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Package 124/514HostnameOS / ArchBUILDCHECKBUILD BIN
cummeRbund 1.0.0
Loyal A. Goff
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/cummeRbund
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: cummeRbund
Version: 1.0.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings cummeRbund_1.0.0.tar.gz
StartedAt: 2012-03-24 00:01:20 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:02:06 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 46.4 seconds
RetCode: 0
Status:  OK 
CheckDir: cummeRbund.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/cummeRbund.Rcheck’
* using R version 2.14.2 (2012-02-29)
* 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 ‘1.0.0’
* 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 ... OK
* 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 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
.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’
.boxplot: no visible binding for global variable ‘sample_name’
.cluster: no visible binding for global variable ‘variable’
.cluster: no visible binding for global variable ‘value’
.cluster: no visible binding for global variable ‘cluster’
.cluster: no visible binding for global variable ‘ids’
.density: no visible binding for global variable ‘sample_name’
.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’
.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’
.volcano: no visible binding for global variable ‘ln_fold_change’
.volcano: no visible binding for global variable ‘p_value’
.volcano: no visible binding for global variable ‘significant’
loadIsoforms: no visible global function definition for ‘sys.stderr’
* 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 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

cummeRbund.Rcheck/00install.out:

* installing *source* package ‘cummeRbund’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘cummeRbund-manual.Rnw’ 
** testing if installed package can be loaded

* DONE (cummeRbund)

cummeRbund.Rcheck/cummeRbund-Ex.timings:

nameusersystemelapsed
CuffData-class0.0000.0000.001
CuffDist-class0.0000.0000.001
CuffFeature-class0.0000.0000.001
CuffFeatureSet-class0.0000.0000.001
CuffGene-class000
CuffGeneSet-class0.0000.0000.001
CuffSet-class0.0000.0000.001
JSdist0.0040.0000.002
JSdistVec000
PINK10.0240.0000.022
addFeatures000
csBoxplot3.4760.0563.531
csCluster0.8640.0000.863
csDensity0.6480.0080.655
csHeatmap0.3600.0000.363
csScatter0.4880.0040.492
csVolcano0.3240.0000.324
diffData0.0080.0000.005
distValues0.0680.0240.093
expressionBarplot0.7720.0000.774
expressionPlot0.7840.0040.787
featureNames0.0080.0000.007
features0.0040.0040.009
findSimilar1.6320.0001.633
fpkm0.0040.0000.007
fpkmMatrix0.0200.0000.019
getGene0.0400.0040.041
getGenes0.1240.0120.148
makeprobs0.0000.0000.001
makeprobsvec000
readCufflinks0.0040.0120.019
sampleGeneSet0.0000.0080.005
sampleIDs0.0040.0000.005
samples0.0160.0080.023
shannon.entropy000