AtlasRDF 1.7.0 James Malone
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AtlasRDF | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AtlasRDF_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AtlasRDF.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.7.0’
* 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 ... [2s/2s] 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’
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’
Undefined global functions or variables:
.set Factor Genename SPARQL has.key hash keys
* 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 ... [1s/4s] 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.