BioC 2.12: CHECK report for AgiMicroRna on petty

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: 2013-10-08 21:32:14 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:44:41 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 747.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AgiMicroRna.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/AgiMicroRna.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 ... [59s/61s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-bioc/meat/AgiMicroRna.Rcheck/00install.out' for details.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [231s/233s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
rmaMicroRna 139.913 14.196 155.532
mvaMicroRna  30.454  0.265  31.736
* 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 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
Warning: package 'KEGG.db' was built under R version 3.1.0
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
* DONE (AgiMicroRna)

name	user	system	elapsed
HeatMapMicroRna	1.190	0.101	1.314
PCAplotMicroRna	0.263	0.014	0.277
RleMicroRna	3.966	0.080	4.050
basicLimma	0.026	0.008	0.034
boxplotMicroRna	1.046	0.051	1.101
cvArray	0.007	0.003	0.011
filterMicroRna	2.813	0.152	2.974
getDecideTests	0.009	0.005	0.015
hierclusMicroRna	0.028	0.013	0.042
mvaBASIC	3.056	0.107	3.208
mvaMicroRna	30.454	0.265	31.736
plotDensityMicroRna	0.400	0.047	0.494
pvalHistogram	0.006	0.003	0.010
qcPlots	0.004	0.006	0.010
readMicroRnaAFE	0.009	0.006	0.014
rmaMicroRna	139.913	14.196	155.532
significantMicroRna	1.109	0.068	1.181
tgsMicroRna	1.654	0.098	1.756
tgsNormalization	0.009	0.008	0.016
uRNAList	0.008	0.004	0.013
writeEset	0.009	0.005	0.014