Package: cummeRbund

Version: 1.2.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings cummeRbund_1.2.0.tar.gz

StartedAt: 2012-04-01 00:32:12 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 00:32:55 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 42.7 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/cummeRbund.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '1.2.0'
* 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
.MAplot: no visible binding for global variable 'A'
.MAplot: no visible binding for global variable 'M'
.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 'sample_name'
.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'
.expressionPlot: no visible binding for global variable 'quant_status'
.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 'log2_fold_change'
.volcano: no visible binding for global variable 'p_value'
.volcano: no visible binding for global variable 'significant'
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'
* 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 was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.

* installing *source* package 'cummeRbund' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'cummeRbund-manual.Rnw' 
** testing if installed package can be loaded

* DONE (cummeRbund)

name	user	system	elapsed
CuffData-class	0.000	0.000	0.001
CuffDist-class	0	0	0
CuffFeature-class	0.000	0.000	0.001
CuffFeatureSet-class	0	0	0
CuffGene-class	0.000	0.000	0.001
CuffGeneSet-class	0.000	0.000	0.001
CuffSet-class	0.000	0.000	0.001
JSdist	0.000	0.000	0.002
JSdistFromP	0.000	0.000	0.001
JSdistVec	0	0	0
MAplot	1.152	0.020	1.179
PINK1	0.020	0.000	0.025
addFeatures	0	0	0
csBoxplot	0.380	0.000	0.384
csCluster	0.044	0.008	0.071
csClusterPlot	1.052	0.012	1.115
csDendro	0.024	0.000	0.028
csDensity	0.356	0.000	0.362
csHeatmap	0.396	0.000	0.402
csScatter	0.332	0.004	0.342
csSpecificity	0.024	0.000	0.031
csVolcano	0.300	0.000	0.305
diffData	0.004	0.000	0.011
distValues	0.040	0.024	0.066
expressionBarplot	0.784	0.004	0.798
expressionPlot	0.836	0.000	0.839
featureNames	0.004	0.000	0.013
features	0.008	0.000	0.018
findSimilar	1.472	0.000	1.476
fpkm	0.004	0.000	0.014
fpkmMatrix	0.016	0.000	0.022
getGene	0.036	0.000	0.041
getGenes	0.080	0.004	0.097
getSig	0.020	0.004	0.023
getSigTable	0.028	0.000	0.033
makeprobs	0	0	0
makeprobsvec	0	0	0
readCufflinks	0.012	0.000	0.019
sampleGeneSet	0.004	0.000	0.015
sampleIDs	0.008	0.000	0.013
samples	0.020	0.000	0.025
shannon.entropy	0	0	0