##############################################################################
##############################################################################
###
### 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_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.29.0’
* 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 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 13.46  0.172  13.712
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Iteration 900: error is 1.152872 (50 iterations in 0.12 seconds)
  Iteration 950: error is 1.151084 (50 iterations in 0.12 seconds)
  Iteration 1000: error is 1.150002 (50 iterations in 0.12 seconds)
  Fitting performed in 2.71 seconds.
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test.post.processing.R:53:5'): Testing the output of the tSNE vis function ──
  TsneVis(...) has type 'object', not 'list'.
  ── Failure ('test.post.processing.R:60:5'): Testing the output of the make.hist function ──
  MakeHist(wand.final, 100, "IL7.fraction.cond.2", "fraction IL7") has type 'object', not 'list'.
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/Sconify.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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 = 0.968600)!
Learning embedding...
Iteration 50: error is 52.066336 (50 iterations in 0.01 seconds)
Iteration 100: error is 52.017971 (50 iterations in 0.01 seconds)
Iteration 150: error is 55.404208 (50 iterations in 0.01 seconds)
Iteration 200: error is 57.708570 (50 iterations in 0.01 seconds)
Iteration 250: error is 55.412284 (50 iterations in 0.01 seconds)
Iteration 300: error is 1.324767 (50 iterations in 0.01 seconds)
Iteration 350: error is 0.899067 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.221409 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.160697 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.161434 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.153291 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.151217 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.152800 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.153167 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.152160 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.152467 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.153116 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.151898 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.154052 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.153237 (50 iterations in 0.01 seconds)
Fitting performed in 0.16 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 0.13 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.885042 (50 iterations in 0.19 seconds)
Iteration 100: error is 60.912024 (50 iterations in 0.18 seconds)
Iteration 150: error is 60.383916 (50 iterations in 0.18 seconds)
Iteration 200: error is 60.218394 (50 iterations in 0.18 seconds)
Iteration 250: error is 60.146295 (50 iterations in 0.17 seconds)
Iteration 300: error is 1.340407 (50 iterations in 0.13 seconds)
Iteration 350: error is 1.229537 (50 iterations in 0.12 seconds)
Iteration 400: error is 1.195518 (50 iterations in 0.12 seconds)
Iteration 450: error is 1.182667 (50 iterations in 0.12 seconds)
Iteration 500: error is 1.175499 (50 iterations in 0.12 seconds)
Iteration 550: error is 1.169952 (50 iterations in 0.13 seconds)
Iteration 600: error is 1.167242 (50 iterations in 0.12 seconds)
Iteration 650: error is 1.165012 (50 iterations in 0.12 seconds)
Iteration 700: error is 1.162255 (50 iterations in 0.12 seconds)
Iteration 750: error is 1.159220 (50 iterations in 0.12 seconds)
Iteration 800: error is 1.156651 (50 iterations in 0.12 seconds)
Iteration 850: error is 1.154300 (50 iterations in 0.12 seconds)
Iteration 900: error is 1.152872 (50 iterations in 0.12 seconds)
Iteration 950: error is 1.151084 (50 iterations in 0.12 seconds)
Iteration 1000: error is 1.150002 (50 iterations in 0.12 seconds)
Fitting performed in 2.71 seconds.
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test.post.processing.R:53:5'): Testing the output of the tSNE vis function ──
TsneVis(...) has type 'object', not 'list'.
── Failure ('test.post.processing.R:60:5'): Testing the output of the make.hist function ──
MakeHist(wand.final, 100, "IL7.fraction.cond.2", "fraction IL7") has type 'object', not 'list'.

[ FAIL 2 | WARN 4 | SKIP 0 | PASS 70 ]
Error: Test failures
Execution halted