BioC 3.0: CHECK report for Risa on perceval

Package: Risa

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Risa_1.8.0.tar.gz

StartedAt: 2015-04-10 05:45:57 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:49:44 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 227.0 seconds

RetCode: 0

Status:  OK

CheckDir: Risa.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 Risa_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Risa.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 ‘Risa/DESCRIPTION’ ... OK
* this is package ‘Risa’ version ‘1.8.0’
* 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 ‘Risa’ can be installed ... [12s/14s] 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 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’ ‘biocViews’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘affy’ ‘Biobase’ ‘biocViews’ ‘methods’ ‘Rcpp’
  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 ... OK
* checking R code for possible problems ... NOTE
getExpressionSet: no visible global function definition for ‘justRMA’
getPackagesInBiocView: no visible global function definition for
  ‘getBiocViews’
getPackagesInBiocView: no visible binding for global variable
  ‘biocViewsVocab’
processAssayXcmsSet: no visible global function definition for
  ‘read.AnnotatedDataFrame’
processAssayXcmsSet: no visible global function definition for
  ‘sampleNames<-’
processAssayXcmsSet: no visible global function definition for ‘pData’
processAssayXcmsSet.1factor: no visible global function definition for
  ‘read.AnnotatedDataFrame’
processAssayXcmsSet.1factor: no visible global function definition for
  ‘sampleNames<-’
processAssayXcmsSet.1factor: no visible global function definition for
  ‘pData’
* 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 ... [93s/96s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet.1factor 41.928  0.863  43.285
processAssayXcmsSet         40.699  0.886  41.873
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/Risa.Rcheck/00check.log’
for details.

* installing *source* package ‘Risa’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Risa)

name	user	system	elapsed
AssayTab-class	0.006	0.001	0.008
ISAtab-class	0.003	0.000	0.005
Risa-package	0.260	0.270	1.834
getAnnotatedDataFrameAssay	0.389	0.034	0.497
getExpressionSet	0.106	0.026	0.194
getMIAMEMetadata	0.126	0.027	0.219
getMSAssayFilenames	0.047	0.003	0.057
getMicroarrayAssayFilenames	0.100	0.024	0.133
getStudyFilename	0.042	0.002	0.045
isMSAssay	0.046	0.002	0.048
isMicroarrayAssay	0.101	0.026	0.190
processAssayXcmsSet.1factor	41.928	0.863	43.285
processAssayXcmsSet	40.699	0.886	41.873
readISAtab	0.120	0.260	0.771
updateAssayMetadata	0.140	0.022	0.161
write.assay.file	0.041	0.002	0.043
write.investigation.file	0.039	0.002	0.041
write.isatab	0.054	0.005	0.077
write.study.file	0.046	0.003	0.049