BioC 3.0: CHECK report for Risa on zin1

Package: Risa

Version: 1.8.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.8.0.tar.gz

StartedAt: 2015-04-10 03:51:26 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:53:46 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 140.7 seconds

RetCode: 0

Status:  OK

CheckDir: Risa.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/Risa.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [8s/8s] 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:
  ‘Biobase’ ‘Rcpp’ ‘affy’ ‘biocViews’ ‘methods’
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [61s/62s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet.1factor 28.514  0.072  28.827
processAssayXcmsSet         26.817  0.052  26.986
* 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
  ‘/home/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	0.008	0.000	0.005
ISAtab-class	0.004	0.000	0.002
Risa-package	0.184	0.048	0.509
getAnnotatedDataFrameAssay	0.252	0.008	0.259
getExpressionSet	0.084	0.004	0.087
getMIAMEMetadata	0.100	0.012	0.110
getMSAssayFilenames	0.040	0.000	0.038
getMicroarrayAssayFilenames	0.080	0.008	0.088
getStudyFilename	0.036	0.000	0.034
isMSAssay	0.036	0.000	0.036
isMicroarrayAssay	0.084	0.000	0.085
processAssayXcmsSet.1factor	28.514	0.072	28.827
processAssayXcmsSet	26.817	0.052	26.986
readISAtab	0.096	0.060	0.311
updateAssayMetadata	0.092	0.012	0.104
write.assay.file	0.036	0.000	0.037
write.investigation.file	0.040	0.000	0.037
write.isatab	0.044	0.004	0.045
write.study.file	0.028	0.004	0.034