AtlasRDF 1.6.0
James Malone
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/AtlasRDF | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && mkdir AtlasRDF.buildbin-libdir AtlasRDF.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AtlasRDF.buildbin-libdir AtlasRDF_1.6.0.tar.gz >AtlasRDF.Rcheck\00install.out 2>&1 && cp AtlasRDF.Rcheck\00install.out AtlasRDF-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=AtlasRDF.buildbin-libdir --install="check:AtlasRDF-install.out" --force-multiarch --no-vignettes --timings AtlasRDF_1.6.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/AtlasRDF.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.6.0'
* 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' ... [44s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
getExperimentsByDescription 0.15 0 12.17
getGeneUriFromEnsemblId 0.03 0 26.10
** running examples for arch 'x64' ... [12s] 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
'D:/biocbld/bbs-3.2-bioc/meat/AtlasRDF.Rcheck/00check.log'
for details.
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_1.6.0.zip
* DONE (AtlasRDF)