CopyNumber450k 1.8.0
Simon Papillon-Cavanagh
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/CopyNumber450k | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 CopyNumber450k_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/CopyNumber450k.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 ‘CopyNumber450k/DESCRIPTION’ ... OK
* this is package ‘CopyNumber450k’ version ‘1.8.0’
* 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 ‘CopyNumber450k’ can be installed ... WARNING
Found the following significant warnings:
Warning: multiple methods tables found for ‘plotPCA’
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/CopyNumber450k.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 ... NOTE
Warning: multiple methods tables found for ‘plotPCA’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
buildControlMatrix450k: no visible binding for global variable ‘median’
extractFromRGChannelSet450k : <anonymous>: no visible global function
definition for ‘quantile’
extractFromRGChannelSet450k: no visible global function definition for
‘seqnames’
getColoring: no visible binding for global variable ‘rainbow’
plotDensity: no visible binding for global variable ‘rainbow’
plotPCA: no visible binding for global variable ‘rainbow’
returnFit: no visible global function definition for ‘prcomp’
returnFit: no visible global function definition for ‘lm’
subgroupDifferenceCNVByType : <anonymous>: no visible global function
definition for ‘fisher.test’
getColoring,CNV450kSet: no visible binding for global variable
‘rainbow’
plotDensity,CNV450kSet: no visible binding for global variable
‘rainbow’
plotDensity,CNV450kSet: no visible global function definition for
‘plot’
plotDensity,CNV450kSet : <anonymous>: no visible global function
definition for ‘lines’
plotDensity,CNV450kSet: no visible global function definition for
‘legend’
plotPCA,CNV450kSet: no visible binding for global variable ‘rainbow’
plotPCA,CNV450kSet: no visible global function definition for ‘prcomp’
plotPCA,CNV450kSet: no visible global function definition for ‘plot’
plotPCA,CNV450kSet: no visible global function definition for ‘legend’
plotSample,CNV450kSet: no visible global function definition for ‘plot’
plotSample,CNV450kSet: no visible global function definition for ‘axis’
plotSample,CNV450kSet: no visible global function definition for
‘abline’
plotSample,CNV450kSet : <anonymous>: no visible binding for global
variable ‘median’
plotSample,CNV450kSet : <anonymous>: no visible global function
definition for ‘points’
segmentize,CNV450kSet: no visible binding for global variable ‘median’
segmentize,CNV450kSet : <anonymous> : <anonymous>: no visible global
function definition for ‘sd’
segmentize,CNV450kSet : <anonymous> : <anonymous>: no visible global
function definition for ‘pnorm’
segmentize,CNV450kSet : <anonymous>: no visible global function
definition for ‘p.adjust’
Undefined global functions or variables:
abline axis fisher.test legend lines lm median p.adjust plot pnorm
points prcomp quantile rainbow sd seqnames
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
"points")
importFrom("stats", "fisher.test", "lm", "median", "p.adjust", "pnorm",
"prcomp", "quantile", "sd")
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 sizes of PDF files under ‘inst/doc’ ... 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
CNV450kSet 46.796 4.682 57.217
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/CopyNumber450k.Rcheck/00check.log’
for details.
* installing *source* package ‘CopyNumber450k’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘plotSample’ in package ‘CopyNumber450k’
Creating a new generic function for ‘plotPCA’ in package ‘CopyNumber450k’
Creating a generic function for ‘write.csv’ from package ‘utils’ in package ‘CopyNumber450k’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for ‘plotPCA’
* DONE (CopyNumber450k)