BioC 3.3: CHECK report for RTCGA on oaxaca

Package: RTCGA

Version: 1.2.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGA_1.2.5.tar.gz

StartedAt: 2016-10-13 06:00:30 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:05:12 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 282.4 seconds

RetCode: 0

Status:  OK

CheckDir: RTCGA.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGA_1.2.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RTCGA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTCGA/DESCRIPTION’ ... OK
* this is package ‘RTCGA’ version ‘1.2.5’
* 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 63.243 12.255  78.124
boxplotTCGA     38.403  7.230  49.798
heatmapTCGA     33.609  6.781  40.426
kmTCGA           9.503  0.515  10.253
survivalTCGA     8.351  0.499   8.855
* 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-3.3-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	0.001	0.000	0.001
boxplotTCGA	38.403	7.230	49.798
checkTCGA	0.754	0.109	3.289
convertTCGA	2.113	0.371	2.490
datasetsTCGA	0.001	0.000	0.001
downloadTCGA	0.190	0.376	1.056
expressionsTCGA	63.243	12.255	78.124
heatmapTCGA	33.609	6.781	40.426
infoTCGA	1.333	0.006	2.790
installTCGA	0.000	0.000	0.001
kmTCGA	9.503	0.515	10.253
mutationsTCGA	3.528	0.257	3.787
pcaTCGA	0	0	0
readTCGA	0.006	0.002	0.007
survivalTCGA	8.351	0.499	8.855
theme_RTCGA	2.941	0.259	3.201