BioC 2.12: CHECK report for Risa on george2

Package: Risa

Version: 1.2.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.2.2.tar.gz

StartedAt: 2013-10-09 04:35:23 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 04:40:27 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 304.0 seconds

RetCode: 0

Status:  OK

CheckDir: Risa.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Risa.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.2.2’
* 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 ... [15s/15s] 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 ... [137s/148s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet.1factor 68.224  0.244  77.406
processAssayXcmsSet         58.668  0.128  59.951
* 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
  ‘/home/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	0.028	0.000	0.029
ISAtab-class	0.02	0.00	0.02
Risa-package	0.564	0.148	0.930
getAnnotatedDataFrameAssay	0.252	0.008	0.272
getExpressionSet	0.136	0.020	0.156
getMIAMEMetadata	0.476	0.024	0.499
getMSAssayFilenames	0.076	0.000	0.076
getMicroarrayAssayFilenames	0.136	0.008	0.156
getStudyFilename	0.072	0.000	0.070
isMSAssay	0.088	0.008	0.094
isMicroarrayAssay	0.120	0.024	0.144
processAssayXcmsSet.1factor	68.224	0.244	77.406
processAssayXcmsSet	58.668	0.128	59.951
readISAtab	0.156	0.192	0.440
updateAssayMetadata	0.180	0.012	0.194
write.assay.file	0.080	0.008	0.086
write.investigation.file	0.072	0.000	0.071
write.isatab	0.084	0.000	0.083
write.study.file	0.072	0.000	0.069