Package: cummeRbund

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cummeRbund_1.2.0.tar.gz

StartedAt: 2012-09-23 23:52:08 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:53:17 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 69.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cummeRbund.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/cummeRbund.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.2.0'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_blank' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_line' is deprecated.
  Warning: 'theme_line' is deprecated.
  Warning: 'theme_rect' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
  Warning: 'opts' is deprecated.
  Warning: 'theme_text' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/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	0.001	0.000	0.001
CuffDist-class	0.000	0.001	0.001
CuffFeature-class	0.001	0.000	0.001
CuffFeatureSet-class	0.000	0.000	0.001
CuffGene-class	0	0	0
CuffGeneSet-class	0.000	0.000	0.001
CuffSet-class	0.001	0.000	0.001
JSdist	0.003	0.000	0.003
JSdistFromP	0.001	0.000	0.001
JSdistVec	0	0	0
MAplot	1.855	0.199	2.167
PINK1	0.039	0.006	0.045
addFeatures	0	0	0
csBoxplot	0.678	0.008	0.687
csCluster	0.099	0.014	0.114
csClusterPlot	1.378	0.044	1.479
csDendro	0.027	0.002	0.029
csDensity	0.458	0.010	0.469
csHeatmap	0.300	0.004	0.304
csScatter	0.501	0.009	0.511
csSpecificity	0.022	0.001	0.022
csVolcano	0.426	0.007	0.433
diffData	0.008	0.001	0.008
distValues	0.080	0.054	0.133
expressionBarplot	0.843	0.008	0.852
expressionPlot	0.959	0.007	0.966
featureNames	0.007	0.001	0.008
features	0.008	0.001	0.010
findSimilar	1.581	0.008	1.590
fpkm	0.007	0.001	0.008
fpkmMatrix	0.016	0.001	0.016
getGene	0.043	0.003	0.046
getGenes	0.103	0.009	0.112
getSig	0.027	0.003	0.030
getSigTable	0.029	0.003	0.032
makeprobs	0.001	0.000	0.001
makeprobsvec	0.000	0.001	0.000
readCufflinks	0.013	0.002	0.015
sampleGeneSet	0.004	0.001	0.005
sampleIDs	0.004	0.000	0.005
samples	0.016	0.002	0.019
shannon.entropy	0.001	0.001	0.001