BioC 3.4: CHECK report for bioCancer on zin1

Package: bioCancer

Version: 1.0.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings bioCancer_1.0.0.tar.gz

StartedAt: 2016-09-20 03:42:39 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:45:14 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 154.1 seconds

RetCode: 0

Status:  OK

CheckDir: bioCancer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings bioCancer_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/bioCancer.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioCancer/DESCRIPTION’ ... OK
* this is package ‘bioCancer’ version ‘1.0.0’
* 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 20.6Mb
  sub-directories of 1Mb or more:
    base        6.2Mb
    bioCancer   3.1Mb
    doc         1.8Mb
    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 ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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	0.000	0.000	0.002
Mutation_obj	0.004	0.000	0.003
Node_Diseases_obj	0.004	0.000	0.003
Node_df_FreqIn	0.000	0.000	0.001
Node_obj_CNA_ProfData	0.004	0.000	0.001
Node_obj_FreqIn	0.000	0.000	0.001
Node_obj_Met_ProfData	0.000	0.000	0.001
Node_obj_mRNA_Classifier	0.000	0.000	0.001
Studies_obj	0.008	0.000	0.006
UnifyRowNames	0.000	0.000	0.001
attriColorGene	0.004	0.000	0.001
attriColorValue	0.000	0.000	0.001
attriColorVector	0.000	0.000	0.001
attriShape2Gene	0.000	0.000	0.001
attriShape2Node	0.004	0.000	0.001
bioCancer	0	0	0
checkDimensions	0.000	0.000	0.001
coffeewheel	0.000	0.000	0.001
coffeewheelOutput	0.000	0.000	0.001
displayTable	0.004	0.004	0.672
getFreqMutData	0.000	0.000	0.001
getListProfData	0.000	0.000	0.002
grepRef	0	0	0
metabologram	0.000	0.000	0.001
reStrColorGene	0.000	0.000	0.002
reStrDimension	0.000	0.000	0.002
reStrDisease	0.000	0.000	0.001
renderCoffeewheel	0	0	0
sampleWheelData	0	0	0
whichGeneList	0.000	0.000	0.001