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BioC 3.5: CHECK report for AtlasRDF on toluca2

This page was generated on 2017-04-23 14:38:00 -0400 (Sun, 23 Apr 2017).

Package 74/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AtlasRDF 1.11.0
Simon Jupp
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AtlasRDF
Last Changed Rev: 122939 / Revision: 129046
Last Changed Date: 2016-10-21 13:19:00 -0400 (Fri, 21 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AtlasRDF
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AtlasRDF_1.11.0.tar.gz
StartedAt: 2017-04-23 00:32:58 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 00:33:34 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 36.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: AtlasRDF.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AtlasRDF_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AtlasRDF.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.11.0’
* 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
  ‘/Users/biocbuild/bbs-3.5-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-package0.6080.0060.911
doFishersEnrichment0.0010.0000.001
doFishersEnrichmentForEnsemblIds0.0010.0000.002
doFishersEnrichmentForGeneNames0.0020.0000.002
drawHeatMapForAtlasExperiment0.0000.0000.001
enrichmentresult-class0.0010.0000.002
excludeSubclasses0.0010.0000.001
factorbackground-class0.0010.0010.001
generef-class0.0010.0000.001
getAllEnsemblGenesForExFactor0.0000.0000.001
getExFactorURIFromLabel0.3230.0020.788
getExperimentIdsForGeneURI0.0000.0000.001
getExperimentURIsForGeneId0.0000.0000.001
getExperimentsByDescription0.0960.0020.485
getGeneListFromPubmedid0.0010.0000.001
getGeneUriFromEnsemblId0.0070.0011.493
getGeneUriFromName0.0000.0000.001
getGenesForExperimentID0.0010.0000.000
getGenesForExperimentURI000
getGenesForPathwayURI000
getLabel0.0090.0000.202
getOntologyMappings000
getPathwayForGeneId000
getPathwayUriFromName000
getPathwaysFromGenesAndCondition0.0010.0000.001
getRankedPathwaysForGeneIds0.0000.0000.001
getSpeciesSpecificEnsemblGenesForExFactor0.0000.0010.001
getTaxonURI0.0050.0000.005
includeOnlySubclasses0.0000.0000.001
orderEnrichmentResults0.0010.0000.001
pathwayresult-class0.0010.0000.001
searchForEFOTerms000
vizPvalues0.0010.0010.000