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BioC 3.0: CHECK report for affycoretools on perceval

This page was generated on 2015-04-10 09:52:47 -0700 (Fri, 10 Apr 2015).

Package 18/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycoretools 1.38.0
James W. MacDonald
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/affycoretools
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  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: affycoretools
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affycoretools_1.38.0.tar.gz
StartedAt: 2015-04-09 22:27:04 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:39:32 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 747.6 seconds
RetCode: 0
Status:  OK 
CheckDir: affycoretools.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 affycoretools_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/affycoretools.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 ‘affycoretools/DESCRIPTION’ ... OK
* this is package ‘affycoretools’ version ‘1.38.0’
* 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 ‘affycoretools’ can be installed ... [75s/91s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gsHeatmap: no visible binding for global variable ‘nam’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [55s/55s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
plotDeg 18.411  0.259  18.698
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘hgu95av2.db’
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/affycoretools.Rcheck/00check.log’
for details.

affycoretools.Rcheck/00install.out:

* installing *source* package ‘affycoretools’ ...
** R
** 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 (affycoretools)

affycoretools.Rcheck/affycoretools-Ex.timings:

nameusersystemelapsed
annBM0.0010.0000.001
entrezLinks0.0010.0000.001
makeVenn0.0010.0000.001
plotDeg18.411 0.25918.698
plotPCA0.1240.0150.164
vennCounts20.1130.0030.176
vennPage0.0010.0000.001