Package: Risa

Version: 1.1.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.1.0.tar.gz

StartedAt: 2013-03-25 04:19:17 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:24:37 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 319.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Risa.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/Risa.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.1.0’
* 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 ... [15s/17s] 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 ... WARNING
Error in eval(expr, envir, enclos) : could not find function "selfStart"
In addition: Warning messages:
1: class "C++Object" is defined (with package slot ‘Rcpp’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘.GlobalEnv’ 
2: class "characterORconnection" is defined (with package slot ‘BiocGenerics’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘xcms’ 
3: class "characterORMIAME" is defined (with package slot ‘Biobase’) but no metadata object found to revise subclass information---not exported?  Making a copy in package ‘xcms’ 
Error: unable to load R code in package ‘xcms’
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... [147s/156s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet         70.061  0.104  75.607
processAssayXcmsSet.1factor 67.300  0.216  70.271
* 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

WARNING: There was 1 warning.
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
   'Risa.Rnw' 
** testing if installed package can be loaded
* DONE (Risa)

name	user	system	elapsed
ISAtab-class	0.012	0.004	0.016
Risa-package	0.272	0.140	0.667
getMSAssayFilenames	0.056	0.000	0.055
getRawDataFiles	0.052	0.004	0.063
is.ms	0.060	0.000	0.063
processAssayXcmsSet.1factor	67.300	0.216	70.271
processAssayXcmsSet	70.061	0.104	75.607
readISAtab	0.152	0.164	0.316
updateAssayMetadata	0.116	0.012	0.130
write.assay.file	0.052	0.000	0.055
write.investigation.file	0.052	0.000	0.051
write.isatab	0.060	0.004	0.062
write.study.file	0.056	0.000	0.058