KEGGSOAP 1.13.0
Robert Gentleman
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGSOAP | | Last Changed Rev: 27716 / Revision: 29143 | | Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | ERROR | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | ERROR | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | ERROR | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | [ ERROR ] | OK |
* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.2-bioc/meat/KEGGSOAP.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'KEGGSOAP/DESCRIPTION' ... OK
* this is package 'KEGGSOAP' version '1.13.0'
* 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.genes.by.motifs
>
> flush(stderr()); flush(stdout())
>
> ### Name: get.genes.by.motifs
> ### Title: Client-side interface to obtain the name of genes that contain
> ### the motifs represented by a set of motif ids
> ### Aliases: get.genes.by.motifs
> ### Keywords: datasets
>
> ### ** Examples
>
> genes <- get.genes.by.motifs(c("pf:DnaJ", "ps:DNAJ_2"), 1, 10)
Error in UseMethod("xmlNamespace") :
no applicable method for "xmlNamespace"
Calls: get.genes.by.motifs ... parseArrayType -> SOAPType -> as -> .class1 -> xmlNamespace
Execution halted
installing R.css in D:/biocbld/bbs-2.2-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-2.2-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-2.2-bioc\meat\KEGGSOAP.Rcheck\00_pkg_src\KEGGSOAP\chm\KEGGSOAP.chm, 35,203 bytes
Compression decreased file by 30,966 bytes.
adding MD5 sums
* DONE (KEGGSOAP)