GEOquery 2.37.0
Sean Davis
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GEOquery | | Last Changed Rev: 109592 / Revision: 116626 | | Last Changed Date: 2015-10-13 12:59:53 -0700 (Tue, 13 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | 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 GEOquery_2.37.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GEOquery.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 ‘GEOquery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEOquery’ version ‘2.37.0’
* 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 ‘GEOquery’ can be installed ... [3s/4s] OK
* checking installed package size ... NOTE
installed size is 13.8Mb
sub-directories of 1Mb or more:
extdata 12.8Mb
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘limma’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Biobase’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘GEOquery/R/zzz.R’:
.onLoad calls:
packageStartupMessage("Setting options('download.file.method.GEOquery'='auto')")
packageStartupMessage("Setting options('GEOquery.inmemory.gpl'=FALSE)")
See section ‘Good practice’ in '?.onAttach'.
GDS2MA: no visible binding for global variable ‘MA’
fastTabRead: no visible global function definition for ‘read.table’
fastTabRead: no visible global function definition for ‘read.delim’
getAndParseGSEMatrices: no visible global function definition for
‘download.file’
getDirListing: no visible global function definition for ‘read.table’
getGEOSuppFiles: no visible global function definition for
‘download.file’
getGEOfile: no visible global function definition for ‘download.file’
getGSEDataTables : <anonymous>: no visible global function definition
for ‘read.delim’
parseGSEMatrix: no visible global function definition for ‘read.table’
parseGSEMatrix: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
MA download.file read.delim read.table
Consider adding
importFrom("utils", "download.file", "read.delim", "read.table")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GEOquery-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGSEDataTables
> ### Title: Get GSE data tables from GEO into R data structures.
> ### Aliases: getGSEDataTables
> ### Keywords: IO
>
> ### ** Examples
>
> dfl = getGSEDataTables("GSE3494")
error : Unknown IO error
I/O warning : failed to load external entity "http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?targ=self&form=xml&view=full&acc=GSE3494"
Error in UseMethod("xmlRoot") :
no applicable method for 'xmlRoot' applied to an object of class "NULL"
Calls: getGSEDataTables -> xmlRoot
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [109s/186s]
[110s/187s] 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 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/GEOquery.Rcheck/00check.log’
for details.