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Package 124/516HostnameOS / ArchBUILDCHECKBUILD BIN
cummeRbund 1.0.0
Loyal A. Goff
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/cummeRbund
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ 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: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch cummeRbund_1.0.0.tar.gz
StartedAt: 2012-01-09 02:22:16 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 02:23:08 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 51.5 seconds
RetCode: 0
Status:  OK  
CheckDir: cummeRbund.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/cummeRbund.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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-class000
CuffDist-class000
CuffFeature-class000
CuffFeatureSet-class000
CuffGene-class000
CuffGeneSet-class000
CuffSet-class000
JSdist000
JSdistVec000
PINK10.040.000.03
addFeatures000
csBoxplot3.840.084.36
csCluster1.640.001.64
csDensity0.920.020.94
csHeatmap0.970.000.96
csScatter0.840.000.84
csVolcano0.870.000.88
diffData000
distValues0.040.040.08
expressionBarplot1.460.001.47
expressionPlot1.860.001.85
featureNames000
features0.020.000.02
findSimilar1.560.001.56
fpkm000
fpkmMatrix0.010.000.01
getGene0.030.000.04
getGenes0.140.000.14
makeprobs000
makeprobsvec000
readCufflinks0.020.000.02
sampleGeneSet000
sampleIDs000
samples0.010.000.01
shannon.entropy000