BioC 2.14: CHECK report for AgiMicroRna on moscato2

Package: AgiMicroRna

Version: 2.14.0

Command: rm -rf AgiMicroRna.buildbin-libdir && mkdir AgiMicroRna.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.14.0.tar.gz >AgiMicroRna-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.14.0.tar.gz

StartedAt: 2014-10-07 22:34:46 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:46:00 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 673.8 seconds

RetCode: 0

Status:  OK

CheckDir: AgiMicroRna.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf AgiMicroRna.buildbin-libdir && mkdir AgiMicroRna.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AgiMicroRna.buildbin-libdir AgiMicroRna_2.14.0.tar.gz >AgiMicroRna-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=AgiMicroRna.buildbin-libdir --install="check:AgiMicroRna-install.out" --force-multiarch --no-vignettes --timings AgiMicroRna_2.14.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/AgiMicroRna.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'AgiMicroRna' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [55s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mvaMicroRna 15.60   0.06   15.80
rmaMicroRna  8.73   0.03    8.79
** running examples for arch 'x64' ... [56s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
mvaMicroRna 16.49   0.04   16.52
rmaMicroRna  7.78   0.01    7.80
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/AgiMicroRna.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'AgiMicroRna' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AgiMicroRna' as AgiMicroRna_2.14.0.zip
* DONE (AgiMicroRna)

name	user	system	elapsed
HeatMapMicroRna	0.86	0.01	1.28
PCAplotMicroRna	0.22	0.00	0.28
RleMicroRna	2.01	0.03	2.04
basicLimma	0	0	0
boxplotMicroRna	0.73	0.00	0.74
cvArray	0	0	0
filterMicroRna	0.53	0.07	0.59
getDecideTests	0	0	0
hierclusMicroRna	0.47	0.00	0.47
mvaBASIC	1.56	0.03	1.59
mvaMicroRna	15.60	0.06	15.80
plotDensityMicroRna	0.30	0.02	0.31
pvalHistogram	0	0	0
qcPlots	0	0	0
readMicroRnaAFE	0	0	0
rmaMicroRna	8.73	0.03	8.79
significantMicroRna	0.61	0.04	0.65
tgsMicroRna	0.18	0.00	0.18
tgsNormalization	0	0	0
uRNAList	0	0	0
writeEset	0	0	0

name	user	system	elapsed
HeatMapMicroRna	1.04	0.00	1.73
PCAplotMicroRna	0.22	0.01	0.28
RleMicroRna	1.80	0.02	1.81
basicLimma	0	0	0
boxplotMicroRna	0.73	0.03	0.76
cvArray	0	0	0
filterMicroRna	0.55	0.06	0.61
getDecideTests	0	0	0
hierclusMicroRna	0.01	0.00	0.01
mvaBASIC	2.17	0.01	2.19
mvaMicroRna	16.49	0.04	16.52
plotDensityMicroRna	0.23	0.03	0.26
pvalHistogram	0	0	0
qcPlots	0	0	0
readMicroRnaAFE	0	0	0
rmaMicroRna	7.78	0.01	7.80
significantMicroRna	1.10	0.03	1.12
tgsMicroRna	0.15	0.00	0.17
tgsNormalization	0	0	0
uRNAList	0.02	0.00	0.02
writeEset	0	0	0