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CHECK report for Sconify on malbec1

This page was generated on 2019-04-16 11:53:23 -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: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Sconify_1.2.1.tar.gz
StartedAt: 2019-04-16 02:55:19 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:57:08 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 109.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Sconify.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Sconify.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Sconify_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Sconify.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘/home/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 18.44      0  18.464
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/Sconify.Rcheck/00check.log’
for details.



Installation output

Sconify.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Sconify
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-pc-linux-gnu (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 0.02 seconds (sparsity = 0.965600)!
Learning embedding...
Iteration 50: error is 51.659531 (50 iterations in 0.02 seconds)
Iteration 100: error is 54.879031 (50 iterations in 0.02 seconds)
Iteration 150: error is 52.444723 (50 iterations in 0.02 seconds)
Iteration 200: error is 52.853914 (50 iterations in 0.02 seconds)
Iteration 250: error is 49.771909 (50 iterations in 0.02 seconds)
Iteration 300: error is 1.539144 (50 iterations in 0.02 seconds)
Iteration 350: error is 0.988978 (50 iterations in 0.01 seconds)
Iteration 400: error is 0.549056 (50 iterations in 0.01 seconds)
Iteration 450: error is 0.258692 (50 iterations in 0.01 seconds)
Iteration 500: error is 0.229307 (50 iterations in 0.01 seconds)
Iteration 550: error is 0.232847 (50 iterations in 0.01 seconds)
Iteration 600: error is 0.228831 (50 iterations in 0.02 seconds)
Iteration 650: error is 0.225772 (50 iterations in 0.01 seconds)
Iteration 700: error is 0.226378 (50 iterations in 0.01 seconds)
Iteration 750: error is 0.225325 (50 iterations in 0.01 seconds)
Iteration 800: error is 0.226548 (50 iterations in 0.01 seconds)
Iteration 850: error is 0.225664 (50 iterations in 0.01 seconds)
Iteration 900: error is 0.225292 (50 iterations in 0.01 seconds)
Iteration 950: error is 0.225378 (50 iterations in 0.01 seconds)
Iteration 1000: error is 0.225044 (50 iterations in 0.01 seconds)
Fitting performed in 0.32 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 0.25 seconds (sparsity = 0.129120)!
Learning embedding...
Iteration 50: error is 65.315189 (50 iterations in 0.59 seconds)
Iteration 100: error is 60.708415 (50 iterations in 0.33 seconds)
Iteration 150: error is 60.346309 (50 iterations in 0.30 seconds)
Iteration 200: error is 60.220633 (50 iterations in 0.30 seconds)
Iteration 250: error is 60.145441 (50 iterations in 0.30 seconds)
Iteration 300: error is 1.341561 (50 iterations in 0.28 seconds)
Iteration 350: error is 1.231059 (50 iterations in 0.27 seconds)
Iteration 400: error is 1.200908 (50 iterations in 0.26 seconds)
Iteration 450: error is 1.187387 (50 iterations in 0.25 seconds)
Iteration 500: error is 1.179544 (50 iterations in 0.26 seconds)
Iteration 550: error is 1.175420 (50 iterations in 0.27 seconds)
Iteration 600: error is 1.172237 (50 iterations in 0.29 seconds)
Iteration 650: error is 1.169081 (50 iterations in 0.28 seconds)
Iteration 700: error is 1.167944 (50 iterations in 0.27 seconds)
Iteration 750: error is 1.165364 (50 iterations in 0.27 seconds)
Iteration 800: error is 1.163662 (50 iterations in 0.26 seconds)
Iteration 850: error is 1.162103 (50 iterations in 0.27 seconds)
Iteration 900: error is 1.160531 (50 iterations in 0.21 seconds)
Iteration 950: error is 1.158884 (50 iterations in 0.24 seconds)
Iteration 1000: error is 1.158317 (50 iterations in 0.23 seconds)
Fitting performed in 5.71 seconds.
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 72 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 27.932   0.160  28.119 

Example timings

Sconify.Rcheck/Sconify-Ex.timings

nameusersystemelapsed
FcsToTibble0.2600.0080.286
Fnn0.4080.4160.824
GetKnnDe0.1240.0000.126
GetMarkerNames0.0400.0040.048
ImputeTesting3.6960.0003.709
MakeHist0.2160.0000.216
MakeKnnList0.2400.0040.243
MeaningOfLife000
ParseMarkers0.0280.0080.036
PostProcessing0.1400.0120.151
ProcessMultipleFiles0.1640.0000.179
QuantNormalizeElements0.2520.0000.252
SconeValues18.440 0.00018.464
SplitFile0.2320.0000.231
StringToNumbers000
SubsampleAndTsne1.8400.0001.848
TsneVis0.1600.0040.166