 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.054556 (50 iterations in 0.39 seconds)
Iteration 100: error is 60.713313 (50 iterations in 0.32 seconds)
Iteration 150: error is 60.308058 (50 iterations in 0.34 seconds)
Iteration 200: error is 60.162988 (50 iterations in 0.33 seconds)
Iteration 250: error is 60.103356 (50 iterations in 0.33 seconds)
Iteration 300: error is 1.331316 (50 iterations in 0.28 seconds)
Iteration 350: error is 1.227081 (50 iterations in 0.28 seconds)
Iteration 400: error is 1.194988 (50 iterations in 0.28 seconds)
Iteration 450: error is 1.181190 (50 iterations in 0.29 seconds)
Iteration 500: error is 1.173521 (50 iterations in 0.32 seconds)
Iteration 550: error is 1.169128 (50 iterations in 0.28 seconds)
Iteration 600: error is 1.165850 (50 iterations in 0.28 seconds)
Iteration 650: error is 1.164087 (50 iterations in 0.28 seconds)
Iteration 700: error is 1.162184 (50 iterations in 0.29 seconds)
Iteration 750: error is 1.159798 (50 iterations in 0.29 seconds)
Iteration 800: error is 1.157176 (50 iterations in 0.29 seconds)
Iteration 850: error is 1.155265 (50 iterations in 0.28 seconds)
Iteration 900: error is 1.153620 (50 iterations in 0.28 seconds)
Iteration 950: error is 1.152435 (50 iterations in 0.29 seconds)
Iteration 1000: error is 1.150842 (50 iterations in 0.29 seconds)
Fitting performed in 6.01 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 32.543   0.473  33.000