Package: cummeRbund

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_2.0.0.tar.gz

StartedAt: 2013-03-24 23:10:59 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:16:14 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 315.3 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/cummeRbund.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '2.0.0'
* 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 whether package 'cummeRbund' can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.11-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
   'cummeRbund-example-workflow.Rnw' 
   'cummeRbund-manual.Rnw' 
** testing if installed package can be loaded

* DONE (cummeRbund)

name	user	system	elapsed
CuffData-class	0.001	0.001	0.002
CuffDist-class	0.000	0.000	0.001
CuffFeature-class	0.001	0.000	0.001
CuffFeatureSet-class	0.001	0.001	0.001
CuffGene-class	0.001	0.000	0.001
CuffGeneSet-class	0.001	0.000	0.009
CuffSet-class	0.001	0.000	0.001
JSdist	0.002	0.000	0.003
JSdistFromP	0.001	0.000	0.001
JSdistVec	0.001	0.000	0.001
MAplot	4.045	0.541	4.861
PINK1	0.012	0.003	0.020
QCplots	0.796	0.040	0.876
addFeatures	0	0	0
count	0.013	0.001	0.013
countMatrix	0.027	0.001	0.028
csBoxplot	0.400	0.014	0.419
csCluster	0.075	0.006	0.090
csClusterPlot	1.098	0.033	1.146
csDendro	0.027	0.003	0.031
csDensity	0.459	0.015	0.474
csDistHeat	0.314	0.006	0.325
csHeatmap	0.278	0.005	0.312
csScatter	0.408	0.014	0.442
csSpecificity	0.028	0.002	0.029
csVolcano	0.344	0.010	0.359
diffData	0.010	0.002	0.012
dimensionality	0.867	0.022	0.905
dispersionPlot	0.493	0.011	0.514
distValues	0.052	0.043	0.095
expressionBarplot	0.913	0.017	0.938
expressionPlot	1.213	0.021	1.265
featureNames	0.013	0.001	0.014
features	0.015	0.002	0.017
findGene	0.068	0.006	0.074
findSimilar	1.759	0.018	1.788
fpkm	0.013	0.001	0.014
fpkmMatrix	0.038	0.003	0.042
getFeatures	0.039	0.005	0.045
getGene	0.125	0.007	0.134
getGeneId	0.094	0.005	0.099
getGenes	0.249	0.020	0.273
getSig	0.030	0.006	0.037
getSigTable	0.030	0.007	0.037
makeprobs	0	0	0
makeprobsvec	0.001	0.000	0.001
readCufflinks	0.021	0.003	0.024
repFpkm	0.014	0.001	0.017
replicates	0.018	0.003	0.022
runInfo	0.018	0.002	0.021
sampleGeneSet	0.009	0.001	0.010
sampleIDs	0.009	0.001	0.010
samples	0.019	0.003	0.022
shannon.entropy	0	0	0
sigMatrix	0.401	0.012	0.417