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BioC 3.3: CHECK report for AnnotationForge on morelia

This page was generated on 2016-04-21 13:23:25 -0700 (Thu, 21 Apr 2016).

Package 46/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationForge 1.13.15
Bioconductor Package Maintainer
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationForge
Last Changed Rev: 116393 / Revision: 116626
Last Changed Date: 2016-04-16 09:07:37 -0700 (Sat, 16 Apr 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationForge
Version: 1.13.15
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationForge_1.13.15.tar.gz
StartedAt: 2016-04-20 23:15:59 -0700 (Wed, 20 Apr 2016)
EndedAt: 2016-04-20 23:17:39 -0700 (Wed, 20 Apr 2016)
EllapsedTime: 100.1 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationForge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationForge_1.13.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/AnnotationForge.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.13.15’
* 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 ... [8s/9s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    AnnDbPkg-templates   1.4Mb
    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 ... NOTE
'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’
.doWeNeedUnigene: no visible global function definition for
  ‘read.table’
.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’
.getAFileSet: no visible binding for global variable ‘download.file’
.getAFileSet: no visible binding for global variable ‘untar’
.getBlast2GO: no visible global function definition for ‘read.delim’
.getBlast2GO: no visible global function definition for ‘unzip’
.getBlast2GOData: no visible global function definition for
  ‘read.delim’
.getBlast2GOData: no visible global function definition for ‘unzip’
.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’
.lookupTableName: no visible global function definition for
  ‘read.delim’
.makeARABIDOPSISCHIP_DB: no visible global function definition for
  ‘new’
.makeAnnDbPkg: no visible global function definition for
  ‘installed.packages’
.makeAnnDbPkg: no visible global function definition for ‘str’
.makeAnnDbPkgList: no visible binding for global variable ‘new’
.makeBOVINECHIP_DB: no visible global function definition for ‘new’
.makeBasicMetadata: no visible global function definition for
  ‘read.delim’
.makeCANINECHIP_DB: no visible global function definition for ‘new’
.makeCHICKENCHIP_DB: no visible global function definition for ‘new’
.makeECOLICHIP_DB: no visible global function definition for ‘new’
.makeFLYCHIP_DB: no visible global function definition for ‘new’
.makeGOTablesFromNCBI: no visible binding for global variable
  ‘GOBPANCESTOR’
.makeGOTablesFromNCBI: no visible binding for global variable
  ‘GOMFANCESTOR’
.makeGOTablesFromNCBI: no visible binding for global variable
  ‘GOCCANCESTOR’
.makeHUMANCHIP_DB: no visible global function definition for ‘new’
.makeMOUSECHIP_DB: no visible global function definition for ‘new’
.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’
.makeOrgPackage: no visible global function definition for ‘new’
.makePIGCHIP_DB: no visible global function definition for ‘new’
.makeRATCHIP_DB: no visible global function definition for ‘new’
.makeRHESUSCHIP_DB: no visible global function definition for ‘new’
.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’
.makeWORMCHIP_DB: no visible global function definition for ‘new’
.makeXENOPUSCHIP_DB: no visible global function definition for ‘new’
.makeYEASTCHIP_DB: no visible global function definition for ‘new’
.makeZEBRAFISHCHIP_DB: no visible global function definition for ‘new’
.prepareData: no visible global function definition for ‘read.delim’
.tryDL: no visible global function definition for ‘is’
.tryDL2: no visible global function definition for ‘is’
.unwindGOs: no visible global function definition for ‘unlist2’
.writeToNCBIDB: no visible global function definition for ‘read.delim’
.writeToNCBIDB2: no visible global function definition for ‘read.delim’
OLD_makeOrgPackageFromNCBI: no visible global function definition for
  ‘new’
appendGeneric: no visible global function definition for ‘read.delim’
appendProbesGeneric: no visible global function definition for
  ‘read.delim’
available.db0pkgs: no visible global function definition for
  ‘available.packages’
available.ensembl.datasets: no visible global function definition for
  ‘useMart’
available.ensembl.datasets: no visible global function definition for
  ‘listDatasets’
cleanSrcMap: no visible global function definition for ‘read.delim’
createCntrTableGeneric: no visible global function definition for
  ‘read.delim’
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 ‘is’
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’
initWithDbMetada: no visible global function definition for ‘slot’
initWithDbMetada: no visible global function definition for ‘slot<-’
makeChipPackage: no visible global function definition for ‘new’
makeOrgPackage: no visible binding for global variable ‘verbose’
makeProbePackage: no visible global function definition for
  ‘packageDescription’
printOutBaseMaps: no visible global function definition for
  ‘write.table’
scrubAffyFileComments: no visible global function definition for
  ‘read.csv’
wrapBaseDBPackages: no visible global function definition for
  ‘installed.packages’
writeTable: no visible global function definition for ‘read.table’
writeTable: no visible global function definition for
  ‘sqliteWriteTable’
Undefined global functions or variables:
  CFILE GO.db GOBPANCESTOR GOCCANCESTOR GOMFANCESTOR GOTERM GO_dbconn
  Lkeys Ontology Stop available.packages cleancdfname curlPerform
  dbFileConnect dbFileDisconnect dbInfo download.file getBM
  getBinaryURL getCurlHandle getNodeSet getURL htmlTreeParse
  installed.packages is listAttributes listDatasets new
  packageDescription read.csv read.delim read.table saveXML select slot
  slot<- sqliteWriteTable str unlist2 untar unzip url.exists useMart
  verbose write.table xmlDoc xmlGetAttr xmlParse xmlValue xpathApply
Consider adding
  importFrom("methods", "is", "new", "slot", "slot<-")
  importFrom("utils", "available.packages", "download.file",
             "installed.packages", "packageDescription", "read.csv",
             "read.delim", "read.table", "str", "untar", "unzip",
             "write.table")
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 ... 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 ... [8s/9s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
makeProbePackage 4.901  0.135   5.175
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘AnnotationForge_unit_tests.R’ [7s/7s]
 [7s/7s] 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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-maker0.0650.0080.073
available.db0pkgs0.1560.0080.909
generateSeqnames_db0.0010.0000.000
getProbeDataAffy000
getProbeData_1lq0.0010.0000.001
makeChipPackageFromDataFrames0.0040.0000.004
makeInpDb0.0010.0000.002
makeOrgPackage0.0010.0000.001
makeOrgPackageFromDataFrames0.0070.0010.007
makeProbePackage4.9010.1355.175
sqlForge-makeCHIPDB0.0010.0000.001
sqlForge-popDB0.0020.0000.002
sqlForge-wrapDBPackages0.0010.0000.001