Package: cummeRbund

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_1.0.0.tar.gz

StartedAt: 2012-03-24 00:33:49 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 00:35:02 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 72.4 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/cummeRbund.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 sizes of PDF files under '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

* 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)

name	user	system	elapsed
CuffData-class	0.002	0.000	0.002
CuffDist-class	0.001	0.000	0.001
CuffFeature-class	0.001	0.001	0.002
CuffFeatureSet-class	0.000	0.000	0.001
CuffGene-class	0.001	0.000	0.001
CuffGeneSet-class	0.000	0.001	0.001
CuffSet-class	0.001	0.001	0.001
JSdist	0.003	0.000	0.004
JSdistVec	0.001	0.001	0.001
PINK1	0.038	0.006	0.045
addFeatures	0.000	0.000	0.001
csBoxplot	3.972	0.404	4.603
csCluster	0.995	0.013	1.017
csDensity	0.618	0.011	0.653
csHeatmap	0.628	0.007	0.647
csScatter	0.479	0.009	0.492
csVolcano	0.426	0.008	0.446
diffData	0.012	0.001	0.013
distValues	0.067	0.051	0.163
expressionBarplot	0.965	0.011	0.983
expressionPlot	0.935	0.008	0.953
featureNames	0.010	0.001	0.011
features	0.012	0.001	0.013
findSimilar	2.150	0.020	2.193
fpkm	0.011	0.002	0.012
fpkmMatrix	0.024	0.001	0.025
getGene	0.057	0.003	0.060
getGenes	0.208	0.015	0.225
makeprobs	0.001	0.000	0.001
makeprobsvec	0	0	0
readCufflinks	0.017	0.002	0.020
sampleGeneSet	0.012	0.001	0.013
sampleIDs	0.007	0.001	0.008
samples	0.021	0.002	0.023
shannon.entropy	0	0	0