BioC 3.0: CHECK report for affycoretools on perceval

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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch affycoretools_1.38.0.tar.gz
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* 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.

* 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)

name	user	system	elapsed
annBM	0.001	0.000	0.001
entrezLinks	0.001	0.000	0.001
makeVenn	0.001	0.000	0.001
plotDeg	18.411	0.259	18.698
plotPCA	0.124	0.015	0.164
vennCounts2	0.113	0.003	0.176
vennPage	0.001	0.000	0.001