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BioC 3.0: CHECK report for AtlasRDF on oaxaca

This page was generated on 2015-04-10 10:08:27 -0700 (Fri, 10 Apr 2015).

Package 62/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AtlasRDF 1.2.0
James Malone
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/AtlasRDF
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: AtlasRDF
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AtlasRDF_1.2.0.tar.gz
StartedAt: 2015-04-09 21:31:26 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:32:13 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 46.7 seconds
RetCode: 0
Status:  OK 
CheckDir: AtlasRDF.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch AtlasRDF_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/AtlasRDF.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AtlasRDF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AtlasRDF’ version ‘1.2.0’
* 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 ‘AtlasRDF’ can be installed ... [4s/4s] 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
Packages in Depends field not imported from:
  ‘SPARQL’ ‘hash’ ‘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
calculateCountsForGeneLists: no visible global function definition for
  ‘hash’
calculateCountsForGeneLists: no visible global function definition for
  ‘has.key’
calculateCountsForGeneLists: no visible global function definition for
  ‘.set’
doFishersEnrichment: no visible global function definition for ‘keys’
drawHeatMapForAtlasExperiment: no visible global function definition
  for ‘SPARQL’
drawHeatMapForAtlasExperiment: no visible binding for global variable
  ‘Genename’
drawHeatMapForAtlasExperiment: no visible binding for global variable
  ‘Factor’
excludeSubclasses: no visible global function definition for ‘SPARQL’
getAllEnsemblGenesForExFactor: no visible global function definition
  for ‘SPARQL’
getExFactorURIFromLabel: no visible global function definition for
  ‘SPARQL’
getExperimentIdsForGeneURI: no visible global function definition for
  ‘SPARQL’
getExperimentURIsForGeneId: no visible global function definition for
  ‘SPARQL’
getExperimentsByDescription: no visible global function definition for
  ‘SPARQL’
getGeneListFromPubmedid: no visible global function definition for
  ‘SPARQL’
getGeneUriFromEnsemblId: no visible global function definition for
  ‘SPARQL’
getGeneUriFromName: no visible global function definition for ‘SPARQL’
getGenesForExperimentID: no visible global function definition for
  ‘SPARQL’
getGenesForExperimentURI: no visible global function definition for
  ‘SPARQL’
getGenesForPathwayURI: no visible global function definition for
  ‘SPARQL’
getLabel: no visible global function definition for ‘SPARQL’
getOntologyMappings: no visible global function definition for ‘SPARQL’
getPathwayForGeneId: no visible global function definition for ‘SPARQL’
getPathwayUriFromName: no visible global function definition for
  ‘SPARQL’
getPathwaysFromGenesAndCondition: no visible global function definition
  for ‘SPARQL’
getRankedPathwaysForGeneIds: no visible global function definition for
  ‘SPARQL’
getSpeciesSpecificEnsemblGenesForExFactor: no visible global function
  definition for ‘SPARQL’
includeOnlySubclasses: no visible global function definition for
  ‘SPARQL’
searchForEFOTerms: no visible global function definition for ‘SPARQL’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/6s] OK
* 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
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/AtlasRDF.Rcheck/00check.log’
for details.

AtlasRDF.Rcheck/00install.out:

* installing *source* package ‘AtlasRDF’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AtlasRDF)

AtlasRDF.Rcheck/AtlasRDF-Ex.timings:

nameusersystemelapsed
AtlasRDF-package0.0180.0010.370
doFishersEnrichment0.0010.0000.002
doFishersEnrichmentForEnsemblIds0.0010.0000.002
doFishersEnrichmentForGeneNames0.0020.0000.002
drawHeatMapForAtlasExperiment0.0010.0000.000
enrichmentresult-class0.0020.0010.002
excludeSubclasses0.0010.0000.001
factorbackground-class0.0010.0000.002
generef-class0.0020.0000.002
getAllEnsemblGenesForExFactor0.0010.0000.001
getExFactorURIFromLabel0.0160.0010.602
getExperimentIdsForGeneURI0.0010.0000.000
getExperimentURIsForGeneId0.0010.0000.001
getExperimentsByDescription0.1680.0050.734
getGeneListFromPubmedid0.0010.0000.001
getGeneUriFromEnsemblId0.0130.0012.376
getGeneUriFromName000
getGenesForExperimentID0.0000.0000.001
getGenesForExperimentURI0.0000.0000.001
getGenesForPathwayURI0.0000.0000.001
getLabel0.0110.0010.328
getOntologyMappings0.0010.0000.001
getPathwayForGeneId0.0010.0010.001
getPathwayUriFromName0.0010.0000.001
getPathwaysFromGenesAndCondition0.0000.0000.001
getRankedPathwaysForGeneIds000
getSpeciesSpecificEnsemblGenesForExFactor0.0000.0010.001
getTaxonURI0.0010.0000.002
includeOnlySubclasses0.0010.0000.001
orderEnrichmentResults0.0010.0010.001
pathwayresult-class0.0010.0000.001
searchForEFOTerms0.0000.0000.001
vizPvalues0.0010.0000.000