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BioC 3.3: CHECK report for AtlasRDF on zin2

This page was generated on 2016-10-13 12:44:22 -0700 (Thu, 13 Oct 2016).

Package 67/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AtlasRDF 1.8.0
James Malone
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AtlasRDF
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AtlasRDF
Version: 1.8.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AtlasRDF_1.8.0.tar.gz
StartedAt: 2016-10-12 23:36:04 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:36:30 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 26.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: AtlasRDF.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AtlasRDF_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AtlasRDF.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 ‘AtlasRDF’ can be installed ... 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:
  ‘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’
doFishersEnrichment: no visible global function definition for
  ‘fisher.test’
doFishersEnrichment: no visible global function definition for ‘new’
drawHeatMapForAtlasExperiment: no visible global function definition
  for ‘SPARQL’
drawHeatMapForAtlasExperiment: no visible binding for global variable
  ‘Genename’
drawHeatMapForAtlasExperiment: no visible binding for global variable
  ‘Factor’
drawHeatMapForAtlasExperiment: no visible global function definition
  for ‘par’
drawHeatMapForAtlasExperiment: no visible global function definition
  for ‘heatmap’
drawHeatMapForAtlasExperiment: no visible global function definition
  for ‘cm.colors’
excludeSubclasses: no visible global function definition for ‘SPARQL’
factorbackground: no visible global function definition for ‘new’
generef: no visible global function definition for ‘new’
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’
getRankedPathwaysForGeneIds: no visible global function definition for
  ‘new’
getSpeciesSpecificEnsemblGenesForExFactor: no visible global function
  definition for ‘SPARQL’
includeOnlySubclasses: no visible global function definition for
  ‘SPARQL’
searchForEFOTerms: no visible global function definition for ‘SPARQL’
vizPvalues: no visible global function definition for ‘setNames’
vizPvalues: no visible global function definition for ‘par’
vizPvalues: no visible global function definition for ‘barplot’
vizPvalues: no visible global function definition for ‘hcl’
vizPvalues: no visible global function definition for ‘title’
Undefined global functions or variables:
  .set Factor Genename SPARQL barplot cm.colors fisher.test has.key
  hash hcl heatmap keys new par setNames title
Consider adding
  importFrom("grDevices", "cm.colors", "hcl")
  importFrom("graphics", "barplot", "par", "title")
  importFrom("methods", "new")
  importFrom("stats", "fisher.test", "heatmap", "setNames")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... 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
  ‘/home/biocbuild/bbs-3.3-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-package0.0130.0000.315
doFishersEnrichment0.0010.0000.000
doFishersEnrichmentForEnsemblIds0.0010.0000.001
doFishersEnrichmentForGeneNames0.0010.0000.001
drawHeatMapForAtlasExperiment000
enrichmentresult-class0.0010.0000.001
excludeSubclasses0.0000.0000.001
factorbackground-class0.0000.0000.001
generef-class0.0000.0000.001
getAllEnsemblGenesForExFactor000
getExFactorURIFromLabel0.0120.0000.623
getExperimentIdsForGeneURI0.0010.0000.001
getExperimentURIsForGeneId0.0010.0000.001
getExperimentsByDescription0.0700.0030.645
getGeneListFromPubmedid0.0000.0000.001
getGeneUriFromEnsemblId0.0080.0002.188
getGeneUriFromName0.0000.0000.001
getGenesForExperimentID000
getGenesForExperimentURI0.0010.0000.000
getGenesForPathwayURI000
getLabel0.0080.0000.306
getOntologyMappings000
getPathwayForGeneId000
getPathwayUriFromName0.0000.0000.001
getPathwaysFromGenesAndCondition0.0010.0000.001
getRankedPathwaysForGeneIds0.0010.0000.000
getSpeciesSpecificEnsemblGenesForExFactor000
getTaxonURI0.0010.0000.001
includeOnlySubclasses000
orderEnrichmentResults0.0000.0000.001
pathwayresult-class0.0000.0000.001
searchForEFOTerms000
vizPvalues000