Package: AgiMicroRna

Version: 2.3.1

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings AgiMicroRna_2.3.1.tar.gz

StartedAt: 2011-05-09 14:34:03 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 14:41:28 -0700 (Mon, 09 May 2011)

EllapsedTime: 444.5 seconds

RetCode: 0

Status:  OK

CheckDir: AgiMicroRna.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/AgiMicroRna.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AgiMicroRna/DESCRIPTION' ... OK
* this is package 'AgiMicroRna' version '2.3.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'AgiMicroRna' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    4.2Mb
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
* 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 'AgiMicroRna' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI

Loading required package: KEGG.db

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'AgiMicroRna.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (AgiMicroRna)

name	user	system	elapsed
HeatMapMicroRna	0.91	0.05	1.95
PCAplotMicroRna	0.21	0.00	0.62
RleMicroRna	3.02	0.00	3.03
basicLimma	0	0	0
boxplotMicroRna	0.55	0.01	0.57
cvArray	0	0	0
filterMicroRna	2.89	0.14	3.36
getDecideTests	0	0	0
hierclusMicroRna	0.03	0.00	0.03
mvaBASIC	1.93	0.00	2.11
mvaMicroRna	18.42	0.04	19.50
plotDensityMicroRna	0.48	0.00	0.49
pvalHistogram	0	0	0
qcPlots	0	0	0
readMicroRnaAFE	0	0	0
rmaMicroRna	106.63	0.12	113.06
significantMicroRna	0.97	0.11	1.36
tgsMicroRna	1.26	0.05	1.40
tgsNormalization	0	0	0
uRNAList	0	0	0
writeEset	0	0	0