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BioC 3.0: CHECK report for Risa on zin1

This page was generated on 2015-04-10 09:40:13 -0700 (Fri, 10 Apr 2015).

Package 753/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Risa 1.8.0
Alejandra Gonzalez-Beltran, ISA Team
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Risa
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Risa
Version: 1.8.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.8.0.tar.gz
StartedAt: 2015-04-10 03:51:26 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:53:46 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 140.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Risa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings Risa_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/Risa.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.8.0’
* 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 ... [8s/8s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘affy’ ‘biocViews’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘Rcpp’ ‘affy’ ‘biocViews’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getExpressionSet: no visible global function definition for ‘justRMA’
getPackagesInBiocView: no visible global function definition for
  ‘getBiocViews’
getPackagesInBiocView: no visible binding for global variable
  ‘biocViewsVocab’
processAssayXcmsSet: no visible global function definition for
  ‘read.AnnotatedDataFrame’
processAssayXcmsSet: no visible global function definition for
  ‘sampleNames<-’
processAssayXcmsSet: no visible global function definition for ‘pData’
processAssayXcmsSet.1factor: no visible global function definition for
  ‘read.AnnotatedDataFrame’
processAssayXcmsSet.1factor: no visible global function definition for
  ‘sampleNames<-’
processAssayXcmsSet.1factor: no visible global function definition for
  ‘pData’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [61s/62s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
processAssayXcmsSet.1factor 28.514  0.072  28.827
processAssayXcmsSet         26.817  0.052  26.986
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-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
** testing if installed package can be loaded
* DONE (Risa)

Risa.Rcheck/Risa-Ex.timings:

nameusersystemelapsed
AssayTab-class0.0080.0000.005
ISAtab-class0.0040.0000.002
Risa-package0.1840.0480.509
getAnnotatedDataFrameAssay0.2520.0080.259
getExpressionSet0.0840.0040.087
getMIAMEMetadata0.1000.0120.110
getMSAssayFilenames0.0400.0000.038
getMicroarrayAssayFilenames0.0800.0080.088
getStudyFilename0.0360.0000.034
isMSAssay0.0360.0000.036
isMicroarrayAssay0.0840.0000.085
processAssayXcmsSet.1factor28.514 0.07228.827
processAssayXcmsSet26.817 0.05226.986
readISAtab0.0960.0600.311
updateAssayMetadata0.0920.0120.104
write.assay.file0.0360.0000.037
write.investigation.file0.0400.0000.037
write.isatab0.0440.0040.045
write.study.file0.0280.0040.034