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Package 148/609HostnameOS / ArchBUILDCHECKBUILD BIN
cummeRbund 2.0.0
Loyal A. Goff
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/cummeRbund
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: cummeRbund
Version: 2.0.0
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings cummeRbund_2.0.0.tar.gz
StartedAt: 2013-03-25 00:30:33 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 00:36:09 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 336.7 seconds
RetCode: 0
Status:  OK 
CheckDir: cummeRbund.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/cummeRbund.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.0.0’
* 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 whether package ‘cummeRbund’ can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/cummeRbund.Rcheck/00check.log’
for details.

cummeRbund.Rcheck/00install.out:

* 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)

cummeRbund.Rcheck/cummeRbund-Ex.timings:

nameusersystemelapsed
CuffData-class0.0000.0000.001
CuffDist-class0.0040.0000.000
CuffFeature-class0.0000.0000.001
CuffFeatureSet-class0.0000.0000.001
CuffGene-class000
CuffGeneSet-class0.0000.0000.001
CuffSet-class000
JSdist0.0000.0000.002
JSdistFromP0.0040.0000.001
JSdistVec000
MAplot4.3250.0924.600
PINK10.0080.0000.011
QCplots0.4480.0040.630
addFeatures000
count0.0120.0000.013
countMatrix0.0320.0000.036
csBoxplot0.8640.0080.876
csCluster0.0680.0000.080
csClusterPlot1.2520.0281.284
csDendro0.0240.0000.026
csDensity0.5200.0080.526
csDistHeat0.4160.0000.422
csHeatmap0.3360.0000.354
csScatter0.3880.0040.400
csSpecificity0.0160.0040.118
csVolcano0.30.00.3
diffData0.0040.0040.020
dimensionality0.7480.0000.756
dispersionPlot0.4480.0000.486
distValues0.0760.0200.116
expressionBarplot1.1080.0001.122
expressionPlot1.3880.0041.394
featureNames0.0080.0000.023
features0.0120.0040.012
findGene0.0520.0000.109
findSimilar1.9720.0042.090
fpkm0.0120.0000.023
fpkmMatrix0.0240.0000.037
getFeatures0.0400.0040.105
getGene0.0920.0040.150
getGeneId0.0640.0000.064
getGenes0.1600.0000.158
getSig0.0240.0000.023
getSigTable0.0240.0000.024
makeprobs000
makeprobsvec000
readCufflinks0.0120.0000.014
repFpkm0.0120.0000.012
replicates0.0160.0000.016
runInfo0.0280.0000.031
sampleGeneSet0.0040.0000.007
sampleIDs0.0040.0000.007
samples0.0120.0040.019
shannon.entropy000
sigMatrix0.3600.0080.368