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CHECK report for bioCancer on merida2

This page was generated on 2018-07-19 11:16:17 -0400 (Thu, 19 Jul 2018).

Package 124/1560HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioCancer 1.8.0
Karim Mezhoud
Snapshot Date: 2018-07-18 16:45:10 -0400 (Wed, 18 Jul 2018)
URL: https://git.bioconductor.org/packages/bioCancer
Branch: RELEASE_3_7
Last Commit: 45c7340
Last Changed Date: 2018-04-30 10:35:42 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: bioCancer
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2018-07-18 22:14:19 -0400 (Wed, 18 Jul 2018)
EndedAt: 2018-07-18 22:17:27 -0400 (Wed, 18 Jul 2018)
EllapsedTime: 187.8 seconds
RetCode: 0
Status:  OK 
CheckDir: bioCancer.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/bioCancer.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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 ... 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-3.7-bioc/meat/bioCancer.Rcheck/00check.log’
for details.



Installation output

bioCancer.Rcheck/00install.out

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###
### 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)

Tests output

bioCancer.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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 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 
  9.132   0.560  13.174 

Example timings

bioCancer.Rcheck/bioCancer-Ex.timings

nameusersystemelapsed
Edges_Diseases_obj0.0070.0000.007
Mutation_obj0.0060.0010.007
Node_Diseases_obj0.0070.0010.008
Node_df_FreqIn0.0020.0000.003
Node_obj_CNA_ProfData0.0020.0010.002
Node_obj_FreqIn0.0030.0000.002
Node_obj_Met_ProfData0.0020.0000.002
Node_obj_mRNA_Classifier0.0030.0010.004
Studies_obj0.0080.0000.009
UnifyRowNames0.0030.0000.003
attriColorGene0.0020.0000.002
attriColorValue0.0030.0000.004
attriColorVector0.0030.0000.004
attriShape2Gene0.0020.0000.002
attriShape2Node0.0010.0000.001
bioCancer0.0010.0000.002
checkDimensions0.0020.0000.004
coffeewheel0.0010.0000.001
coffeewheelOutput0.0010.0000.001
displayTable0.0130.0020.255
findPhantom0.0020.0000.002
getFreqMutData0.0030.0000.003
getGenesClassification0.0090.0010.252
getListProfData0.0030.0000.003
getList_Cases0.0080.0010.261
getList_GenProfs0.0080.0020.249
getMegaProfData0.0020.0000.002
getSequensed_SampleSize0.0010.0010.002
grepRef0.0020.0000.002
metabologram0.0010.0000.002
metabologramOutput0.0010.0000.002
reStrColorGene0.0030.0010.003
reStrDimension0.0030.0000.004
reStrDisease0.0020.0010.004
renderCoffeewheel0.0010.0000.002
renderMetabologram0.0010.0010.001
returnTextAreaInput0.0020.0000.002
whichGeneList0.0020.0000.001
widgetThumbnail0.0020.0000.002