BioC 3.1: CHECK report for AtlasRDF on petty

Package: AtlasRDF

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AtlasRDF_1.4.0.tar.gz

StartedAt: 2015-10-08 21:32:12 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 21:33:09 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 57.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AtlasRDF.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AtlasRDF_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/AtlasRDF.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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:
  ‘hash’ ‘methods’ ‘SPARQL’
  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’
getExperimentsByDescription: no visible global function definition for
  ‘SPARQL’
getExperimentURIsForGeneId: no visible global function definition for
  ‘SPARQL’
getGeneListFromPubmedid: 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’
getGeneUriFromEnsemblId: no visible global function definition for
  ‘SPARQL’
getGeneUriFromName: 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’
getPathwaysFromGenesAndCondition: no visible global function definition
  for ‘SPARQL’
getPathwayUriFromName: 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 ... WARNING
Undocumented code objects:
  ‘getConditionsForGeneName’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/AtlasRDF.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
AtlasRDF-package	0.020	0.002	0.333
doFishersEnrichment	0.002	0.000	0.002
doFishersEnrichmentForEnsemblIds	0.002	0.001	0.003
doFishersEnrichmentForGeneNames	0.001	0.000	0.001
drawHeatMapForAtlasExperiment	0.000	0.000	0.001
enrichmentresult-class	0.002	0.000	0.002
excludeSubclasses	0.001	0.001	0.001
factorbackground-class	0.002	0.000	0.002
generef-class	0.002	0.000	0.002
getAllEnsemblGenesForExFactor	0	0	0
getExFactorURIFromLabel	0.018	0.001	0.589
getExperimentIdsForGeneURI	0.000	0.001	0.001
getExperimentURIsForGeneId	0.001	0.000	0.000
getExperimentsByDescription	0.173	0.004	0.720
getGeneListFromPubmedid	0.001	0.000	0.001
getGeneUriFromEnsemblId	0.015	0.001	2.464
getGeneUriFromName	0.001	0.000	0.001
getGenesForExperimentID	0.001	0.000	0.001
getGenesForExperimentURI	0.002	0.000	0.002
getGenesForPathwayURI	0.000	0.000	0.001
getLabel	0.016	0.001	0.328
getOntologyMappings	0.000	0.000	0.001
getPathwayForGeneId	0.000	0.000	0.001
getPathwayUriFromName	0.000	0.000	0.001
getPathwaysFromGenesAndCondition	0.001	0.000	0.001
getRankedPathwaysForGeneIds	0.001	0.000	0.001
getSpeciesSpecificEnsemblGenesForExFactor	0.001	0.000	0.002
getTaxonURI	0.002	0.000	0.003
includeOnlySubclasses	0.001	0.000	0.001
orderEnrichmentResults	0.000	0.000	0.001
pathwayresult-class	0.002	0.000	0.002
searchForEFOTerms	0.000	0.000	0.001
vizPvalues	0	0	0