AffyCompatible 1.28.0
Martin Morgan
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/AffyCompatible | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 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 | OK | OK |  |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| morelia | 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-3.1-bioc/R/bin/R CMD check --no-vignettes --timings AffyCompatible_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/AffyCompatible.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AffyCompatible/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AffyCompatible’ version ‘1.28.0’
* 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 ‘AffyCompatible’ can be installed ... [20s/21s] 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.readXmlAsClass: no visible global function definition for
‘xmlTreeParse’
.xassn: no visible global function definition for ‘xpathApply’
.xattrs: no visible global function definition for ‘xmlAttrs’
.xclass: no visible global function definition for ‘xmlName’
.xclass: no visible global function definition for ‘xpathApply’
.xclass: no visible binding for global variable ‘xmlName’
.xmlDoc: no visible global function definition for ‘xmlDoc’
.xpcdata: no visible global function definition for ‘xpathApply’
.xvalue: no visible global function definition for ‘xpathApply’
readXml: no visible global function definition for ‘xmlTreeParse’
xclass: no visible global function definition for ‘xpathApply’
* 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘AffyCompatible-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NetAffxResource-class
> ### Title: Manage NetAffx annotations
> ### Aliases: NetAffxResource-class
> ### [[,NetAffxResource,numeric,missing-method
> ### [[,NetAffxResource,numeric,character-method
> ### [[,NetAffxResource,numeric,numeric-method
> ### [[,NetAffxResource,character,missing-method
> ### [[,NetAffxResource,character,numeric-method
> ### [[,NetAffxResource,character,character-method
> ### affxLicence,NetAffxResource-method affxUrl,NetAffxResource-method
> ### annotationsFile,NetAffxResource-method
> ### directory,NetAffxResource-method names,NetAffxResource-method
> ### password,NetAffxResource-method readAnnotation
> ### readAnnotation,NetAffxResource,character,character-method
> ### readAnnotation,NetAffxResource,character,numeric-method
> ### readAnnotation,NetAffxResource,missing,AffxAnnotation-method
> ### readAnnotation,NetAffxResource,numeric,character-method
> ### readAnnotation,NetAffxResource,numeric,numeric-method
> ### show,NetAffxResource-method user,NetAffxResource-method
> ### Keywords: classes
>
> ### ** Examples
>
> ## Don't show:
> password = acpassword
> ## End(Don't show)
> ## password must be obtained by the user
> rsrc <- NetAffxResource(user="mtmorgan@fhcrc.org", password=password)
> head(names(rsrc))
Document is empty
Start tag expected, '<' not found
Error: 1: Document is empty
2: Start tag expected, '<' not found
Execution halted
* 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, 1 NOTE
See
‘/home/biocbuild/bbs-3.1-bioc/meat/AffyCompatible.Rcheck/00check.log’
for details.