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BioC 3.2: CHECK report for AnnotationForge on oaxaca

This page was generated on 2016-04-23 10:25:57 -0700 (Sat, 23 Apr 2016).

Package 45/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationForge 1.12.2
Bioconductor Package Maintainer
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/AnnotationForge
Last Changed Rev: 112616 / Revision: 116712
Last Changed Date: 2016-01-15 14:29:01 -0800 (Fri, 15 Jan 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationForge
Version: 1.12.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationForge_1.12.2.tar.gz
StartedAt: 2016-04-22 21:48:02 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 21:50:02 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 120.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: AnnotationForge.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationForge_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/AnnotationForge.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.12.2’
* 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 5.45  0.143   5.634
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationForge_unit_tests.R’ [7s/16s]
 [7s/16s] 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.


AnnotationForge.Rcheck/00install.out:

* installing *source* package ‘AnnotationForge’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationForge)

AnnotationForge.Rcheck/AnnotationForge-Ex.timings:

nameusersystemelapsed
AnnDbPkg-maker0.1450.0060.152
available.db0pkgs0.1860.0130.939
generateSeqnames_db000
getProbeDataAffy0.0010.0000.001
getProbeData_1lq0.0010.0000.001
makeChipPackageFromDataFrames0.0040.0000.005
makeInpDb0.0010.0000.001
makeOrgPackage0.0010.0000.001
makeOrgPackageFromDataFrames0.0080.0010.010
makeProbePackage5.4500.1435.634
sqlForge-makeCHIPDB0.0010.0000.001
sqlForge-popDB0.0020.0000.003
sqlForge-wrapDBPackages0.0000.0000.001