Package: cummeRbund

Version: 2.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_2.1.0.tar.gz

StartedAt: 2013-03-25 01:59:24 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:04:51 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 327.3 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cummeRbund.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '2.1.0'
* 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 ... [31s/34s] 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 ... [32s/32s] 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 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
   'cummeRbund-example-workflow.Rnw' 
   'cummeRbund-manual.Rnw' 
** testing if installed package can be loaded
* DONE (cummeRbund)

name	user	system	elapsed
CuffData-class	0.007	0.007	0.015
CuffDist-class	0.006	0.006	0.013
CuffFeature-class	0.007	0.006	0.013
CuffFeatureSet-class	0.006	0.006	0.013
CuffGene-class	0.008	0.007	0.016
CuffGeneSet-class	0.008	0.007	0.015
CuffSet-class	0.005	0.006	0.011
JSdist	0.009	0.008	0.017
JSdistFromP	0.010	0.008	0.018
JSdistVec	0.009	0.008	0.018
MAplot	3.687	0.412	4.299
PINK1	0.023	0.007	0.030
QCplots	0.483	0.023	0.526
addFeatures	0.005	0.004	0.009
count	0.025	0.007	0.032
countMatrix	0.048	0.010	0.058
csBoxplot	0.408	0.019	0.428
csCluster	0.071	0.011	0.083
csClusterPlot	1.080	0.051	1.152
csDendro	0.034	0.009	0.043
csDensity	0.407	0.024	0.432
csDistHeat	0.334	0.013	0.350
csHeatmap	0.274	0.011	0.287
csScatter	0.404	0.025	0.433
csSpecificity	0.036	0.010	0.045
csVolcano	0.329	0.016	0.346
diffData	0.015	0.006	0.021
dimensionality	1.078	0.034	1.115
dispersionPlot	0.554	0.018	0.573
distValues	0.094	0.070	0.165
expressionBarplot	1.106	0.031	1.142
expressionPlot	1.719	0.033	1.754
featureNames	0.037	0.010	0.052
features	0.033	0.011	0.047
findGene	0.101	0.014	0.117
findSimilar	2.052	0.022	2.074
fpkm	0.020	0.007	0.028
fpkmMatrix	0.057	0.013	0.071
getFeatures	0.044	0.011	0.055
getGene	0.172	0.014	0.187
getGeneId	0.117	0.013	0.131
getGenes	0.260	0.022	0.282
getSig	0.039	0.012	0.051
getSigTable	0.055	0.013	0.069
makeprobs	0.009	0.007	0.016
makeprobsvec	0.009	0.007	0.015
readCufflinks	0.026	0.009	0.035
repFpkm	0.025	0.007	0.033
replicates	0.025	0.010	0.035
runInfo	0.030	0.012	0.042
sampleGeneSet	0.016	0.007	0.025
sampleIDs	0.020	0.010	0.029
samples	0.027	0.011	0.039
shannon.entropy	0.008	0.008	0.018
sigMatrix	0.430	0.024	0.455