AnnotationHubData 1.5.38
Bioconductor Package Maintainer
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnotationHubData | | Last Changed Rev: 128892 / Revision: 129046 | | Last Changed Date: 2017-04-19 11:01:25 -0400 (Wed, 19 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / 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 AnnotationHubData_1.5.38.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationHubData.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.5.38’
* package encoding: UTF-8
* 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 ‘AnnotationHubData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘BiocInstaller’
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' call to ‘BiocInstaller’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘AnnotationHub:::.db_connection’
Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.NCBIMetadataFromUrl: no visible binding for global variable ‘results’
.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’
.makeComplexGR: no visible binding for global variable ‘seqname’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Title’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Description’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘BiocVersion’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Genome’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘SourceType’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘SourceUrl’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘SourceVersion’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Species’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘TaxonomyId’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Coordinate_1_based’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘DataProvider’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Maintainer’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘RDataClass’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘RDataDateAdded’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘RDataPath’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘DispatchClass’
makeAnnotationHubMetadata : <anonymous> : <anonymous>: no visible
binding for global variable ‘Location_Prefix’
test_BioPaxImportPreparer_recipe: no visible binding for global
variable ‘ahroot’
test_BioPaxImportPreparer_recipe: no visible binding for global
variable ‘BiocVersion’
test_BioPaxImportPreparer_recipe: no visible global function definition
for ‘checkTrue’
test_Inparanoid8ImportPreparer_recipe: no visible global function
definition for ‘suppresWarnings’
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
variable ‘ahroot’
test_Inparanoid8ImportPreparer_recipe: no visible binding for global
variable ‘BiocVersion’
test_Inparanoid8ImportPreparer_recipe: no visible global function
definition for ‘checkTrue’
trackWithAuxiliaryTablesToGRanges: no visible binding for global
variable ‘seqname’
Undefined global functions or variables:
BiocVersion Coordinate_1_based DataProvider Description DispatchClass
Genome Location_Prefix Maintainer RDataClass RDataDateAdded RDataPath
SourceType SourceUrl SourceVersion Species TaxonomyId Title ahroot
checkTrue results seqname specData suppresWarnings
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'AnnotationHubMetadata-class' but not in code:
jsonPath constructAnnotationHubMetadataFromSourceFilePath
constructMetadataFromJsonPath
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 ‘AnnotationHubData_unit_tests.R’
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
‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.