Package: bioCancer

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioCancer_1.6.0.tar.gz

StartedAt: 2018-04-12 00:54:43 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:57:23 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 160.4 seconds

RetCode: 0

Status:  OK

CheckDir: bioCancer.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioCancer_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/bioCancer.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.6.0’
* 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 ‘bioCancer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    app   3.1Mb
    doc   2.8Mb
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘dplyr’ ‘import’ ‘methods’ ‘shinythemes’
  All declared Imports should be used.
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/bioCancer.Rcheck/00check.log’
for details.

* installing *source* package ‘bioCancer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bioCancer)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(bioCancer)
Loading required package: radiant.data
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

Loading required package: ggplot2
Loading required package: lubridate

Attaching package: 'lubridate'

The following object is masked from 'package:base':

    date

Loading required package: tidyr

Attaching package: 'tidyr'

The following object is masked from 'package:magrittr':

    extract

Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:lubridate':

    intersect, setdiff, union

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'radiant.data'

The following object is masked from 'package:dplyr':

    mutate_each

The following objects are masked from 'package:lubridate':

    month, wday

The following object is masked from 'package:ggplot2':

    diamonds

The following object is masked from 'package:testthat':

    describe

Loading required package: cgdsr
Please send questions to cbioportal@googlegroups.com
Loading required package: XML


> 
> test_check("bioCancer")
getCancerStudies...  OK
getCaseLists (1/2) ...  OK
getCaseLists (2/2) ...  OK
getGeneticProfiles (1/2) ...  OK
getGeneticProfiles (2/2) ...  OK
getClinicalData (1/1) ...  OK
getProfileData (1/6) ...  OK
getProfileData (2/6) ...  OK
getProfileData (3/6) ...  OK
getProfileData (4/6) ...  OK
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
ReactomeFI connection...  OK
══ testthat results  ═══════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
OK: 0 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  7.591   0.308  11.420 

name	user	system	elapsed
Edges_Diseases_obj	0.004	0.000	0.004
Mutation_obj	0.086	0.001	0.088
Node_Diseases_obj	0.005	0.001	0.004
Node_df_FreqIn	0.001	0.000	0.001
Node_obj_CNA_ProfData	0.001	0.000	0.002
Node_obj_FreqIn	0.001	0.001	0.001
Node_obj_Met_ProfData	0.002	0.000	0.002
Node_obj_mRNA_Classifier	0.003	0.000	0.003
Studies_obj	0.006	0.001	0.006
UnifyRowNames	0.001	0.000	0.002
attriColorGene	0.001	0.000	0.001
attriColorValue	0.002	0.001	0.002
attriColorVector	0.001	0.000	0.002
attriShape2Gene	0.001	0.001	0.000
attriShape2Node	0.001	0.000	0.001
bioCancer	0.001	0.000	0.001
checkDimensions	0.002	0.001	0.002
coffeewheel	0.001	0.000	0.001
coffeewheelOutput	0.001	0.000	0.001
displayTable	0.094	0.002	0.752
getFreqMutData	0.001	0.000	0.002
getGenesClassification	0.005	0.001	0.235
getListProfData	0.001	0.001	0.002
getList_Cases	0.005	0.001	0.244
getList_GenProfs	0.005	0.001	0.235
getMegaProfData	0.001	0.000	0.001
getSequensed_SampleSize	0.000	0.000	0.001
grepRef	0.001	0.000	0.001
reStrColorGene	0.001	0.000	0.004
reStrDimension	0.002	0.000	0.003
reStrDisease	0.002	0.000	0.002
renderCoffeewheel	0.000	0.001	0.000
returnTextAreaInput	0.001	0.000	0.001
whichGeneList	0.000	0.000	0.001