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BioC 3.1: CHECK report for AtlasRDF on moscato2

This page was generated on 2015-10-09 09:30:53 -0700 (Fri, 09 Oct 2015).

Package 63/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AtlasRDF 1.4.0
James Malone
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/AtlasRDF
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
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
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: AtlasRDF
Version: 1.4.0
Command: rm -rf AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && mkdir AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AtlasRDF.buildbin-libdir AtlasRDF_1.4.0.tar.gz >AtlasRDF.Rcheck\00install.out 2>&1 && cp AtlasRDF.Rcheck\00install.out AtlasRDF-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AtlasRDF.buildbin-libdir --install="check:AtlasRDF-install.out" --force-multiarch --no-vignettes --timings AtlasRDF_1.4.0.tar.gz
StartedAt: 2015-10-08 23:27:00 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 23:27:59 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 58.9 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AtlasRDF.buildbin-libdir AtlasRDF_1.4.0.tar.gz >AtlasRDF.Rcheck\00install.out 2>&1 && cp AtlasRDF.Rcheck\00install.out AtlasRDF-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=AtlasRDF.buildbin-libdir --install="check:AtlasRDF-install.out" --force-multiarch --no-vignettes --timings AtlasRDF_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/AtlasRDF.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.4.0'
* 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 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'
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 ... 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' ... [5s] OK
** running examples for arch 'x64' ... [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
  'E:/biocbld/bbs-3.1-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_1.4.0.zip
* DONE (AtlasRDF)

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

nameusersystemelapsed
AtlasRDF-package0.030.000.35
doFishersEnrichment000
doFishersEnrichmentForEnsemblIds000
doFishersEnrichmentForGeneNames000
drawHeatMapForAtlasExperiment000
enrichmentresult-class000
excludeSubclasses000
factorbackground-class000
generef-class000
getAllEnsemblGenesForExFactor000
getExFactorURIFromLabel0.000.000.58
getExperimentIdsForGeneURI000
getExperimentURIsForGeneId000
getExperimentsByDescription0.090.000.64
getGeneListFromPubmedid000
getGeneUriFromEnsemblId0.020.002.45
getGeneUriFromName000
getGenesForExperimentID000
getGenesForExperimentURI000
getGenesForPathwayURI000
getLabel0.010.000.32
getOntologyMappings000
getPathwayForGeneId000
getPathwayUriFromName000
getPathwaysFromGenesAndCondition000
getRankedPathwaysForGeneIds000
getSpeciesSpecificEnsemblGenesForExFactor000
getTaxonURI000
includeOnlySubclasses0.020.000.02
orderEnrichmentResults000
pathwayresult-class000
searchForEFOTerms000
vizPvalues000

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

nameusersystemelapsed
AtlasRDF-package0.020.020.34
doFishersEnrichment000
doFishersEnrichmentForEnsemblIds000
doFishersEnrichmentForGeneNames000
drawHeatMapForAtlasExperiment000
enrichmentresult-class000
excludeSubclasses000
factorbackground-class000
generef-class000
getAllEnsemblGenesForExFactor0.010.000.01
getExFactorURIFromLabel0.020.000.56
getExperimentIdsForGeneURI000
getExperimentURIsForGeneId000
getExperimentsByDescription0.160.000.72
getGeneListFromPubmedid000
getGeneUriFromEnsemblId0.000.002.47
getGeneUriFromName000
getGenesForExperimentID000
getGenesForExperimentURI000
getGenesForPathwayURI000
getLabel0.000.000.31
getOntologyMappings0.010.000.02
getPathwayForGeneId000
getPathwayUriFromName000
getPathwaysFromGenesAndCondition000
getRankedPathwaysForGeneIds000
getSpeciesSpecificEnsemblGenesForExFactor000
getTaxonURI000
includeOnlySubclasses000
orderEnrichmentResults000
pathwayresult-class000
searchForEFOTerms000
vizPvalues000