Package: bioCancer

Version: 1.10.11

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioCancer_1.10.11.tar.gz

StartedAt: 2019-04-15 22:34:28 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:37:55 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 206.3 seconds

RetCode: 0

Status:  OK

CheckDir: bioCancer.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bioCancer.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioCancer_1.10.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/bioCancer.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.11’
* 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 ‘bioCancer’ can be installed ... OK
* 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 ... 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 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/bioCancer.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘bioCancer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bioCancer)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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(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 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) ...  FAILED!
getProfileData (2/6) ...  OK
getProfileData (3/6) ...  OK
getProfileData (4/6) ...  FAILED!
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
ReactomeFI connection...  OK
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 2 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  9.987   0.552  13.678 

name	user	system	elapsed
Edges_Diseases_obj	0.005	0.000	0.005
Mutation_obj	0.005	0.000	0.006
Node_Diseases_obj	0.005	0.000	0.005
Node_df_FreqIn	0.001	0.000	0.001
Node_obj_CNA_ProfData	0.000	0.000	0.001
Node_obj_FreqIn	0.001	0.000	0.001
Node_obj_Met_ProfData	0.001	0.001	0.001
Node_obj_mRNA_Classifier	0.002	0.000	0.002
Studies_obj	0.007	0.001	0.007
UnifyRowNames	0.001	0.000	0.001
attriColorGene	0.001	0.000	0.001
attriColorValue	0.000	0.000	0.001
attriColorVector	0.001	0.000	0.002
attriShape2Gene	0	0	0
attriShape2Node	0.000	0.000	0.001
bioCancer	0	0	0
checkDimensions	0.001	0.000	0.001
coffeewheel	0	0	0
coffeewheelOutput	0	0	0
displayTable	0.009	0.002	0.252
findPhantom	0.000	0.001	0.000
getFreqMutData	0.002	0.000	0.002
getGenesClassification	0.008	0.002	0.242
getListProfData	0.001	0.000	0.001
getList_Cases	0.008	0.001	0.260
getList_GenProfs	0.006	0.001	0.260
getMegaProfData	0	0	0
getSequensed_SampleSize	0	0	0
grepRef	0	0	0
metabologram	0	0	0
metabologramOutput	0	0	0
reStrColorGene	0.001	0.001	0.001
reStrDimension	0.001	0.000	0.001
reStrDisease	0.001	0.000	0.002
renderCoffeewheel	0	0	0
renderMetabologram	0.000	0.000	0.001
returnTextAreaInput	0.001	0.000	0.000
whichGeneList	0.001	0.000	0.001
widgetThumbnail	0.001	0.000	0.000