BioC 3.2: CHECK report for Risa on oaxaca

Package: Risa

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Risa_1.11.1.tar.gz

StartedAt: 2015-08-24 03:22:24 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:25:07 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 162.9 seconds

RetCode: 0

Status:  OK

CheckDir: Risa.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Risa_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Risa.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Risa/DESCRIPTION’ ... OK
* this is package ‘Risa’ version ‘1.11.1’
* 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 ... [9s/9s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [72s/75s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet.1factor 30.038  3.115  33.684
processAssayXcmsSet         29.674  3.302  33.399
* 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

Status: OK

* 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	0.007	0.001	0.007
ISAtab-class	0.004	0.000	0.004
Risa-package	0.205	0.145	2.168
getAnnotatedDataFrameAssay	0.184	0.018	0.217
getExpressionSet	0.092	0.012	0.120
getMIAMEMetadata	0.121	0.012	0.148
getMSAssayFilenames	0.045	0.002	0.047
getMicroarrayAssayFilenames	0.091	0.013	0.123
getStudyFilename	0.042	0.001	0.043
isMSAssay	0.044	0.001	0.045
isMicroarrayAssay	0.096	0.013	0.125
processAssayXcmsSet.1factor	30.038	3.115	33.684
processAssayXcmsSet	29.674	3.302	33.399
readISAtab	0.112	0.132	0.553
updateAssayMetadata	0.125	0.013	0.140
write.assay.file	0.048	0.001	0.048
write.investigation.file	0.041	0.000	0.042
write.isatab	0.047	0.002	0.049
write.study.file	0.043	0.001	0.044