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BioC 3.2: CHECK report for GEOquery on oaxaca

This page was generated on 2016-04-23 10:23:13 -0700 (Sat, 23 Apr 2016).

Package 432/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEOquery 2.36.0
Sean Davis
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GEOquery
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  ERROR 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  ERROR  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: GEOquery
Version: 2.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GEOquery_2.36.0.tar.gz
StartedAt: 2016-04-23 00:37:22 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 00:41:09 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 226.6 seconds
RetCode: 1
Status:  ERROR 
CheckDir: GEOquery.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GEOquery_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GEOquery.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘2.36.0’
* 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’
* 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’ [93s/184s]
 [93s/184s] 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-3.2-bioc/meat/GEOquery.Rcheck/00check.log’
for details.

GEOquery.Rcheck/00install.out:

* installing *source* package ‘GEOquery’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GEOquery)

GEOquery.Rcheck/GEOquery-Ex.timings:

nameusersystemelapsed
GDS2MA0.0010.0000.001
getGEO000
getGEOSuppFiles0.0010.0000.000
getGEOfile0.0010.0000.000