Package: cummeRbund

Version: 2.1.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings cummeRbund_2.1.0.tar.gz

StartedAt: 2013-03-25 01:02:26 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:10:41 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 494.9 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/cummeRbund.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [47s/48s] OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    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 ... [50s/51s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
MAplot 5.98  0.128   6.111
* 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
  ‘/home/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	0.016	0.008	0.025
CuffDist-class	0.028	0.000	0.030
CuffFeature-class	0.016	0.000	0.016
CuffFeatureSet-class	0.024	0.000	0.023
CuffGene-class	0.016	0.000	0.016
CuffGeneSet-class	0.028	0.000	0.027
CuffSet-class	0.008	0.008	0.017
JSdist	0.020	0.012	0.030
JSdistFromP	0.024	0.000	0.023
JSdistVec	0.024	0.000	0.024
MAplot	5.980	0.128	6.111
PINK1	0.068	0.000	0.068
QCplots	0.712	0.032	0.748
addFeatures	0.024	0.008	0.034
count	0.048	0.000	0.051
countMatrix	0.084	0.004	0.090
csBoxplot	1.537	0.004	1.543
csCluster	0.096	0.008	0.103
csClusterPlot	1.608	0.020	1.631
csDendro	0.048	0.008	0.055
csDensity	0.636	0.012	0.648
csDistHeat	0.520	0.008	0.527
csHeatmap	0.420	0.004	0.424
csScatter	0.624	0.004	0.628
csSpecificity	0.056	0.000	0.058
csVolcano	0.520	0.004	0.526
diffData	0.028	0.000	0.028
dimensionality	1.252	0.012	1.276
dispersionPlot	0.744	0.012	0.755
distValues	0.116	0.032	0.150
expressionBarplot	1.380	0.008	1.389
expressionPlot	1.772	0.012	1.786
featureNames	0.028	0.008	0.035
features	0.036	0.008	0.043
findGene	0.088	0.008	0.094
findSimilar	2.068	0.008	2.088
fpkm	0.036	0.000	0.043
fpkmMatrix	0.064	0.000	0.063
getFeatures	0.076	0.004	0.080
getGene	0.156	0.008	0.213
getGeneId	0.088	0.012	0.099
getGenes	0.280	0.000	0.282
getSig	0.060	0.004	0.067
getSigTable	0.072	0.000	0.073
makeprobs	0.012	0.000	0.013
makeprobsvec	0.020	0.000	0.018
readCufflinks	0.048	0.004	0.051
repFpkm	0.044	0.000	0.044
replicates	0.036	0.000	0.040
runInfo	0.04	0.00	0.04
sampleGeneSet	0.028	0.000	0.028
sampleIDs	0.020	0.000	0.019
samples	0.032	0.004	0.037
shannon.entropy	0.016	0.000	0.013
sigMatrix	1.433	0.000	1.475