STATegRa 1.0.0
David Gomez-Cabrero , Patricia Sebastián-León , Gordon Ball
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/STATegRa | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | 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 --no-multiarch STATegRa_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/STATegRa.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STATegRa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STATegRa’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘STATegRa’ can be installed ... [6s/9s] OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 2.4Mb
doc 2.7Mb
* 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
biplotRes,caClass-character-numeric-character: no visible binding for
global variable ‘values.1’
biplotRes,caClass-character-numeric-character: no visible binding for
global variable ‘values.2’
biplotRes,caClass-character-numeric-character: no visible binding for
global variable ‘color’
plotVAF,caClass: no visible binding for global variable ‘comp’
plotVAF,caClass: no visible binding for global variable ‘VAF’
plotVAF,caClass: no visible binding for global variable ‘block’
selectCommonComps,matrix-matrix-numeric: no visible binding for global
variable ‘comps’
selectCommonComps,matrix-matrix-numeric: no visible binding for global
variable ‘block’
selectCommonComps,matrix-matrix-numeric: no visible binding for global
variable ‘comp’
selectCommonComps,matrix-matrix-numeric: no visible binding for global
variable ‘ratio’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/66s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
STATegRa_plotRes 7.737 0.532 8.303
STATegRa_biplotRes 7.660 0.443 8.122
STATegRa_caClass 7.281 0.413 7.702
STATegRa_plotVAF 7.230 0.429 7.678
STATegRa_omicsCompAnalysis 6.557 0.569 7.126
STATegRa_loadings 3.218 2.249 5.962
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [7s/7s]
Running ‘STATEgRa_Example.omicsCLUST.R’ [50s/50s]
Running ‘STATEgRa_Example.omicsPCA.R’ [23s/23s]
[80s/80s] 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
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/STATegRa.Rcheck/00check.log’
for details.