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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings Sconify_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/Sconify.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.18.0’
* 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 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 ... 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 13.094    0.2  13.294
* 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-3.16-bioc/R/bin/R CMD INSTALL Sconify
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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 version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 = 0.967400)!
Learning embedding...
Iteration 50: error is 51.853260 (50 iterations in 0.01 seconds)
Iteration 100: error is 52.105486 (50 iterations in 0.01 seconds)
Iteration 150: error is 52.659803 (50 iterations in 0.01 seconds)
Iteration 200: error is 52.354884 (50 iterations in 0.01 seconds)
Iteration 250: error is 53.276192 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.368106 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.696348 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.297884 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.157699 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.154835 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.151375 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.154718 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.155483 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.155130 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.154208 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.154208 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.152205 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.154358 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.155360 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.156241 (50 iterations in 0.01 seconds)
Fitting performed in 0.17 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 0.11 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 65.946446 (50 iterations in 0.23 seconds)
Iteration 100: error is 60.647812 (50 iterations in 0.16 seconds)
Iteration 150: error is 60.309844 (50 iterations in 0.15 seconds)
Iteration 200: error is 60.212697 (50 iterations in 0.15 seconds)
Iteration 250: error is 60.140360 (50 iterations in 0.15 seconds)
Iteration 300: error is 1.329192 (50 iterations in 0.14 seconds)
Iteration 350: error is 1.220690 (50 iterations in 0.14 seconds)
Iteration 400: error is 1.188825 (50 iterations in 0.14 seconds)
Iteration 450: error is 1.177104 (50 iterations in 0.14 seconds)
Iteration 500: error is 1.169518 (50 iterations in 0.14 seconds)
Iteration 550: error is 1.165434 (50 iterations in 0.14 seconds)
Iteration 600: error is 1.162922 (50 iterations in 0.14 seconds)
Iteration 650: error is 1.160623 (50 iterations in 0.14 seconds)
Iteration 700: error is 1.158831 (50 iterations in 0.14 seconds)
Iteration 750: error is 1.156489 (50 iterations in 0.13 seconds)
Iteration 800: error is 1.154142 (50 iterations in 0.14 seconds)
Iteration 850: error is 1.152967 (50 iterations in 0.14 seconds)
Iteration 900: error is 1.151544 (50 iterations in 0.14 seconds)
Iteration 950: error is 1.149554 (50 iterations in 0.14 seconds)
Iteration 1000: error is 1.148102 (50 iterations in 0.14 seconds)
Fitting performed in 2.91 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 18.570   0.431  19.004