##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Sconify.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Sconify_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Sconify.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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 9.73  0.194   9.957
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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!
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.01 seconds (sparsity = 0.961400)!
Learning embedding...
Iteration 50: error is 52.305871 (50 iterations in 0.01 seconds)
Iteration 100: error is 54.528001 (50 iterations in 0.01 seconds)
Iteration 150: error is 55.223938 (50 iterations in 0.01 seconds)
Iteration 200: error is 57.713216 (50 iterations in 0.01 seconds)
Iteration 250: error is 53.611555 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.599816 (50 iterations in 0.01 seconds)
Iteration 350: error is 1.147987 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.624252 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.213955 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.206769 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.206347 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.205980 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.205121 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.204904 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.208031 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.208691 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.207082 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.208119 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.207051 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.208366 (50 iterations in 0.01 seconds)
Fitting performed in 0.12 seconds.
Read the 1000 x 27 data matrix successfully!
Using no_dims = 2, perplexity = 30.000000, and theta = 0.500000
Computing input similarities...
Building tree...
Done in 0.10 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.468747 (50 iterations in 0.14 seconds)
Iteration 100: error is 60.658830 (50 iterations in 0.11 seconds)
Iteration 150: error is 60.344232 (50 iterations in 0.11 seconds)
Iteration 200: error is 60.223004 (50 iterations in 0.12 seconds)
Iteration 250: error is 60.159349 (50 iterations in 0.13 seconds)
Iteration 300: error is 1.338169 (50 iterations in 0.10 seconds)
Iteration 350: error is 1.226905 (50 iterations in 0.10 seconds)
Iteration 400: error is 1.197924 (50 iterations in 0.09 seconds)
Iteration 450: error is 1.185387 (50 iterations in 0.09 seconds)
Iteration 500: error is 1.177108 (50 iterations in 0.09 seconds)
Iteration 550: error is 1.171774 (50 iterations in 0.09 seconds)
Iteration 600: error is 1.166507 (50 iterations in 0.09 seconds)
Iteration 650: error is 1.162244 (50 iterations in 0.09 seconds)
Iteration 700: error is 1.158641 (50 iterations in 0.09 seconds)
Iteration 750: error is 1.155810 (50 iterations in 0.09 seconds)
Iteration 800: error is 1.153945 (50 iterations in 0.09 seconds)
Iteration 850: error is 1.152785 (50 iterations in 0.09 seconds)
Iteration 900: error is 1.150799 (50 iterations in 0.09 seconds)
Iteration 950: error is 1.149334 (50 iterations in 0.09 seconds)
Iteration 1000: error is 1.147368 (50 iterations in 0.09 seconds)
Fitting performed in 1.95 seconds.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 72 ]
> 
> proc.time()
   user  system elapsed 
 15.163   0.603  15.952