BioC 3.6: CHECK report for bioCancer on veracruz1

Package: bioCancer

Version: 1.5.04

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioCancer_1.5.04.tar.gz

StartedAt: 2017-08-16 00:24:30 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:27:38 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 188.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: bioCancer.Rcheck

Warnings: 1

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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_1.5.04.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/bioCancer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.04’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘magrittr’ ‘ggplot2’ ‘lubridate’ ‘tidyr’ ‘cgdsr’ ‘RCurl’ ‘XML’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 21.8Mb
  sub-directories of 1Mb or more:
    base        6.5Mb
    bioCancer   3.1Mb
    doc         2.8Mb
    quant       7.7Mb
* 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 ... WARNING
Undocumented code objects:
  ‘getSequensed_SampleSize’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/bioCancer.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
Edges_Diseases_obj	0.002	0.001	0.003
Mutation_obj	0.086	0.001	0.088
Node_Diseases_obj	0.004	0.000	0.004
Node_df_FreqIn	0.001	0.000	0.002
Node_obj_CNA_ProfData	0.002	0.000	0.002
Node_obj_FreqIn	0.001	0.000	0.002
Node_obj_Met_ProfData	0.001	0.000	0.001
Node_obj_mRNA_Classifier	0.001	0.001	0.002
Studies_obj	0.007	0.000	0.007
UnifyRowNames	0.002	0.000	0.002
attriColorGene	0.002	0.000	0.002
attriColorValue	0.002	0.000	0.002
attriColorVector	0.002	0.000	0.002
attriShape2Gene	0.000	0.000	0.001
attriShape2Node	0.001	0.000	0.000
bioCancer	0.000	0.000	0.001
checkDimensions	0.001	0.000	0.002
coffeewheel	0.001	0.000	0.001
coffeewheelOutput	0.000	0.000	0.001
displayTable	0.110	0.002	0.684
getFreqMutData	0.002	0.000	0.002
getGenesClassification	0.006	0.001	0.264
getListProfData	0.002	0.001	0.002
getList_Cases	0.005	0.001	0.274
getList_GenProfs	0.006	0.001	0.279
getMegaProfData	0.001	0.000	0.001
grepRef	0.001	0.000	0.001
metabologram	0.001	0.000	0.001
reStrColorGene	0.002	0.000	0.002
reStrDimension	0.002	0.001	0.002
reStrDisease	0.002	0.000	0.001
renderCoffeewheel	0.000	0.000	0.001
sampleWheelData	0.001	0.000	0.001
whichGeneList	0.001	0.001	0.000