Package: Risa

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Risa_1.2.1.tar.gz

StartedAt: 2013-05-01 10:19:47 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:24:01 -0700 (Wed, 01 May 2013)

EllapsedTime: 253.6 seconds

RetCode: 0

Status:  OK

CheckDir: Risa.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/Risa.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'Risa/DESCRIPTION' ... OK
* this is package 'Risa' version '1.2.1'
* 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 ... [13s/14s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [120s/127s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet.1factor 55.370  2.537  61.327
processAssayXcmsSet         50.284  2.469  53.978
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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	0.022	0.003	0.026
ISAtab-class	0.009	0.001	0.011
Risa-package	0.467	0.304	1.651
getAnnotatedDataFrameAssay	0.288	0.043	0.371
getExpressionSet	0.164	0.035	0.287
getMIAMEMetadata	0.182	0.032	0.305
getMSAssayFilenames	0.070	0.006	0.085
getMicroarrayAssayFilenames	0.150	0.029	0.255
getStudyFilename	0.075	0.005	0.131
isMSAssay	0.070	0.004	0.121
isMicroarrayAssay	0.144	0.036	0.265
processAssayXcmsSet.1factor	55.370	2.537	61.327
processAssayXcmsSet	50.284	2.469	53.978
readISAtab	0.179	0.278	0.638
updateAssayMetadata	0.167	0.025	0.192
write.assay.file	0.065	0.005	0.070
write.investigation.file	0.064	0.006	0.074
write.isatab	0.076	0.010	0.107
write.study.file	0.059	0.004	0.071