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BioC 2.14: CHECK report for AgiMicroRna on petty

This page was generated on 2014-10-08 08:58:49 -0700 (Wed, 08 Oct 2014).

Package 31/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.14.0
Pedro Lopez-Romero
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/AgiMicroRna
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.

AgiMicroRna.Rcheck/00install.out:

* 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)

AgiMicroRna.Rcheck/AgiMicroRna-Ex.timings:

nameusersystemelapsed
HeatMapMicroRna1.9300.0672.080
PCAplotMicroRna0.3240.0340.359
RleMicroRna2.7610.0742.845
basicLimma0.0030.0000.004
boxplotMicroRna1.1860.0311.221
cvArray0.0010.0000.002
filterMicroRna0.8000.0700.874
getDecideTests0.0010.0000.002
hierclusMicroRna0.0220.0090.032
mvaBASIC3.0760.1073.204
mvaMicroRna28.340 0.21829.129
plotDensityMicroRna0.3710.0280.440
pvalHistogram0.0010.0000.001
qcPlots0.0010.0010.002
readMicroRnaAFE0.0010.0000.001
rmaMicroRna13.675 0.49114.230
significantMicroRna1.2970.0511.441
tgsMicroRna0.2700.0170.288
tgsNormalization0.0010.0010.002
uRNAList0.0010.0000.001
writeEset0.0010.0000.001