BioC 2.13: CHECK report for AgiMicroRna on zin1

Package: AgiMicroRna

Version: 2.12.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings AgiMicroRna_2.12.0.tar.gz

StartedAt: 2014-04-04 23:25:19 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:32:21 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 421.2 seconds

RetCode: 0

Status:  OK

CheckDir: AgiMicroRna.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/AgiMicroRna.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AgiMicroRna/DESCRIPTION’ ... OK
* this is package ‘AgiMicroRna’ version ‘2.12.0’
* 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 ... [37s/37s] 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 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘AgiMicroRna.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [97s/97s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
rmaMicroRna 58.891  0.012  59.025
mvaMicroRna 12.597  0.032  12.685
* 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 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	0.456	0.084	0.550
PCAplotMicroRna	0.544	0.040	0.583
RleMicroRna	1.440	0.020	1.462
basicLimma	0.008	0.000	0.008
boxplotMicroRna	0.640	0.004	0.645
cvArray	0.004	0.000	0.004
filterMicroRna	1.644	0.012	1.659
getDecideTests	0.004	0.000	0.004
hierclusMicroRna	0.012	0.004	0.015
mvaBASIC	1.228	0.032	1.263
mvaMicroRna	12.597	0.032	12.685
plotDensityMicroRna	0.236	0.000	0.239
pvalHistogram	0.000	0.000	0.001
qcPlots	0.000	0.004	0.003
readMicroRnaAFE	0.000	0.000	0.004
rmaMicroRna	58.891	0.012	59.025
significantMicroRna	1.044	0.004	1.051
tgsMicroRna	0.201	0.008	0.209
tgsNormalization	0.004	0.000	0.005
uRNAList	0.000	0.000	0.001
writeEset	0.004	0.000	0.004