BioC 2.14: CHECK report for AgiMicroRna on petty

Package: AgiMicroRna

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AgiMicroRna_2.14.0.tar.gz

StartedAt: 2014-10-07 20:38:50 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:53:34 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 883.1 seconds

RetCode: 0

Status:  OK

CheckDir: AgiMicroRna.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AgiMicroRna_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/AgiMicroRna.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.14.0’
* 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 ... [84s/87s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘affy’ ‘affycoretools’ ‘preprocessCore’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘affy’ ‘affycoretools’ ‘limma’ ‘methods’ ‘preprocessCore’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to 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 files in ‘vignettes’ ... OK
* checking examples ... [96s/97s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mvaMicroRna 28.340  0.218  29.129
rmaMicroRna 13.675  0.491  14.230
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	1.930	0.067	2.080
PCAplotMicroRna	0.324	0.034	0.359
RleMicroRna	2.761	0.074	2.845
basicLimma	0.003	0.000	0.004
boxplotMicroRna	1.186	0.031	1.221
cvArray	0.001	0.000	0.002
filterMicroRna	0.800	0.070	0.874
getDecideTests	0.001	0.000	0.002
hierclusMicroRna	0.022	0.009	0.032
mvaBASIC	3.076	0.107	3.204
mvaMicroRna	28.340	0.218	29.129
plotDensityMicroRna	0.371	0.028	0.440
pvalHistogram	0.001	0.000	0.001
qcPlots	0.001	0.001	0.002
readMicroRnaAFE	0.001	0.000	0.001
rmaMicroRna	13.675	0.491	14.230
significantMicroRna	1.297	0.051	1.441
tgsMicroRna	0.270	0.017	0.288
tgsNormalization	0.001	0.001	0.002
uRNAList	0.001	0.000	0.001
writeEset	0.001	0.000	0.001