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BioC 3.5: CHECK report for AtlasRDF on tokay2

This page was generated on 2017-07-13 13:23:03 -0400 (Thu, 13 Jul 2017).

Package 75/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AtlasRDF 1.12.0
Simon Jupp
Snapshot Date: 2017-07-12 17:17:29 -0400 (Wed, 12 Jul 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/AtlasRDF
Last Changed Rev: 129126 / Revision: 131152
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
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
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: 1.12.0
Command: rm -rf AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && mkdir AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AtlasRDF.buildbin-libdir AtlasRDF_1.12.0.tar.gz >AtlasRDF.Rcheck\00install.out 2>&1 && cp AtlasRDF.Rcheck\00install.out AtlasRDF-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AtlasRDF.buildbin-libdir --install="check:AtlasRDF-install.out" --force-multiarch --no-vignettes --timings AtlasRDF_1.12.0.tar.gz
StartedAt: 2017-07-12 22:07:23 -0400 (Wed, 12 Jul 2017)
EndedAt: 2017-07-12 22:09:02 -0400 (Wed, 12 Jul 2017)
EllapsedTime: 98.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: AtlasRDF.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && mkdir AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AtlasRDF.buildbin-libdir AtlasRDF_1.12.0.tar.gz >AtlasRDF.Rcheck\00install.out 2>&1 && cp AtlasRDF.Rcheck\00install.out AtlasRDF-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=AtlasRDF.buildbin-libdir --install="check:AtlasRDF-install.out" --force-multiarch --no-vignettes --timings AtlasRDF_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/AtlasRDF.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AtlasRDF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AtlasRDF' version '1.12.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/AtlasRDF.Rcheck/00check.log'
for details.


AtlasRDF.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'AtlasRDF' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AtlasRDF' as AtlasRDF_1.12.0.zip
* DONE (AtlasRDF)

AtlasRDF.Rcheck/examples_i386/AtlasRDF-Ex.timings:

nameusersystemelapsed
AtlasRDF-package0.060.000.35
doFishersEnrichment000
doFishersEnrichmentForEnsemblIds000
doFishersEnrichmentForGeneNames000
drawHeatMapForAtlasExperiment000
enrichmentresult-class000
excludeSubclasses000
factorbackground-class000
generef-class000
getAllEnsemblGenesForExFactor000
getExFactorURIFromLabel0.280.000.69
getExperimentIdsForGeneURI000
getExperimentURIsForGeneId000
getExperimentsByDescription0.080.000.51
getGeneListFromPubmedid000
getGeneUriFromEnsemblId0.020.001.40
getGeneUriFromName000
getGenesForExperimentID000
getGenesForExperimentURI000
getGenesForPathwayURI000
getLabel0.000.000.19
getOntologyMappings0.020.000.01
getPathwayForGeneId000
getPathwayUriFromName000
getPathwaysFromGenesAndCondition000
getRankedPathwaysForGeneIds000
getSpeciesSpecificEnsemblGenesForExFactor000
getTaxonURI000
includeOnlySubclasses000
orderEnrichmentResults000
pathwayresult-class000
searchForEFOTerms000
vizPvalues000

AtlasRDF.Rcheck/examples_x64/AtlasRDF-Ex.timings:

nameusersystemelapsed
AtlasRDF-package0.050.010.25
doFishersEnrichment000
doFishersEnrichmentForEnsemblIds000
doFishersEnrichmentForGeneNames000
drawHeatMapForAtlasExperiment000
enrichmentresult-class0.020.000.02
excludeSubclasses000
factorbackground-class000
generef-class000
getAllEnsemblGenesForExFactor000
getExFactorURIFromLabel0.340.020.76
getExperimentIdsForGeneURI000
getExperimentURIsForGeneId000
getExperimentsByDescription0.130.000.49
getGeneListFromPubmedid000
getGeneUriFromEnsemblId0.030.001.78
getGeneUriFromName000
getGenesForExperimentID000
getGenesForExperimentURI000
getGenesForPathwayURI000
getLabel0.010.000.20
getOntologyMappings000
getPathwayForGeneId000
getPathwayUriFromName000
getPathwaysFromGenesAndCondition000
getRankedPathwaysForGeneIds000
getSpeciesSpecificEnsemblGenesForExFactor000
getTaxonURI000
includeOnlySubclasses000
orderEnrichmentResults000
pathwayresult-class000
searchForEFOTerms000
vizPvalues000