Package: BiocOncoTK

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocOncoTK_1.0.3.tar.gz

StartedAt: 2018-10-16 20:06:26 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:08:26 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 119.8 seconds

RetCode: 0

Status:  OK

CheckDir: BiocOncoTK.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocOncoTK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocOncoTK_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/BiocOncoTK.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 ‘BiocOncoTK/DESCRIPTION’ ... OK
* this is package ‘BiocOncoTK’ version ‘1.0.3’
* 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 ‘BiocOncoTK’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.rainfall.bq.df: no visible global function definition for ‘seqlengths’
.rainfall.maeGRL.df: no visible global function definition for ‘genome’
.rainfall.maeGRL.df: no visible global function definition for
  ‘seqlengths’
checkCache_patel: no visible global function definition for
  ‘BiocFileCache’
chrbounds_basic: no visible global function definition for ‘seqlengths’
rainfall: no visible global function definition for ‘genome’
rainfall: no visible global function definition for ‘ggplot’
rainfall: no visible global function definition for ‘aes’
rainfall: no visible global function definition for ‘geom_point’
rainfall: no visible global function definition for ‘theme’
rainfall: no visible global function definition for ‘element_blank’
rainfall: no visible global function definition for ‘ylab’
rainfall: no visible global function definition for ‘xlab’
rainfall: no visible global function definition for ‘geom_vline’
rainfall: no visible global function definition for
  ‘scale_x_continuous’
rainfall: no visible global function definition for ‘ggtitle’
rainfall: no visible global function definition for ‘geom_text’
Undefined global functions or variables:
  BiocFileCache aes element_blank genome geom_point geom_text
  geom_vline ggplot ggtitle scale_x_continuous seqlengths theme xlab
  ylab
* 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
Examples with CPU or elapsed time > 5s
         user system elapsed
brcaMAE 5.928  0.274   6.259
* 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/BiocOncoTK.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BiocOncoTK’ ...
** 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 (BiocOncoTK)

name	user	system	elapsed
CCLE_DRUG_BROAD	0.088	0.019	0.110
TcgaMutCounts	0.002	0.001	0.002
TcgaNIndWithAnyMut	0.002	0.000	0.004
annotTabs	0.002	0.000	0.002
brcaMAE	5.928	0.274	6.259
cell_70138	0.002	0.001	0.002
clueDemos	0.002	0.000	0.001
clueServiceNames	0.001	0.000	0.001
darmGBMcls	0.344	0.040	0.387
icd10_c	0.107	0.018	0.126
loadPatel	0.002	0.000	0.003
oncoPrintISB	0.003	0.000	0.003
pancan.clin.varnames	0.024	0.001	0.024
pancan_BQ	0.002	0.000	0.002
pancan_app	0.001	0.000	0.002
pancan_clinicalTabVarnames	0.001	0.000	0.001
pancan_longname	0.002	0.000	0.002
pancan_sampTypeMap	0.003	0.001	0.003
pancan_tabulate	0.002	0.000	0.002
pertClasses	0.002	0.001	0.001
pert_70138	0.002	0.001	0.003
query_clue	0.003	0.000	0.003
utils	0.747	0.085	0.843