Package: slingshot

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:slingshot.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings slingshot_1.0.0.tar.gz

StartedAt: 2019-03-18 02:58:14 -0400 (Mon, 18 Mar 2019)

EndedAt: 2019-03-18 03:03:48 -0400 (Mon, 18 Mar 2019)

EllapsedTime: 333.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: slingshot.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:slingshot.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings slingshot_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/slingshot.Rcheck’
* using R version 3.5.2 Patched (2018-12-20 r75875)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘slingshot/DESCRIPTION’ ... OK
* this is package ‘slingshot’ version ‘1.0.0’
* 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 ‘slingshot’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘slingshot’
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/slingshot.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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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/slingshot.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL slingshot
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘slingshot’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘slingshot’
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘slingshot.Rmd’ using ‘UTF-8’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘SingleCellExperiment::weights’ by ‘stats::weights’ when loading ‘slingshot’
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (slingshot)

R version 3.5.2 Patched (2018-12-20 r75875) -- "Eggshell Igloo"
Copyright (C) 2018 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(slingshot)
Loading required package: princurve
Warning messages:
1: replacing previous import 'SingleCellExperiment::weights' by 'stats::weights' when loading 'slingshot' 
2: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
3: 'rgl_init' failed, running with rgl.useNULL = TRUE 
> 
> test_check("slingshot")
class: SlingshotDataSet 

 Samples Dimensions
     140          2

lineages: 2 
Lineage1: 1  2  3  5  
Lineage2: 1  2  3  4  

curves: 2 
Curve1: Length: 15.045	Samples: 100.61
Curve2: Length: 15.126	Samples: 103.49
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 107 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 26.989   0.984  28.154 

name	user	system	elapsed
SlingshotDataSet-class	0.004	0.001	0.006
getCurves	0.416	0.020	0.444
getLineages	0.393	0.019	0.419
newSlingshotDataSet	0.002	0.000	0.002
pairs-SlingshotDataSet	0.804	0.086	0.892
plot-SlingshotDataSet	0.381	0.015	0.398
plot3d-SlingshotDataSet	0.000	0.000	0.001
plotGenePseudotime	0.411	0.014	0.432
predict.SlingshotDataSet	0.374	0.006	0.382
slingAdjacency	0.023	0.001	0.024
slingCurves	0.381	0.015	0.400
slingLineages	0.034	0.001	0.035
slingParams	0.226	0.004	0.237
slingPseudotime	0.757	0.010	0.771
slingshot	0.337	0.005	0.345