BioC 2.1: CHECK report for KEGGSOAP on lemming

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.1-bioc/meat/KEGGSOAP.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-06-03 r41797)
* checking for file 'KEGGSOAP/DESCRIPTION' ... OK
* this is package 'KEGGSOAP' version '1.11.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'KEGGSOAP' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating KEGGSOAP-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'KEGGSOAP-Ex.R' failed.
The error most likely occurred in:

> ### * get.motifs.by.gene
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: get.motifs.by.gene
> ### Title: Client-side interface to obtain the name of genes that are
> ###   homologous to a given gene
> ### Aliases: get.motifs.by.gene
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     if(require("SSOAP") && require("XML")){
+         motifs <- get.motifs.by.gene("eco:b0002", "pfam")
+         sapply(motifs, function(x) x$motif_id)
+     } 
Error in UseMethod("as.integer") : no applicable method for "as.integer"
Execution halted

installing R.css in D:/biocbld/bbs-2.1-bioc/meat/KEGGSOAP.Rcheck


---------- Making package KEGGSOAP ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  preparing package KEGGSOAP for lazy loading
Loading required package: XML
Loading required package: SSOAP
Loading required package: RCurl
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'KEGGSOAP'
     Formats: text html latex example chm 
  KEGGserver                        text    html    latex           chm
  bget                              text    html    latex   example chm
  get.genes.by.motifs               text    html    latex   example chm
  get.genes.by.organism             text    html    latex   example chm
  get.genes.by.pathway              text    html    latex   example chm
  get.motifs.by.gene                text    html    latex   example chm
  get.paralogs.by.gene              text    html    latex   example chm
  get.pathways.by.genes             text    html    latex   example chm
  getBestNeighbors                  text    html    latex   example chm
  list.organisms                    text    html    latex   example chm
  mark.pathway.by.objects           text    html    latex   example chm
  search.compounds.by.name          text    html    latex   example chm
  search.glycans.by.name            text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.1-bioc\meat\KEGGSOAP.Rcheck\00_pkg_src\KEGGSOAP\chm\KEGGSOAP.chm


Compile time: 0 minutes, 0 seconds
14	Topics
64	Local links
15	Internet links
1	Graphic


Created d:\biocbld\bbs-2.1-bioc\meat\KEGGSOAP.Rcheck\00_pkg_src\KEGGSOAP\chm\KEGGSOAP.chm, 35,317 bytes
Compression decreased file by 31,432 bytes.
  adding MD5 sums

* DONE (KEGGSOAP)

Package 114/238	Hostname	OS	Arch	BUILD	CHECK	BUILD BIN
KEGGSOAP 1.11.0 J. Zhang Last Changed Date: 2007-04-24 11:31:42 -0700 Last Changed Rev: 24217	lamb1	Linux (SUSE 10.1)	x86_64	OK	ERROR
	wellington	Linux (SUSE 9.2)	i686	OK	ERROR
	churchill	Solaris 2.9	sparc	OK	ERROR
	lemming	Windows Server 2003 (32-bit)	x64	OK	[ ERROR ]	skipped

KEGGSOAP

1.11.0

Command output