Package: cummeRbund

Version: 1.99.2

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_1.99.2.tar.gz

StartedAt: 2012-06-20 23:12:38 -0700 (Wed, 20 Jun 2012)

EndedAt: 2012-06-20 23:14:09 -0700 (Wed, 20 Jun 2012)

EllapsedTime: 90.6 seconds

RetCode: 0

Status:  OK

CheckDir: cummeRbund.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/cummeRbund.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.99.2'
* 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 ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   3.1Mb
* 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 'condition'
.density: no visible binding for global variable 'condition'
.dispersionPlot: no visible binding for global variable 'dispersion'
.dispersionPlot: 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 sizes of PDF files under 'inst/doc' ... 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-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-example-workflow.Rnw' 
   'cummeRbund-manual.Rnw' 
** testing if installed package can be loaded

* DONE (cummeRbund)

name	user	system	elapsed
CuffData-class	0.001	0.001	0.002
CuffDist-class	0.001	0.000	0.000
CuffFeature-class	0.001	0.000	0.001
CuffFeatureSet-class	0.000	0.000	0.003
CuffGene-class	0.001	0.000	0.001
CuffGeneSet-class	0.001	0.001	0.002
CuffSet-class	0.001	0.001	0.002
JSdist	0.004	0.000	0.004
JSdistFromP	0.01	0.00	0.01
JSdistVec	0.001	0.000	0.000
MAplot	4.713	0.520	5.744
PINK1	0.047	0.005	0.053
addFeatures	0.000	0.000	0.001
count	0.018	0.001	0.018
countMatrix	0.029	0.002	0.031
csBoxplot	0.646	0.010	0.686
csCluster	0.109	0.009	0.119
csClusterPlot	1.832	0.042	1.976
csDendro	0.040	0.002	0.043
csDensity	0.637	0.017	0.664
csHeatmap	0.490	0.006	0.512
csScatter	0.490	0.011	0.513
csSpecificity	0.034	0.002	0.036
csVolcano	0.465	0.009	0.508
diffData	0.013	0.001	0.015
dispersionPlot	0.459	0.010	0.508
distValues	0.076	0.058	0.157
expressionBarplot	1.265	0.015	1.393
expressionPlot	1.354	0.012	1.392
featureNames	0.015	0.002	0.016
features	0.017	0.002	0.019
findSimilar	2.278	0.019	2.342
fpkm	0.016	0.001	0.017
fpkmMatrix	0.030	0.002	0.033
getFeatures	0.042	0.005	0.047
getGene	0.157	0.006	0.165
getGeneId	0.124	0.004	0.131
getGenes	0.298	0.019	0.316
getSig	0.030	0.004	0.036
getSigTable	0.042	0.003	0.046
makeprobs	0.001	0.000	0.001
makeprobsvec	0	0	0
readCufflinks	0.019	0.002	0.020
repFpkm	0.017	0.001	0.019
repFpkmMatrix	0.031	0.002	0.038
replicates	0.021	0.002	0.024
runInfo	0.027	0.003	0.031
sampleGeneSet	0.012	0.001	0.013
sampleIDs	0.012	0.001	0.013
samples	0.021	0.001	0.022
shannon.entropy	0	0	0