BioC 2.13: CHECK report for cummeRbund on perceval

Package: cummeRbund

Version: 2.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_2.4.1.tar.gz

StartedAt: 2014-04-05 00:38:47 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:45:37 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 410.1 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/cummeRbund.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.4.1’
* 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 ... [38s/39s] 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 ‘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’ ... 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 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 ... [36s/37s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
MAplot 5.446  0.199    5.69
* 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 7 notes.
See
  ‘/Users/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	0.018	0.003	0.022
CuffDist-class	0.009	0.003	0.014
CuffFeature-class	0.009	0.003	0.012
CuffFeatureSet-class	0.009	0.004	0.014
CuffGene-class	0.008	0.002	0.011
CuffGeneSet-class	0.010	0.004	0.014
CuffSet-class	0.010	0.001	0.011
JSdist	0.010	0.002	0.014
JSdistFromP	0.013	0.005	0.017
JSdistVec	0.007	0.003	0.009
MAplot	5.446	0.199	5.690
PINK1	0.018	0.003	0.021
QCplots	0.522	0.039	0.563
addFeatures	0.011	0.001	0.013
count	0.038	0.003	0.042
countMatrix	0.054	0.004	0.058
csBoxplot	0.511	0.010	1.337
csCluster	0.101	0.006	0.107
csClusterPlot	1.292	0.029	1.328
csDendro	0.038	0.003	0.041
csDensity	0.890	0.012	0.904
csDistHeat	0.311	0.006	0.317
csHeatmap	0.266	0.006	0.272
csScatter	0.411	0.010	0.422
csSpecificity	0.038	0.003	0.041
csVolcano	0.300	0.005	0.307
diffData	0.022	0.005	0.026
dimensionality	0.901	0.014	0.918
dispersionPlot	0.495	0.009	0.505
distValues	0.148	0.050	0.198
expressionBarplot	0.912	0.010	0.924
expressionPlot	1.115	0.010	1.129
featureNames	0.022	0.003	0.025
features	0.024	0.005	0.029
findGene	0.067	0.006	0.072
findSimilar	1.759	0.040	1.808
fpkm	0.017	0.003	0.020
fpkmMatrix	0.038	0.005	0.043
getFeatures	0.036	0.005	0.040
getGene	0.221	0.015	0.235
getGeneId	0.091	0.006	0.097
getGenes	0.304	0.019	0.324
getSig	0.029	0.004	0.034
getSigTable	0.033	0.005	0.038
makeprobs	0.007	0.002	0.010
makeprobsvec	0.006	0.003	0.009
readCufflinks	0.021	0.004	0.025
repFpkm	0.020	0.004	0.024
replicates	0.023	0.005	0.028
runInfo	0.023	0.004	0.027
sampleGeneSet	0.014	0.003	0.016
sampleIDs	0.014	0.003	0.017
samples	0.023	0.004	0.027
shannon.entropy	0.006	0.002	0.009
sigMatrix	0.369	0.010	0.380