Package: AgiMicroRna

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AgiMicroRna_2.10.0.tar.gz

StartedAt: 2013-05-01 02:08:05 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 02:19:50 -0700 (Wed, 01 May 2013)

EllapsedTime: 704.5 seconds

RetCode: 0

Status:  OK

CheckDir: AgiMicroRna.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/AgiMicroRna.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'AgiMicroRna/DESCRIPTION' ... OK
* this is package 'AgiMicroRna' version '2.10.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'AgiMicroRna' can be installed ... [51s/53s] OK
* checking installed package size ... OK
* checking package directory ... 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 installed files from 'inst/doc' ... OK
* checking examples ... [227s/230s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
rmaMicroRna 158.679  3.875 164.583
mvaMicroRna  23.411  0.203  23.781
* 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-2.12-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
** testing if installed package can be loaded
* DONE (AgiMicroRna)

name	user	system	elapsed
HeatMapMicroRna	1.021	0.094	1.150
PCAplotMicroRna	0.218	0.016	0.235
RleMicroRna	3.659	0.089	3.754
basicLimma	0.025	0.009	0.035
boxplotMicroRna	0.975	0.050	1.029
cvArray	0.007	0.005	0.012
filterMicroRna	2.459	0.144	2.627
getDecideTests	0.008	0.004	0.013
hierclusMicroRna	0.026	0.013	0.041
mvaBASIC	2.564	0.113	2.749
mvaMicroRna	23.411	0.203	23.781
plotDensityMicroRna	0.958	0.045	1.030
pvalHistogram	0.002	0.005	0.007
qcPlots	0.003	0.007	0.011
readMicroRnaAFE	0.002	0.004	0.007
rmaMicroRna	158.679	3.875	164.583
significantMicroRna	0.890	0.071	0.989
tgsMicroRna	0.975	0.107	1.100
tgsNormalization	0.003	0.005	0.007
uRNAList	0.002	0.003	0.005
writeEset	0.009	0.006	0.014