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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Sconify_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.29.0’
* 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 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 ... 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 12.159  0.167  12.327
* 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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Sconify
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Sconify’ ...
** this is package ‘Sconify’ version ‘1.29.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(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 52.914372 (50 iterations in 0.01 seconds)
Iteration 100: error is 54.147226 (50 iterations in 0.01 seconds)
Iteration 150: error is 55.038904 (50 iterations in 0.01 seconds)
Iteration 200: error is 56.875102 (50 iterations in 0.01 seconds)
Iteration 250: error is 52.827510 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.306829 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.730696 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.263669 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.211911 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.196591 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.179608 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.175821 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.174723 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.174540 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.175000 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.174674 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.175993 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.174793 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.175409 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.175153 (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 0.12 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.218054 (50 iterations in 0.32 seconds)
Iteration 100: error is 60.770685 (50 iterations in 0.21 seconds)
Iteration 150: error is 60.347557 (50 iterations in 0.21 seconds)
Iteration 200: error is 60.206791 (50 iterations in 0.22 seconds)
Iteration 250: error is 60.136961 (50 iterations in 0.23 seconds)
Iteration 300: error is 1.351523 (50 iterations in 0.16 seconds)
Iteration 350: error is 1.234916 (50 iterations in 0.14 seconds)
Iteration 400: error is 1.204872 (50 iterations in 0.14 seconds)
Iteration 450: error is 1.192685 (50 iterations in 0.14 seconds)
Iteration 500: error is 1.184534 (50 iterations in 0.14 seconds)
Iteration 550: error is 1.179233 (50 iterations in 0.14 seconds)
Iteration 600: error is 1.175378 (50 iterations in 0.14 seconds)
Iteration 650: error is 1.171730 (50 iterations in 0.14 seconds)
Iteration 700: error is 1.168308 (50 iterations in 0.14 seconds)
Iteration 750: error is 1.164948 (50 iterations in 0.14 seconds)
Iteration 800: error is 1.162806 (50 iterations in 0.14 seconds)
Iteration 850: error is 1.160631 (50 iterations in 0.14 seconds)
Iteration 900: error is 1.158373 (50 iterations in 0.14 seconds)
Iteration 950: error is 1.158963 (50 iterations in 0.14 seconds)
Iteration 1000: error is 1.158316 (50 iterations in 0.14 seconds)
Fitting performed in 3.32 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 18.630   0.394  19.012