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CHECK report for Sconify on merida1

This page was generated on 2019-04-16 12:07:56 -0400 (Tue, 16 Apr 2019).

Package 1402/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Sconify 1.2.1
Tyler J Burns
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/Sconify
Branch: RELEASE_3_8
Last Commit: 940b0c7
Last Changed Date: 2019-01-04 13:49:48 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Sconify
Version: 1.2.1
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_1.2.1.tar.gz
StartedAt: 2019-04-16 02:39:39 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:41:46 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 126.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Sconify.Rcheck
Warnings: 1

Command output

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### Running 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_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Sconify.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.1’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘flowCore::view’ by ‘tibble::view’ when loading ‘Sconify’
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/Sconify.Rcheck/00install.out’ for details.
* 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 19.425  0.235  19.851
* 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 WARNING
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/Sconify.Rcheck/00check.log’
for details.



Installation output

Sconify.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Sconify’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘flowCore::view’ by ‘tibble::view’ when loading ‘Sconify’
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
Warning: replacing previous import ‘flowCore::view’ by ‘tibble::view’ when loading ‘Sconify’
* DONE (Sconify)

Tests output

Sconify.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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)
Warning message:
replacing previous import 'flowCore::view' by 'tibble::view' when loading '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 = 0.968400)!
Learning embedding...
Iteration 50: error is 52.541348 (50 iterations in 0.02 seconds)
Iteration 100: error is 50.301482 (50 iterations in 0.02 seconds)
Iteration 150: error is 50.720392 (50 iterations in 0.02 seconds)
Iteration 200: error is 53.794649 (50 iterations in 0.02 seconds)
Iteration 250: error is 54.346872 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.755357 (50 iterations in 0.02 seconds)
Iteration 350: error is 1.426610 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.957451 (50 iterations in 0.02 seconds)
Iteration 450: error is 0.551079 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.372644 (50 iterations in 0.02 seconds)
Iteration 550: error is 0.250135 (50 iterations in 0.02 seconds)
Iteration 600: error is 0.197773 (50 iterations in 0.02 seconds)
Iteration 650: error is 0.189173 (50 iterations in 0.02 seconds)
Iteration 700: error is 0.189606 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.189099 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.191222 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.190973 (50 iterations in 0.02 seconds)
Iteration 900: error is 0.190731 (50 iterations in 0.02 seconds)
Iteration 950: error is 0.190411 (50 iterations in 0.02 seconds)
Iteration 1000: error is 0.190162 (50 iterations in 0.02 seconds)
Fitting performed in 0.34 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 0.21 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 64.742169 (50 iterations in 0.40 seconds)
Iteration 100: error is 60.723454 (50 iterations in 0.28 seconds)
Iteration 150: error is 60.336675 (50 iterations in 0.26 seconds)
Iteration 200: error is 60.201969 (50 iterations in 0.28 seconds)
Iteration 250: error is 60.129577 (50 iterations in 0.27 seconds)
Iteration 300: error is 1.344808 (50 iterations in 0.23 seconds)
Iteration 350: error is 1.234169 (50 iterations in 0.21 seconds)
Iteration 400: error is 1.202658 (50 iterations in 0.21 seconds)
Iteration 450: error is 1.191721 (50 iterations in 0.21 seconds)
Iteration 500: error is 1.183939 (50 iterations in 0.22 seconds)
Iteration 550: error is 1.178289 (50 iterations in 0.20 seconds)
Iteration 600: error is 1.174018 (50 iterations in 0.21 seconds)
Iteration 650: error is 1.169910 (50 iterations in 0.20 seconds)
Iteration 700: error is 1.166344 (50 iterations in 0.21 seconds)
Iteration 750: error is 1.164059 (50 iterations in 0.21 seconds)
Iteration 800: error is 1.162860 (50 iterations in 0.22 seconds)
Iteration 850: error is 1.160694 (50 iterations in 0.21 seconds)
Iteration 900: error is 1.159335 (50 iterations in 0.19 seconds)
Iteration 950: error is 1.157873 (50 iterations in 0.21 seconds)
Iteration 1000: error is 1.156596 (50 iterations in 0.21 seconds)
Fitting performed in 4.64 seconds.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 72 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 30.306   0.553  31.142 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.3180.0090.333
Fnn0.7060.6981.418
GetKnnDe0.0900.0050.095
GetMarkerNames0.0440.0020.046
ImputeTesting4.0790.0184.121
MakeHist0.2930.0050.298
MakeKnnList0.3220.0100.334
MeaningOfLife0.0010.0000.000
ParseMarkers0.0310.0080.039
PostProcessing0.2660.0050.272
ProcessMultipleFiles0.2840.0060.296
QuantNormalizeElements0.4230.0060.436
SconeValues19.425 0.23519.851
SplitFile0.2490.0030.257
StringToNumbers0.0010.0000.001
SubsampleAndTsne2.4920.0082.521
TsneVis0.3050.0030.314