AnnotationForge 1.14.2
Bioconductor Package Maintainer
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AnnotationForge | | Last Changed Rev: 117513 / Revision: 122332 | | Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationForge_1.14.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/AnnotationForge.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* this is package ‘AnnotationForge’ version ‘1.14.2’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘AnnotationForge’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
AnnDbPkg-templates 1.8Mb
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:
‘RSQLite’ ‘XML’
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.
* 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 binding for global variable ‘GO.db’
.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’
.filterGOFrame: no visible binding for global variable ‘GOTERM’
.getEnsemblData: no visible global function definition for ‘useMart’
.getEnsemblData: no visible global function definition for ‘getBM’
.getGODate: no visible global function definition for ‘GO_dbconn’
.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 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’
.makeUnWoundGOTables: no visible binding for global variable
‘GOBPANCESTOR’
.makeUnWoundGOTables: no visible binding for global variable
‘GOMFANCESTOR’
.makeUnWoundGOTables: no visible binding for global variable
‘GOCCANCESTOR’
available.ensembl.datasets: no visible global function definition for
‘useMart’
available.ensembl.datasets: no visible global function definition for
‘listDatasets’
getFastaSpeciesDirs: no visible global function definition for
‘getCurlHandle’
getFastaSpeciesDirs: no visible global function definition for ‘getURL’
getProbeDataAffy: no visible global function definition for
‘cleancdfname’
listMappings: no visible global function definition for
‘NCBIORG_DB_SeedGenerator’
writeTable: no visible global function definition for
‘sqliteWriteTable’
Undefined global functions or variables:
CFILE GO.db GOBPANCESTOR GOCCANCESTOR GOMFANCESTOR GOTERM GO_dbconn
NCBIORG_DB_SeedGenerator Stop cleancdfname curlPerform getBM
getBinaryURL getCurlHandle getURL listAttributes listDatasets
sqliteWriteTable url.exists useMart
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘AnnotationForge_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘Biostrings’
* 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
‘/home/biocbuild/bbs-3.3-bioc/meat/AnnotationForge.Rcheck/00check.log’
for details.