ExperimentHubData 0.99.11
Bioconductor Package Maintainer
| Snapshot Date: 2016-05-01 17:20:12 -0700 (Sun, 01 May 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ExperimentHubData | | Last Changed Rev: 114071 / Revision: 116962 | | Last Changed Date: 2016-02-27 21:17:39 -0800 (Sat, 27 Feb 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ExperimentHubData_0.99.11.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ExperimentHubData.Rcheck’
* using R version 3.3.0 RC (2016-04-26 r70550)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExperimentHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExperimentHubData’ version ‘0.99.11’
* 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 ‘ExperimentHubData’ can be installed ... [16s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* checking S3 generic/method consistency ... WARNING
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘Title’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘Description’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘BiocVersion’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘Genome’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘SourceType’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘SourceUrl’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘SourceVersion’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘Species’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘TaxonomyId’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘Coordinate_1_based’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘DataProvider’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘Maintainer’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘RDataClass’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘Tags’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘RDataDateAdded’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘RDataPath’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘DispatchClass’
makeExperimentHubMetadata : <anonymous>: no visible binding for global
variable ‘PreparerClass’
readMetadataFromCsv: no visible global function definition for
‘read.csv’
Undefined global functions or variables:
BiocVersion Coordinate_1_based DataProvider Description DispatchClass
Genome Maintainer PreparerClass RDataClass RDataDateAdded RDataPath
SourceType SourceUrl SourceVersion Species Tags TaxonomyId Title
read.csv
Consider adding
importFrom("utils", "read.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘ExperimentHub’
* checking for missing documentation entries ... WARNING
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
* checking Rd \usage sections ... NOTE
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [9s/9s] 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: 4 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/ExperimentHubData.Rcheck/00check.log’
for details.