BioC 3.5: CHECK report for STATegRa on oaxaca

Package: STATegRa

Version: 1.9.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings STATegRa_1.9.2.tar.gz

StartedAt: 2017-03-04 09:43:13 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:48:10 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 296.4 seconds

RetCode: 0

Status:  OK

CheckDir: STATegRa.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 STATegRa_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/STATegRa.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.2’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.0Mb
* 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’
Undefined global functions or variables:
  VAF block color comp comps ratio values.1 values.2
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotRes           7.484  0.309   7.805
biplotRes         7.386  0.183   7.575
plotVAF           7.041  0.308   7.357
omicsCompAnalysis 5.479  0.288   5.770
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘STATEgRa_Example.omicsCLUST.R’
  Running ‘STATEgRa_Example.omicsPCA.R’
  Running ‘STATegRa_Example.omicsNPC.R’
  Running ‘runTests.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/STATegRa.Rcheck/00check.log’
for details.

* installing *source* package ‘STATegRa’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (STATegRa)

name	user	system	elapsed
PCA.selection	0.176	0.008	0.185
STATegRaUsersGuide	0.001	0.000	0.002
STATegRa_data	0.330	0.017	0.347
STATegRa_data_TCGA_BRCA	0.002	0.001	0.003
bioDist	0.884	0.039	0.924
bioDistFeature	1.605	0.023	1.632
bioDistFeaturePlot	0.512	0.021	0.536
bioDistW	0.364	0.017	0.383
bioDistWPlot	0.394	0.021	0.416
bioMap	0.003	0.003	0.007
biplotRes	7.386	0.183	7.575
combiningMappings	0.103	0.001	0.104
createOmicsExpressionSet	0.173	0.004	0.178
getInitialData	1.304	0.176	1.481
getLoadings	2.200	1.374	3.581
getMethodInfo	0.848	0.119	0.969
getPreprocessing	1.111	0.430	1.541
getScores	0.826	0.173	0.999
getVAF	0.840	0.142	0.983
holistOmics	0.003	0.000	0.004
modelSelection	0.519	0.022	0.541
omicsCompAnalysis	5.479	0.288	5.770
omicsNPC	0.004	0.001	0.005
plotRes	7.484	0.309	7.805
plotVAF	7.041	0.308	7.357
selectCommonComps	0.957	0.019	0.977