BioC 2.14: CHECK report for cummeRbund on petty

Package: cummeRbund

Version: 2.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_2.6.1.tar.gz

StartedAt: 2014-10-07 21:33:02 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:43:13 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 611.4 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_2.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/cummeRbund.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cummeRbund/DESCRIPTION’ ... OK
* this is package ‘cummeRbund’ version ‘2.6.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘RSQLite’ ‘ggplot2’ ‘reshape2’ ‘fastcluster’
  ‘rtracklayer’ ‘Gviz’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [54s/60s] OK
* checking installed package size ... NOTE
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘plyr’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘fastcluster’ ‘ggplot2’ ‘Gviz’ ‘reshape2’ ‘RSQLite’ ‘rtracklayer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.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’
.CVdensity: no visible binding for global variable ‘CV’
.CVdensity: 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’
.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’
.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’
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’
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’
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’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [49s/52s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
MAplot 7.199  0.221    7.51
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.003	0.000	0.004
CuffDist-class	0.002	0.001	0.002
CuffFeature-class	0.002	0.000	0.003
CuffFeatureSet-class	0.002	0.000	0.003
CuffGene-class	0.003	0.001	0.003
CuffGeneSet-class	0.003	0.001	0.003
CuffSet-class	0.002	0.000	0.003
JSdist	0.004	0.001	0.004
JSdistFromP	0.003	0.000	0.002
JSdistVec	0.002	0.001	0.002
MAplot	7.199	0.221	7.510
PINK1	0.015	0.001	0.016
QCplots	0.669	0.004	0.675
addFeatures	0	0	0
count	0.020	0.001	0.021
countMatrix	0.048	0.002	0.050
csBoxplot	0.639	0.004	0.645
csCluster	0.156	0.004	0.160
csClusterPlot	1.884	0.022	2.288
csDendro	0.041	0.003	0.374
csDensity	0.578	0.004	0.858
csDistHeat	0.447	0.002	0.779
csHeatmap	0.452	0.003	0.476
csScatter	0.540	0.005	0.547
csSpecificity	0.032	0.001	0.034
csVolcano	0.499	0.004	0.506
diffData	0.014	0.001	0.014
dimensionality	1.200	0.008	1.210
dispersionPlot	0.740	0.005	0.750
distValues	0.204	0.054	0.258
expressionBarplot	1.631	0.009	1.683
expressionPlot	1.672	0.017	1.726
featureNames	0.020	0.001	0.021
features	0.026	0.002	0.028
findGene	0.107	0.004	0.111
findSimilar	2.998	0.047	3.051
fpkm	0.015	0.001	0.020
fpkmMatrix	0.043	0.002	0.044
getFeatures	0.062	0.003	0.065
getGene	0.375	0.021	0.397
getGeneId	0.124	0.006	0.130
getGenes	0.517	0.028	0.547
getSig	0.044	0.003	0.047
getSigTable	0.048	0.003	0.051
makeprobs	0.001	0.000	0.002
makeprobsvec	0.001	0.001	0.001
readCufflinks	0.021	0.001	0.023
repFpkm	0.022	0.001	0.023
replicates	0.023	0.002	0.024
runInfo	0.027	0.002	0.029
sampleGeneSet	0.012	0.001	0.012
sampleIDs	0.013	0.001	0.014
samples	0.030	0.002	0.031
shannon.entropy	0.001	0.000	0.001
sigMatrix	0.589	0.006	0.598