BioC 3.5: CHECK report for RTCGA on malbec2

Package: RTCGA

Version: 1.6.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RTCGA_1.6.0.tar.gz

StartedAt: 2017-10-18 02:15:30 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:23:21 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 470.7 seconds

RetCode: 0

Status:  OK

CheckDir: RTCGA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RTCGA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/RTCGA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.6.0’
* 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 ‘RTCGA’ 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
availableDates: no visible binding for global variable ‘.’
downloadTCGA: no visible binding for global variable ‘.’
ggbiplot: no visible binding for global variable ‘xvar’
ggbiplot: no visible binding for global variable ‘yvar’
ggbiplot: no visible global function definition for ‘muted’
ggbiplot: no visible binding for global variable ‘varname’
ggbiplot: no visible binding for global variable ‘angle’
ggbiplot: no visible binding for global variable ‘hjust’
read.mutations: no visible binding for global variable ‘.’
read.rnaseq: no visible binding for global variable ‘.’
survivalTCGA: no visible binding for global variable ‘times’
whichDateToUse: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . angle hjust muted times varname xvar yvar
* 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
Examples with CPU or elapsed time > 5s
                   user system elapsed
expressionsTCGA 157.752  0.488 159.581
heatmapTCGA     103.296  0.116 103.669
boxplotTCGA      75.264  0.764  77.356
kmTCGA           15.620  0.008  15.764
survivalTCGA     12.964  0.012  12.986
mutationsTCGA     6.948  0.000   6.954
theme_RTCGA       6.120  0.004   6.133
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/RTCGA.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
RTCGA-package	0.000	0.000	0.001
boxplotTCGA	75.264	0.764	77.356
checkTCGA	1.196	0.004	2.413
convertTCGA	1.324	0.148	1.471
datasetsTCGA	0	0	0
downloadTCGA	0.216	0.100	0.785
expressionsTCGA	157.752	0.488	159.581
heatmapTCGA	103.296	0.116	103.669
infoTCGA	1.248	0.004	1.565
installTCGA	0	0	0
kmTCGA	15.620	0.008	15.764
mutationsTCGA	6.948	0.000	6.954
pcaTCGA	0.004	0.000	0.001
readTCGA	0.000	0.004	0.005
survivalTCGA	12.964	0.012	12.986
theme_RTCGA	6.120	0.004	6.133