BioC 2.13: CHECK report for cummeRbund on zin1

Package: cummeRbund

Version: 2.4.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings cummeRbund_2.4.1.tar.gz

StartedAt: 2014-04-05 00:34:55 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:38:42 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 227.4 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/cummeRbund.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.4.1’
* 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 ... [22s/22s] 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 ‘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:
  ‘Gviz’ ‘RSQLite’ ‘fastcluster’ ‘ggplot2’ ‘reshape2’ ‘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
.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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘cummeRbund-example-workflow.Rnw’, ‘cummeRbund-manual.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [21s/21s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 6 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.232	0.004	0.240
CuffDist-class	0.004	0.000	0.004
CuffFeature-class	0.004	0.000	0.002
CuffFeatureSet-class	0.000	0.000	0.003
CuffGene-class	0.004	0.000	0.003
CuffGeneSet-class	0.004	0.000	0.002
CuffSet-class	0.000	0.000	0.002
JSdist	0.004	0.000	0.005
JSdistFromP	0.004	0.000	0.005
JSdistVec	0.004	0.000	0.005
MAplot	2.692	0.032	2.739
PINK1	0.008	0.000	0.010
QCplots	0.348	0.000	0.348
addFeatures	0.004	0.000	0.006
count	0.020	0.000	0.021
countMatrix	0.028	0.000	0.029
csBoxplot	0.324	0.004	0.330
csCluster	0.048	0.004	0.051
csClusterPlot	0.832	0.016	0.849
csDendro	0.032	0.000	0.032
csDensity	0.584	0.004	0.590
csDistHeat	0.256	0.004	0.258
csHeatmap	0.204	0.004	0.210
csScatter	0.284	0.004	0.287
csSpecificity	0.020	0.000	0.019
csVolcano	0.244	0.004	0.249
diffData	0.008	0.000	0.008
dimensionality	0.649	0.000	0.646
dispersionPlot	0.356	0.000	0.360
distValues	0.060	0.016	0.076
expressionBarplot	0.656	0.008	0.669
expressionPlot	0.840	0.000	0.841
featureNames	0.016	0.000	0.014
features	0.016	0.000	0.015
findGene	0.048	0.004	0.049
findSimilar	1.408	0.004	1.416
fpkm	0.016	0.000	0.016
fpkmMatrix	0.028	0.000	0.028
getFeatures	0.028	0.000	0.028
getGene	0.16	0.00	0.16
getGeneId	0.064	0.000	0.060
getGenes	0.224	0.004	0.227
getSig	0.028	0.000	0.025
getSigTable	0.028	0.000	0.024
makeprobs	0.004	0.000	0.006
makeprobsvec	0.004	0.000	0.003
readCufflinks	0.012	0.000	0.013
repFpkm	0.012	0.000	0.012
replicates	0.008	0.004	0.016
runInfo	0.016	0.000	0.015
sampleGeneSet	0.004	0.000	0.006
sampleIDs	0.008	0.000	0.008
samples	0.016	0.000	0.015
shannon.entropy	0.004	0.000	0.003
sigMatrix	0.288	0.004	0.292