BioC 2.13: CHECK report for Risa on perceval

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/Risa.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.4.1’
* 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/13s] 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’ 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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
getPackagesInBiocView: no visible binding for global variable
  ‘biocViewsVocab’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Risa.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [104s/110s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet.1factor 50.332  1.305  53.980
processAssayXcmsSet         42.580  1.432  46.159
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/Risa.Rcheck/00check.log’
for details.

* installing *source* package ‘Risa’ ...
** R
** inst
** preparing package for lazy loading
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.0)
than is installed on your system (0.11.1). This might lead to errors
when loading mzR. If you encounter such issues, please send
a report, including the output of sessionInfo() to the Bioc
mailing list -- http://www.bioconductor.org/help/mailing-list.
* DONE (Risa)

name	user	system	elapsed
AssayTab-class	0.016	0.001	0.017
ISAtab-class	0.008	0.002	0.010
Risa-package	0.276	0.269	1.756
getAnnotatedDataFrameAssay	0.216	0.034	0.436
getExpressionSet	0.118	0.028	0.171
getMIAMEMetadata	0.139	0.028	0.179
getMSAssayFilenames	0.063	0.005	0.070
getMicroarrayAssayFilenames	0.112	0.030	0.156
getStudyFilename	0.061	0.002	0.064
isMSAssay	0.061	0.003	0.064
isMicroarrayAssay	0.123	0.034	0.174
processAssayXcmsSet.1factor	50.332	1.305	53.980
processAssayXcmsSet	42.580	1.432	46.159
readISAtab	0.146	0.265	0.441
updateAssayMetadata	0.160	0.025	0.186
write.assay.file	0.052	0.006	0.058
write.investigation.file	0.048	0.006	0.053
write.isatab	0.059	0.010	0.072
write.study.file	0.050	0.005	0.060

BioC 2.13: CHECK report for Risa on perceval

Summary

Command output