Package: cummeRbund

Version: 1.0.0

Command: E:\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 02:44:15 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 02:45:04 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 48.7 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/cummeRbund.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-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

* 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	0.01	0.00	0.02
CuffDist-class	0	0	0
CuffFeature-class	0	0	0
CuffFeatureSet-class	0	0	0
CuffGene-class	0	0	0
CuffGeneSet-class	0	0	0
CuffSet-class	0	0	0
JSdist	0	0	0
JSdistVec	0	0	0
PINK1	0.03	0.00	0.03
addFeatures	0	0	0
csBoxplot	3.03	0.06	3.15
csCluster	1.13	0.00	1.14
csDensity	0.87	0.00	0.90
csHeatmap	0.69	0.00	0.68
csScatter	0.77	0.00	1.02
csVolcano	0.78	0.00	0.78
diffData	0	0	0
distValues	0.06	0.00	0.06
expressionBarplot	1.23	0.00	1.24
expressionPlot	1.44	0.00	1.45
featureNames	0.00	0.02	0.02
features	0	0	0
findSimilar	1.22	0.02	1.23
fpkm	0.02	0.00	0.02
fpkmMatrix	0.01	0.00	0.01
getGene	0.03	0.00	0.03
getGenes	0.13	0.00	0.13
makeprobs	0	0	0
makeprobsvec	0	0	0
readCufflinks	0	0	0
sampleGeneSet	0.01	0.00	0.02
sampleIDs	0	0	0
samples	0.02	0.00	0.01
shannon.entropy	0	0	0