AnnotationForge 1.12.0
Bioconductor Package Maintainer
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/AnnotationForge | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationForge_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/AnnotationForge.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* this is package ‘AnnotationForge’ 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 ... NOTE
Found the following hidden files and directories:
inst/ProbePkg-template/data/.dummy.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationForge’ can be installed ... [9s/9s] OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
AnnDbPkg-templates 1.3Mb
extdata 3.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘utils’ ‘BiocGenerics’ ‘Biobase’ ‘DBI’ ‘RSQLite’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘GenomeInfoDb’
'library' or 'require' calls not declared from:
‘biomaRt’ ‘httr’
'library' or 'require' calls in package code:
‘GO.db’ ‘RCurl’ ‘RSQLite’ ‘XML’ ‘affy’ ‘biomaRt’ ‘httr’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
‘methods’ ‘utils’
All declared Imports should be used.
Packages in Depends field not imported from:
‘AnnotationDbi’ ‘methods’ ‘org.Hs.eg.db’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘AnnotationDbi:::.filterSeeds’
‘AnnotationDbi:::NCBICHIP_DB_SeedGenerator’
‘AnnotationDbi:::NCBIORG_DB_SeedGenerator’
‘AnnotationDbi:::dbGetTable’ ‘AnnotationDbi:::getOrgPkgForSchema’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.addEssentialMetadata’ ‘.addMeta’ ‘.createMetadataTables’
‘.makeARABIDOPSISCHIP_DB’ ‘.makeBOVINECHIP_DB’ ‘.makeCANINECHIP_DB’
‘.makeCHICKENCHIP_DB’ ‘.makeECOLICHIP_DB’ ‘.makeFLYCHIP_DB’
‘.makeGenesTable’ ‘.makeHUMANCHIP_DB’ ‘.makeLegacyProbesTable’
‘.makeMOUSECHIP_DB’ ‘.makePIGCHIP_DB’ ‘.makeProbesTable’
‘.makeRATCHIP_DB’ ‘.makeRHESUSCHIP_DB’ ‘.makeWORMCHIP_DB’
‘.makeXENOPUSCHIP_DB’ ‘.makeYEASTCHIP_DB’ ‘.makeZEBRAFISHCHIP_DB’
‘popANOPHELESDB’ ‘popARABIDOPSISCHIPDB’ ‘popARABIDOPSISDB’
‘popBOVINECHIPDB’ ‘popBOVINEDB’ ‘popCANINECHIPDB’ ‘popCANINEDB’
‘popCHICKENCHIPDB’ ‘popCHICKENDB’ ‘popCHIMPDB’ ‘popECOLICHIPDB’
‘popECOLIDB’ ‘popFLYCHIPDB’ ‘popFLYDB’ ‘popHUMANCHIPDB’ ‘popHUMANDB’
‘popMALARIADB’ ‘popMOUSECHIPDB’ ‘popMOUSEDB’ ‘popPIGCHIPDB’
‘popPIGDB’ ‘popRATCHIPDB’ ‘popRATDB’ ‘popRHESUSCHIPDB’ ‘popRHESUSDB’
‘popWORMCHIPDB’ ‘popWORMDB’ ‘popXENOPUSCHIPDB’ ‘popXENOPUSDB’
‘popYEASTCHIPDB’ ‘popYEASTDB’ ‘popZEBRAFISHCHIPDB’ ‘popZEBRAFISHDB’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addOntologyData: no visible global function definition for ‘select’
.addOntologyData: no visible binding for global variable ‘GO.db’
.checkRetrieveNode: no visible global function definition for
‘xpathApply’
.checkRetrieveNode: no visible binding for global variable ‘xmlValue’
.downloadAndPopulateAltGOData: no visible global function definition
for ‘CFILE’
.downloadAndPopulateAltGOData: no visible global function definition
for ‘curlPerform’
.downloadAndSaveToTemp: no visible global function definition for
‘url.exists’
.downloadAndSaveToTemp: no visible global function definition for
‘getBinaryURL’
.ensemblMapsToEntrezId: no visible global function definition for
‘useMart’
.ensemblMapsToEntrezId: no visible global function definition for
‘listAttributes’
.expandGOFrame: no visible global function definition for ‘unlist2’
.filterGOFrame: no visible global function definition for ‘Lkeys’
.filterGOFrame: no visible binding for global variable ‘GOTERM’
.getBlast2GOData: no visible global function definition for ‘Ontology’
.getDBTag: no visible global function definition for ‘xpathApply’
.getDBTag: no visible binding for global variable ‘xmlValue’
.getEnsemblData: no visible global function definition for ‘useMart’
.getEnsemblData: no visible global function definition for ‘getBM’
.getGODate: no visible global function definition for ‘dbInfo’
.getGODate: no visible global function definition for ‘GO_dbconn’
.getOtherSrcDocs: no visible global function definition for
‘getNodeSet’
.getOtherSrcDocs: no visible binding for global variable ‘xmlDoc’
.getSubDirs : getLinks : <anonymous>: no visible global function
definition for ‘xmlGetAttr’
.getSubDirs: no visible global function definition for ‘htmlTreeParse’
.getSubNodeInfo: no visible global function definition for ‘Stop’
.makeGOTablesFromNCBI: no visible binding for global variable
‘GOBPANCESTOR’
.makeGOTablesFromNCBI: no visible binding for global variable
‘GOMFANCESTOR’
.makeGOTablesFromNCBI: no visible binding for global variable
‘GOCCANCESTOR’
.makeNewGOTables: no visible global function definition for ‘Lkeys’
.makeNewGOTables: no visible binding for global variable ‘GOTERM’
.makeNewGOTables: no visible binding for global variable ‘GOBPANCESTOR’
.makeNewGOTables: no visible binding for global variable ‘GOMFANCESTOR’
.makeNewGOTables: no visible binding for global variable ‘GOCCANCESTOR’
.makeSimpleDF: no visible global function definition for ‘unlist2’
.makeUnWoundGOTables: no visible global function definition for
‘unlist2’
.makeUnWoundGOTables: no visible global function definition for
‘Ontology’
.makeUnWoundGOTables: no visible binding for global variable
‘GOBPANCESTOR’
.makeUnWoundGOTables: no visible binding for global variable
‘GOMFANCESTOR’
.makeUnWoundGOTables: no visible binding for global variable
‘GOCCANCESTOR’
.unwindGOs: no visible global function definition for ‘unlist2’
available.ensembl.datasets: no visible global function definition for
‘useMart’
available.ensembl.datasets: no visible global function definition for
‘listDatasets’
getEntrezGenesFromTaxId: no visible global function definition for
‘xmlParse’
getEntrezGenesFromTaxId: no visible global function definition for
‘xpathApply’
getEntrezGenesFromTaxId: no visible binding for global variable
‘xmlValue’
getFastaSpeciesDirs: no visible global function definition for
‘getCurlHandle’
getFastaSpeciesDirs: no visible global function definition for ‘getURL’
getGeneStuff: no visible global function definition for ‘xmlParse’
getGeneStuff: no visible global function definition for ‘getNodeSet’
getGeneStuff: no visible binding for global variable ‘xmlDoc’
getGeneStuff: no visible global function definition for ‘saveXML’
getProbeDataAffy: no visible global function definition for
‘cleancdfname’
initWithDbDoc: no visible global function definition for
‘dbFileConnect’
initWithDbDoc: no visible global function definition for
‘dbFileDisconnect’
initWithDbMetada: no visible global function definition for
‘dbFileConnect’
initWithDbMetada: no visible global function definition for
‘dbFileDisconnect’
writeTable: no visible global function definition for
‘sqliteWriteTable’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/11s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
makeProbePackage 4.967 0.169 5.377
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘AnnotationForge_unit_tests.R’ [6s/29s]
[6s/30s] 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/AnnotationForge.Rcheck/00check.log’
for details.