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BioC 3.0: CHECK report for AgiMicroRna on perceval

This page was generated on 2015-04-10 09:54:40 -0700 (Fri, 10 Apr 2015).

Package 31/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AgiMicroRna 2.16.0
Pedro Lopez-Romero
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/AgiMicroRna
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: AgiMicroRna
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AgiMicroRna_2.16.0.tar.gz
StartedAt: 2015-04-09 22:32:59 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:45:46 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 767.3 seconds
RetCode: 0
Status:  OK 
CheckDir: AgiMicroRna.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AgiMicroRna_2.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/AgiMicroRna.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘2.16.0’
* 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 ... [70s/71s] 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.
'library' or 'require' calls in package code:
  ‘codelink’ ‘gdata’ ‘geneplotter’ ‘gplots’ ‘gtools’ ‘marray’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
* 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 chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
basicLimma: no visible global function definition for ‘lmFit’
basicLimma: no visible global function definition for ‘contrasts.fit’
basicLimma: no visible global function definition for ‘eBayes’
getDecideTests: no visible global function definition for ‘decideTests’
HeatMapMicroRna: no visible global function definition for ‘maPalette’
HeatMapMicroRna: no visible global function definition for ‘heatmap.2’
PCAplotMicroRna: no visible global function definition for ‘plotPCA’
read.agiMicroRna: no visible global function definition for
  ‘read.columns’
rmaMicroRna: no visible global function definition for
  ‘rma.background.correct’
rmaMicroRna: no visible global function definition for
  ‘normalizeBetweenArrays’
tgsNormalization: no visible global function definition for
  ‘normalizeBetweenArrays’
* 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 ... [78s/80s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mvaMicroRna 19.649  0.197  20.509
rmaMicroRna 11.691  0.402  12.118
* 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
* DONE

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/AgiMicroRna.Rcheck/00check.log’
for details.

AgiMicroRna.Rcheck/00install.out:

* installing *source* package ‘AgiMicroRna’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "colnames<-" from package "annaffy" (malformed exports?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "colnames<-" from package "annaffy" (malformed exports?)
* DONE (AgiMicroRna)

AgiMicroRna.Rcheck/AgiMicroRna-Ex.timings:

nameusersystemelapsed
HeatMapMicroRna1.7540.1072.380
PCAplotMicroRna0.1650.0070.177
RleMicroRna2.4030.0842.498
basicLimma0.0020.0010.002
boxplotMicroRna1.2410.0271.289
cvArray0.0010.0000.001
filterMicroRna0.5220.0660.647
getDecideTests000
hierclusMicroRna0.0160.0100.031
mvaBASIC2.7880.0813.010
mvaMicroRna19.649 0.19720.509
plotDensityMicroRna0.2900.0260.440
pvalHistogram0.0010.0010.001
qcPlots0.0010.0000.002
readMicroRnaAFE0.0010.0000.001
rmaMicroRna11.691 0.40212.118
significantMicroRna0.9770.0571.197
tgsMicroRna0.1800.0180.199
tgsNormalization0.0010.0000.001
uRNAList0.0010.0010.001
writeEset0.0010.0000.000