BioC 3.4: CHECK report for RTCGA on morelia

Package: RTCGA

Version: 1.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGA_1.3.3.tar.gz

StartedAt: 2016-09-20 12:38:37 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:42:41 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 243.7 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_1.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘1.3.3’
* 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 ‘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 54.602 10.858  67.835
boxplotTCGA     33.870  6.511  43.406
heatmapTCGA     30.758  5.872  36.680
kmTCGA           8.036  0.429   8.705
survivalTCGA     7.127  0.335   7.464
* 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-3.4-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	33.870	6.511	43.406
checkTCGA	0.767	0.112	2.955
convertTCGA	1.642	0.301	1.945
datasetsTCGA	0.001	0.000	0.001
downloadTCGA	0.180	0.349	0.986
expressionsTCGA	54.602	10.858	67.835
heatmapTCGA	30.758	5.872	36.680
infoTCGA	1.305	0.006	2.624
installTCGA	0.000	0.001	0.000
kmTCGA	8.036	0.429	8.705
mutationsTCGA	3.070	0.253	3.331
pcaTCGA	0.001	0.001	0.001
readTCGA	0.007	0.001	0.009
survivalTCGA	7.127	0.335	7.464
theme_RTCGA	2.683	0.210	2.896