Package: slingshot

Version: 1.1.2

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_1.1.2.tar.gz

StartedAt: 2019-04-09 05:35:52 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:43:18 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 446.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: slingshot.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running 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_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/slingshot.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.2’
* 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
See ‘/Users/biocbuild/bbs-3.9-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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
splatterParameters 28.196  2.361   30.58
* 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-3.9-bioc/meat/slingshot.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘slingshot’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
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
** testing if installed package can be loaded from temporary location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** testing if installed package can be loaded from final location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** testing if installed package keeps a record of temporary installation path
* DONE (slingshot)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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(slingshot)
Loading required package: princurve
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: '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: 948 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 33.873   2.241  36.070 

name	user	system	elapsed
SlingshotDataSet-class	0.004	0.002	0.005
getCurves	0.529	0.030	0.562
getLineages	0.684	0.080	0.796
newSlingshotDataSet	0.002	0.001	0.003
pairs-SlingshotDataSet	1.154	0.084	1.239
plot-SlingshotDataSet	0.454	0.020	0.475
plot3d-SlingshotDataSet	0	0	0
plotGenePseudotime	0.442	0.022	0.466
predict.SlingshotDataSet	0.482	0.012	0.494
slingAdjacency	0.033	0.002	0.035
slingCurves	0.431	0.052	0.483
slingLineages	0.039	0.005	0.044
slingParams	0.149	0.005	0.153
slingPseudotime	0.938	0.049	0.988
slingshot	0.415	0.019	0.435
slingshotExample	0.410	0.017	0.426
splatterParameters	28.196	2.361	30.580