SigCheck 2.3.5
Rory Stark
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SigCheck | | Last Changed Rev: 114644 / Revision: 116626 | | Last Changed Date: 2016-03-11 09:32:18 -0800 (Fri, 11 Mar 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SigCheck_2.3.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SigCheck.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SigCheck/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SigCheck’ version ‘2.3.5’
* 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 ‘SigCheck’ can be installed ... [13s/14s] WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/SigCheck.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 loading without being on the library search path ... 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
.sigCheckClassifierSurvival: no visible binding for global variable
‘median’
.sigCheckPCA1: no visible global function definition for ‘prcomp’
.sigCheckPlotClassifierKM: no visible global function definition for
‘quantile’
.sigCheckPlotKM: no visible global function definition for ‘pchisq’
.sigCheckPlotKM: no visible global function definition for ‘plot’
.sigCheckPlotKM: no visible global function definition for ‘text’
.sigCheckSurvivalCategories: no visible global function definition for
‘quantile’
sigCheck: no visible binding for global variable ‘median’
sigCheckKnown: no visible binding for global variable ‘knownSignatures’
sigCheckPlotClassifier: no visible global function definition for
‘plot’
sigCheckPlotClassifier: no visible global function definition for
‘density’
sigCheckPlotSurvival: no visible global function definition for ‘plot’
sigCheckPlotSurvival: no visible global function definition for
‘density’
Undefined global functions or variables:
density knownSignatures median pchisq plot prcomp quantile text
Consider adding
importFrom("graphics", "plot", "text")
importFrom("stats", "density", "median", "pchisq", "prcomp",
"quantile")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [270s/272s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
sigCheckAll 125.177 13.614 138.944
sigCheckKnown 55.848 6.255 63.019
sigCheckPermuted 15.546 1.318 16.899
sigCheck 15.443 1.184 16.789
sigCheckPlot 14.707 1.319 16.048
sigCheckRandom 11.172 0.935 12.119
* 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-3.3-bioc/meat/SigCheck.Rcheck/00check.log’
for details.
* installing *source* package ‘SigCheck’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Creating a new generic function for ‘signature’ in package ‘SigCheck’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (SigCheck)