BioC 2.12: CHECK report for cummeRbund on petty

Package: cummeRbund

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_2.2.0.tar.gz

StartedAt: 2013-10-08 22:06:18 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:13:55 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 457.5 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cummeRbund.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '2.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.RData
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'cummeRbund' can be installed ... [41s/42s] OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   5.6Mb
* checking package 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 for unstated 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
.CVdensity: no visible binding for global variable 'CV'
.CVdensity: no visible binding for global variable 'sample_name'
.MAplot: no visible binding for global variable 'A'
.MAplot: no visible binding for global variable 'M'
.MDSplot: no visible binding for global variable 'M1'
.MDSplot: no visible binding for global variable 'M2'
.PCAplot: no visible binding for global variable 'obsnames'
.PCAplot: no visible binding for global variable 'v1'
.PCAplot: no visible binding for global variable 'v2'
.PCAplot: no visible binding for global variable 'varnames'
.barplot: no visible binding for global variable 'sample_name'
.barplot: no visible binding for global variable 'conf_lo'
.barplot: no visible binding for global variable 'conf_hi'
.barplot: no visible binding for global variable 'quant_status'
.boxplot: no visible binding for global variable 'condition'
.confidencePlot: no visible binding for global variable 'CV'
.confidencePlot: no visible binding for global variable 'sample_name'
.density: no visible binding for global variable 'condition'
.dispersionPlot: no visible binding for global variable 'dispersion'
.dispersionPlot: no visible binding for global variable 'sample_name'
.distheat: no visible binding for global variable 'X1'
.distheat: no visible binding for global variable 'X2'
.distheat: no visible binding for global variable 'value'
.expressionPlot: no visible binding for global variable 'sample_name'
.expressionPlot: no visible binding for global variable 'tracking_id'
.expressionPlot: no visible binding for global variable 'conf_lo'
.expressionPlot: no visible binding for global variable 'conf_hi'
.expressionPlot: no visible binding for global variable 'quant_status'
.fpkmSCVPlot: no visible binding for global variable 'stdev'
.fpkmSCVPlot: no visible binding for global variable 'sample_name'
.ggheat: no visible binding for global variable 'colInd'
.ggheat: no visible binding for global variable 'rowInd'
.ggheat: no visible binding for global variable 'value'
.heatmap: no visible binding for global variable 'tracking_id'
.heatmap: no visible binding for global variable 'sample_name'
.plotmatrix: no visible binding for global variable 'x'
.plotmatrix: no visible binding for global variable 'y'
.plotmatrix: no visible binding for global variable '..scaled..'
.sigMatrix: no visible binding for global variable 'sample_1'
.sigMatrix: no visible binding for global variable 'sample_2'
.sigMatrix: no visible binding for global variable '..n..'
.volcano: no visible binding for global variable 'log2_fold_change'
.volcano: no visible binding for global variable 'p_value'
.volcano: no visible binding for global variable 'significant'
.volcanoMatrix: no visible binding for global variable 'label'
csClusterPlot: no visible binding for global variable 'variable'
csClusterPlot: no visible binding for global variable 'value'
csClusterPlot: no visible binding for global variable 'cluster'
csClusterPlot: no visible binding for global variable 'ids'
PCAplot,CuffData: no visible binding for global variable 'obsnames'
PCAplot,CuffData: no visible binding for global variable 'v1'
PCAplot,CuffData: no visible binding for global variable 'v2'
PCAplot,CuffData: no visible binding for global variable 'varnames'
csDistHeat,CuffData: no visible binding for global variable 'X1'
csDistHeat,CuffData: no visible binding for global variable 'X2'
csDistHeat,CuffData: no visible binding for global variable 'value'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X1'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X2'
csDistHeat,CuffFeatureSet: no visible binding for global variable
  'value'
dispersionPlot,CuffData: no visible binding for global variable
  'dispersion'
dispersionPlot,CuffData: no visible binding for global variable
  'sample_name'
sigMatrix,CuffSet: no visible binding for global variable 'sample_1'
sigMatrix,CuffSet: no visible binding for global variable 'sample_2'
sigMatrix,CuffSet: no visible binding for global variable '..n..'
* 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' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'cuffData_schema.pdf' from 703Kb to 546Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [47s/48s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
MAplot 6.195  0.271    6.71
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.

* installing *source* package 'cummeRbund' ...
** 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 (cummeRbund)

name	user	system	elapsed
CuffData-class	0.474	0.005	0.481
CuffDist-class	0.007	0.003	0.011
CuffFeature-class	0.008	0.003	0.011
CuffFeatureSet-class	0.007	0.002	0.010
CuffGene-class	0.008	0.003	0.011
CuffGeneSet-class	0.012	0.003	0.016
CuffSet-class	0.008	0.003	0.011
JSdist	0.011	0.005	0.015
JSdistFromP	0.015	0.004	0.019
JSdistVec	0.015	0.005	0.022
MAplot	6.195	0.271	6.710
PINK1	0.022	0.005	0.027
QCplots	0.769	0.030	0.803
addFeatures	0.007	0.003	0.011
count	0.027	0.004	0.030
countMatrix	0.060	0.007	0.067
csBoxplot	0.737	0.008	0.778
csCluster	0.109	0.005	0.116
csClusterPlot	2.014	0.045	2.078
csDendro	0.050	0.005	0.056
csDensity	0.740	0.022	0.763
csDistHeat	0.600	0.009	0.612
csHeatmap	0.489	0.007	0.501
csScatter	0.685	0.012	0.700
csSpecificity	0.052	0.003	0.054
csVolcano	0.580	0.008	0.599
diffData	0.029	0.003	0.033
dimensionality	1.959	0.024	2.091
dispersionPlot	0.815	0.009	0.844
distValues	0.083	0.051	0.135
expressionBarplot	1.484	0.012	1.504
expressionPlot	1.954	0.018	1.998
featureNames	0.026	0.003	0.030
features	0.032	0.005	0.037
findGene	0.116	0.007	0.123
findSimilar	3.242	0.042	3.357
fpkm	0.041	0.002	0.042
fpkmMatrix	0.052	0.006	0.057
getFeatures	0.073	0.007	0.078
getGene	0.409	0.020	0.429
getGeneId	0.146	0.006	0.153
getGenes	0.569	0.031	0.600
getSig	0.051	0.004	0.055
getSigTable	0.064	0.004	0.069
makeprobs	0.009	0.003	0.012
makeprobsvec	0.008	0.002	0.011
readCufflinks	0.033	0.005	0.038
repFpkm	0.031	0.003	0.034
replicates	0.039	0.005	0.044
runInfo	0.043	0.004	0.048
sampleGeneSet	0.020	0.002	0.023
sampleIDs	0.020	0.003	0.024
samples	0.039	0.003	0.043
shannon.entropy	0.552	0.005	0.564
sigMatrix	0.677	0.014	0.695