RTCGA 1.5.0
Marcin Kosinski
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RTCGA | | Last Changed Rev: 128787 / Revision: 129046 | | Last Changed Date: 2017-04-17 15:24:16 -0400 (Mon, 17 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RTCGA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.5.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘ggplot2::%+%’ by ‘survminer::%+%’ when loading ‘RTCGA’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/RTCGA.Rcheck/00install.out’ for details.
* 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 66.158 11.494 77.852
boxplotTCGA 45.010 7.273 52.437
heatmapTCGA 37.111 6.460 43.657
kmTCGA 13.570 0.407 14.056
survivalTCGA 12.395 0.285 12.706
mutationsTCGA 5.304 0.208 5.522
theme_RTCGA 4.921 0.236 5.163
* 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 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/RTCGA.Rcheck/00check.log’
for details.
* installing *source* package ‘RTCGA’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::%+%’ by ‘survminer::%+%’ when loading ‘RTCGA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::%+%’ by ‘survminer::%+%’ when loading ‘RTCGA’
* DONE (RTCGA)