##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Sconify.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Sconify_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Sconify.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Sconify/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Sconify' version '1.25.0'
* 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 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 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 13.88   0.46   14.34
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 0.02 seconds (sparsity = 0.966000)!
Learning embedding...
Iteration 50: error is 51.307760 (50 iterations in 0.01 seconds)
Iteration 100: error is 53.346034 (50 iterations in 0.01 seconds)
Iteration 150: error is 48.866196 (50 iterations in 0.01 seconds)
Iteration 200: error is 50.988402 (50 iterations in 0.01 seconds)
Iteration 250: error is 48.852688 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.329247 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.652700 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.231507 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.175620 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.154193 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.153391 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.152748 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.154172 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.153878 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.154348 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.153743 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.154376 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.153809 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.152397 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.152658 (50 iterations in 0.01 seconds)
Fitting performed in 0.24 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 0.24 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 65.454186 (50 iterations in 0.28 seconds)
Iteration 100: error is 60.752716 (50 iterations in 0.23 seconds)
Iteration 150: error is 60.355303 (50 iterations in 0.18 seconds)
Iteration 200: error is 60.225079 (50 iterations in 0.21 seconds)
Iteration 250: error is 60.160827 (50 iterations in 0.24 seconds)
Iteration 300: error is 1.346947 (50 iterations in 0.14 seconds)
Iteration 350: error is 1.234848 (50 iterations in 0.16 seconds)
Iteration 400: error is 1.202559 (50 iterations in 0.16 seconds)
Iteration 450: error is 1.194179 (50 iterations in 0.16 seconds)
Iteration 500: error is 1.186126 (50 iterations in 0.16 seconds)
Iteration 550: error is 1.179932 (50 iterations in 0.12 seconds)
Iteration 600: error is 1.175315 (50 iterations in 0.12 seconds)
Iteration 650: error is 1.171646 (50 iterations in 0.13 seconds)
Iteration 700: error is 1.168255 (50 iterations in 0.10 seconds)
Iteration 750: error is 1.165094 (50 iterations in 0.10 seconds)
Iteration 800: error is 1.161851 (50 iterations in 0.10 seconds)
Iteration 850: error is 1.160356 (50 iterations in 0.10 seconds)
Iteration 900: error is 1.158948 (50 iterations in 0.10 seconds)
Iteration 950: error is 1.157291 (50 iterations in 0.11 seconds)
Iteration 1000: error is 1.155374 (50 iterations in 0.10 seconds)
Fitting performed in 3.02 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
  19.93    9.67   29.45