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Package 502/609HostnameOS / ArchBUILDCHECKBUILD BIN
Risa 1.0.0
Alejandra Gonzalez-Beltran, ISA Team
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/Risa
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

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

Command output

* 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.

Risa.Rcheck/00install.out:

* 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)

Risa.Rcheck/Risa-Ex.timings:

nameusersystemelapsed
ISAtab-class0.0000.0000.002
Risa-package0.2640.1201.981
processAssayXcmsSet42.246 0.42847.438
readISAtab0.0720.1200.651
updateAssayMetadata0.0640.0120.077
write.assay.file0.0320.0005.506
write.investigation.file0.0280.0000.027
write.isatab0.040.000.49
write.study.file0.0240.0040.029