##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ChromSCape_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChromSCape.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ChromSCape’ 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 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 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
peaks_to_bins               14.738  6.622   8.473
filter_scExp                13.202  0.084  13.300
differential_analysis_scExp  9.930  0.256  10.201
CompareedgeRGLM              7.896  0.286   8.196
create_scDataset_raw         7.618  0.461   8.087
CompareWilcox                6.758  0.218   6.984
consensus_clustering_scExp   5.172  0.530   5.716
import_scExp                 5.555  0.084   5.692
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (ChromSCape)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(ChromSCape)
> 
> test_check("ChromSCape")
Read the 285 x 50 data matrix successfully!
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.02 seconds!
Learning embedding...
Iteration 50: error is 69.899664 (50 iterations in 0.07 seconds)
Iteration 100: error is 68.902778 (50 iterations in 0.06 seconds)
Iteration 150: error is 69.435150 (50 iterations in 0.06 seconds)
Iteration 200: error is 75.483312 (50 iterations in 0.07 seconds)
Iteration 250: error is 72.362121 (50 iterations in 0.07 seconds)
Iteration 300: error is 2.383375 (50 iterations in 0.06 seconds)
Iteration 350: error is 2.095224 (50 iterations in 0.06 seconds)
Iteration 400: error is 1.994822 (50 iterations in 0.07 seconds)
Iteration 450: error is 1.820434 (50 iterations in 0.07 seconds)
Iteration 500: error is 1.717651 (50 iterations in 0.08 seconds)
Iteration 550: error is 1.681820 (50 iterations in 0.06 seconds)
Iteration 600: error is 1.651323 (50 iterations in 0.06 seconds)
Iteration 650: error is 1.625209 (50 iterations in 0.06 seconds)
Iteration 700: error is 1.600104 (50 iterations in 0.06 seconds)
Iteration 750: error is 1.580099 (50 iterations in 0.06 seconds)
Iteration 800: error is 1.568410 (50 iterations in 0.06 seconds)
Iteration 850: error is 1.561593 (50 iterations in 0.06 seconds)
Iteration 900: error is 1.556643 (50 iterations in 0.06 seconds)
Iteration 950: error is 1.553253 (50 iterations in 0.07 seconds)
Iteration 1000: error is 1.549877 (50 iterations in 0.07 seconds)
Fitting performed in 1.26 seconds.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 38.200   2.376  40.608