AtlasRDF 1.10.0
Simon Jupp
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/AtlasRDF | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings AtlasRDF_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/AtlasRDF.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.10.0’
* 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 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-3.4-bioc/meat/AtlasRDF.Rcheck/00check.log’
for details.