Package: Risa

Version: 1.0.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.0.0.tar.gz

StartedAt: 2013-03-25 04:27:53 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:30:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 150.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Risa.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/Risa.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.0.0’
* 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 whether package ‘Risa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 message:
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’ 
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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
processAssayXcmsSet 42.246  0.428  47.438
write.assay.file     0.032  0.000   5.506
* 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.
See
  ‘/loc/home/biocbuild/bbs-2.11-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	0.000	0.000	0.002
Risa-package	0.264	0.120	1.981
processAssayXcmsSet	42.246	0.428	47.438
readISAtab	0.072	0.120	0.651
updateAssayMetadata	0.064	0.012	0.077
write.assay.file	0.032	0.000	5.506
write.investigation.file	0.028	0.000	0.027
write.isatab	0.04	0.00	0.49
write.study.file	0.024	0.004	0.029