Package: TCGAWorkflowData

Version: 1.2.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.2.1.tar.gz

StartedAt: 2018-04-12 10:41:31 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:46:18 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 286.9 seconds

RetCode: 0

Status:  OK

CheckDir: TCGAWorkflowData.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TCGAWorkflowData_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/TCGAWorkflowData.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TCGAWorkflowData/DESCRIPTION’ ... OK
* this is package ‘TCGAWorkflowData’ version ‘1.2.1’
* 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 ‘TCGAWorkflowData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 76.8Mb
  sub-directories of 1Mb or more:
    data  76.1Mb
* 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 loading without being on the library search path ... 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
Examples with CPU or elapsed time > 5s
                   user system elapsed
TCGAWorkflowData 36.916  0.304  37.246
GBMmut           15.076  0.092  15.180
LGGmut           13.144  0.032  13.186
tmp.biogrid      12.652  0.012  12.670
mut              10.940  0.048  10.993
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/TCGAWorkflowData.Rcheck/00check.log’
for details.

* installing *source* package ‘TCGAWorkflowData’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCGAWorkflowData)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(TCGAWorkflowData)
> 
> test_check("TCGAWorkflowData")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 38.760   0.520  39.299 

name	user	system	elapsed
GBMmut	15.076	0.092	15.180
LGGmut	13.144	0.032	13.186
TCGAWorkflowData	36.916	0.304	37.246
cnvMatrix	0.008	0.000	0.007
exp	0.568	0.016	0.587
gbm.exp	0.420	0.008	0.428
gbm.samples	0.576	0.012	0.590
genes	0.196	0.004	0.196
genes_GR	0.196	0.008	0.206
gistic.allbygene	0.008	0.000	0.009
gistic.thresholedbygene	0.008	0.000	0.008
histone.marks	1.592	0.040	1.635
lgg.exp	0.660	0.004	0.666
lgg.samples	0.532	0.016	0.546
markersMatrix	2.828	0.024	2.857
met	0.548	0.008	0.558
mut	10.940	0.048	10.993
tmp.biogrid	12.652	0.012	12.670