BioC 3.2: CHECK report for STATegRa on perceval

Package: STATegRa

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings STATegRa_1.4.0.tar.gz

StartedAt: 2015-11-10 09:55:48 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 10:00:45 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 297.4 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/STATegRa.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.4.0’
* 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 ... [5s/6s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  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 ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
biplotRes         7.752  0.159   7.912
plotRes           7.344  0.368   7.713
plotVAF           6.353  0.318   6.704
omicsCompAnalysis 6.315  0.314   6.628
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
  Running ‘STATegRa_Example.holistOmics.R’ [120s/120s]
  Running ‘STATEgRa_Example.omicsCLUST.R’ [36s/36s]
  Running ‘STATEgRa_Example.omicsPCA.R’ [19s/19s]
 [181s/181s] 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-3.2-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	0.298	0.016	0.314
STATegRaUsersGuide	0.001	0.000	0.001
STATegRa_data	0.377	0.037	0.414
STATegRa_data_TCGA_BRCA	0.003	0.001	0.004
bioDist	0.599	0.041	0.641
bioDistFeature	0.529	0.030	0.559
bioDistFeaturePlot	0.610	0.039	0.650
bioDistW	0.510	0.029	0.542
bioDistWPlot	0.513	0.025	0.538
bioMap	0.005	0.009	0.014
biplotRes	7.752	0.159	7.912
createOmicsExpressionSet	0.202	0.006	0.209
getInitialData	0.980	0.124	1.104
getLoadings	2.692	1.583	4.276
getMethodInfo	1.062	0.157	1.220
getPreprocessing	1.587	0.505	2.149
getScores	1.178	0.166	1.344
getVAF	1.061	0.171	1.232
holistOmics	0.004	0.001	0.004
modelSelection	0.695	0.026	0.721
omicsCompAnalysis	6.315	0.314	6.628
plotRes	7.344	0.368	7.713
plotVAF	6.353	0.318	6.704
selectCommonComps	0.850	0.026	0.877