Package: AgiMicroRna

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AgiMicroRna_2.8.0.tar.gz

StartedAt: 2013-03-24 22:28:25 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:35:51 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 446.2 seconds

RetCode: 0

Status:  OK

CheckDir: AgiMicroRna.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/AgiMicroRna.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'AgiMicroRna/DESCRIPTION' ... OK
* this is package 'AgiMicroRna' version '2.8.0'
* 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 'AgiMicroRna' 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 for left-over 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 ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
HeatMapMicroRna: warning in heatmap.2(DD.s, labCol = samples, labRow =
  names, scale = "none", col = rbg, margin = c(10, 10), tracecol =
  "cyan"): partial argument match of 'margin' to 'margins'
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
rmaMicroRna 100.841 76.647 180.963
mvaMicroRna  18.924  0.316  19.520
* 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/AgiMicroRna.Rcheck/00check.log'
for details.

* installing *source* package 'AgiMicroRna' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'AgiMicroRna.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (AgiMicroRna)

name	user	system	elapsed
HeatMapMicroRna	1.048	0.179	1.369
PCAplotMicroRna	0.432	0.047	0.491
RleMicroRna	2.416	0.100	2.617
basicLimma	0.000	0.001	0.000
boxplotMicroRna	0.596	0.069	0.736
cvArray	0.000	0.000	0.001
filterMicroRna	2.132	0.784	3.262
getDecideTests	0.000	0.000	0.001
hierclusMicroRna	0.015	0.004	0.019
mvaBASIC	1.625	0.100	1.987
mvaMicroRna	18.924	0.316	19.520
plotDensityMicroRna	0.328	0.046	0.383
pvalHistogram	0	0	0
qcPlots	0	0	0
readMicroRnaAFE	0	0	0
rmaMicroRna	100.841	76.647	180.963
significantMicroRna	0.743	0.241	1.008
tgsMicroRna	0.980	0.197	1.211
tgsNormalization	0	0	0
uRNAList	0	0	0
writeEset	0	0	0