Package: Sconify

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Sconify.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Sconify_1.6.0.tar.gz

StartedAt: 2020-04-15 05:31:23 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:34:41 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 197.2 seconds

RetCode: 0

Status:  OK

CheckDir: Sconify.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Sconify.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Sconify_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Sconify.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Sconify/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sconify’ version ‘1.6.0’
* 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 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 or elapsed time > 5s
                user system elapsed
SconeValues   36.858  0.158  37.600
ImputeTesting 19.104  0.084  19.407
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Sconify
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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 = 0.965600)!
Learning embedding...
Iteration 50: error is 50.060977 (50 iterations in 0.02 seconds)
Iteration 100: error is 55.877951 (50 iterations in 0.02 seconds)
Iteration 150: error is 51.897560 (50 iterations in 0.02 seconds)
Iteration 200: error is 53.970836 (50 iterations in 0.02 seconds)
Iteration 250: error is 52.173658 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.543913 (50 iterations in 0.02 seconds)
Iteration 350: error is 1.037818 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.536102 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.291860 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.214156 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.208892 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.209358 (50 iterations in 0.01 seconds)
Iteration 650: error is 0.208439 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.208686 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.208942 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.208787 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.208873 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.208644 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.209141 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.208729 (50 iterations in 0.01 seconds)
Fitting performed in 0.29 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 0.18 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.482415 (50 iterations in 0.28 seconds)
Iteration 100: error is 60.758300 (50 iterations in 0.24 seconds)
Iteration 150: error is 60.324340 (50 iterations in 0.28 seconds)
Iteration 200: error is 60.185819 (50 iterations in 0.26 seconds)
Iteration 250: error is 60.125940 (50 iterations in 0.24 seconds)
Iteration 300: error is 1.338595 (50 iterations in 0.22 seconds)
Iteration 350: error is 1.231580 (50 iterations in 0.20 seconds)
Iteration 400: error is 1.202672 (50 iterations in 0.15 seconds)
Iteration 450: error is 1.187586 (50 iterations in 0.15 seconds)
Iteration 500: error is 1.177621 (50 iterations in 0.20 seconds)
Iteration 550: error is 1.173024 (50 iterations in 0.19 seconds)
Iteration 600: error is 1.167919 (50 iterations in 0.20 seconds)
Iteration 650: error is 1.164655 (50 iterations in 0.16 seconds)
Iteration 700: error is 1.162221 (50 iterations in 0.16 seconds)
Iteration 750: error is 1.158981 (50 iterations in 0.18 seconds)
Iteration 800: error is 1.156964 (50 iterations in 0.19 seconds)
Iteration 850: error is 1.154320 (50 iterations in 0.21 seconds)
Iteration 900: error is 1.152086 (50 iterations in 0.19 seconds)
Iteration 950: error is 1.150783 (50 iterations in 0.19 seconds)
Iteration 1000: error is 1.149392 (50 iterations in 0.18 seconds)
Fitting performed in 4.08 seconds.
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 72 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 69.392   0.636  71.638 

name	user	system	elapsed
FcsToTibble	0.157	0.019	0.178
Fnn	0.702	0.701	1.413
GetKnnDe	0.086	0.005	0.092
GetMarkerNames	0.038	0.004	0.043
ImputeTesting	19.104	0.084	19.407
MakeHist	0.439	0.006	0.447
MakeKnnList	0.644	0.014	0.663
MeaningOfLife	0	0	0
ParseMarkers	0.018	0.006	0.024
PostProcessing	0.136	0.001	0.139
ProcessMultipleFiles	0.161	0.003	0.170
QuantNormalizeElements	0.203	0.002	0.209
SconeValues	36.858	0.158	37.600
SplitFile	0.128	0.002	0.131
StringToNumbers	0.000	0.000	0.001
SubsampleAndTsne	2.839	0.006	3.078
TsneVis	0.313	0.002	0.320