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: 2013-05-01 04:16:16 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 04:23:02 -0700 (Wed, 01 May 2013)

EllapsedTime: 405.3 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cummeRbund.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* 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 ... [37s/40s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [39s/41s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
MAplot 5.585  0.273   6.425
* 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-2.12-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	0.434	0.004	0.439
CuffDist-class	0.009	0.004	0.012
CuffFeature-class	0.008	0.003	0.012
CuffFeatureSet-class	0.007	0.004	0.012
CuffGene-class	0.011	0.004	0.015
CuffGeneSet-class	0.008	0.003	0.012
CuffSet-class	0.013	0.003	0.017
JSdist	0.010	0.003	0.013
JSdistFromP	0.013	0.006	0.019
JSdistVec	0.008	0.003	0.010
MAplot	5.585	0.273	6.425
PINK1	0.033	0.004	0.049
QCplots	0.603	0.014	0.829
addFeatures	0.481	0.007	0.537
count	0.022	0.005	0.027
countMatrix	0.041	0.006	0.047
csBoxplot	0.525	0.025	0.565
csCluster	0.090	0.008	0.116
csClusterPlot	1.374	0.043	1.456
csDendro	0.040	0.005	0.046
csDensity	0.497	0.016	0.520
csDistHeat	0.432	0.011	0.447
csHeatmap	0.357	0.009	0.370
csScatter	0.514	0.014	0.533
csSpecificity	0.040	0.006	0.045
csVolcano	0.457	0.010	0.474
diffData	0.024	0.004	0.028
dimensionality	1.107	0.019	1.142
dispersionPlot	0.654	0.011	0.683
distValues	0.088	0.063	0.153
expressionBarplot	1.170	0.018	1.208
expressionPlot	1.973	0.029	2.051
featureNames	0.021	0.005	0.025
features	0.025	0.005	0.030
findGene	0.141	0.006	0.148
findSimilar	2.796	0.058	2.898
fpkm	0.021	0.005	0.026
fpkmMatrix	0.045	0.006	0.052
getFeatures	0.067	0.006	0.085
getGene	0.488	0.020	0.508
getGeneId	0.185	0.008	0.192
getGenes	0.674	0.027	0.707
getSig	0.045	0.006	0.053
getSigTable	0.048	0.006	0.055
makeprobs	0.008	0.003	0.011
makeprobsvec	0.017	0.004	0.022
readCufflinks	0.025	0.003	0.029
repFpkm	0.023	0.004	0.029
replicates	0.028	0.005	0.034
runInfo	0.032	0.005	0.039
sampleGeneSet	0.020	0.004	0.025
sampleIDs	0.021	0.005	0.026
samples	0.028	0.004	0.033
shannon.entropy	0.015	0.004	0.019
sigMatrix	0.535	0.012	0.554