[BioC] KEGGSOAP

[John Zhang]

One reason might be changes in the APIs at the server site (it happend many 
times in the past) but I am not sure. I will try to have a look to see what 
might be the problem when I get the chance.



>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>X-Spam-Checker-Version: SpamAssassin 3.1.0 (2005-09-13) on hypatia.math.ethz.ch
>X-Spam-Level: 
>X-Spam-Status: No, score=0.4 required=5.0 tests=BAYES_50, FORGED_RCVD_HELO 
autolearn=no version=3.1.0
>Mime-Version: 1.0 (Apple Message framework v746.3)
>To: bioconductor at stat.math.ethz.ch
>From: "Dr. Mayhaus Manuel" <manuel.mayhaus at unimib.it>
>Date: Mon, 20 Mar 2006 17:09:09 +0100
>X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.2.0.0, Antispam-Data: 
2006.03.20.065110
>X-PerlMx-Spam: Gauge=IIIIIII, Probability=7%, Report='__CT 0, __CTE 0, 
__CT_TEXT_PLAIN 0, __HAS_MSGID 0, __HAS_X_MAILER 0, __MIME_TEXT_ONLY 0, 
__MIME_VERSION 0, __SANE_MSGID 0'
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>Subject: [BioC] KEGGSOAP
>X-BeenThere: bioconductor at stat.math.ethz.ch
>X-Mailman-Version: 2.1.7
>List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch>
>List-Unsubscribe: <https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
<mailto:bioconductor-request at stat.math.ethz.ch?subject=unsubscribe>
>List-Archive: <https://stat.ethz.ch/pipermail/bioconductor>
>List-Post: <mailto:bioconductor at stat.math.ethz.ch>
>List-Help: <mailto:bioconductor-request at stat.math.ethz.ch?subject=help>
>List-Subscribe: <https://stat.ethz.ch/mailman/listinfo/bioconductor>, 
<mailto:bioconductor-request at stat.math.ethz.ch?subject=subscribe>
>Content-Transfer-Encoding: 7bit
>X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.2.0.0, Antispam-Data: 
2006.03.20.071106
>X-PMX-Spam: Probability=7%, Report='__CT 0, __CTE 0, __CTYPE_CHARSET_QUOTED 0, 
__CT_TEXT_PLAIN 0, __HAS_MSGID 0, __HAS_X_MAILER 0, __MIME_TEXT_ONLY 0, 
__MIME_VERSION 0, __SANE_MSGID 0, __STOCK_CRUFT 0'
>
>Hi Folks,
>
>I used to have a working KEGGSOAP installation - with RCurl, SSOAP,  
>XML at their proper place...I remember that istallation was a bit  
>tricky.
>Now I try to reuse some code and it doesn't work anymore.
>Even trying the example from the help doesn' t work
>
>>> url <- mark.pathway.by.objects("path:eco00260",  c("eco:b0002",  
>>> "eco:c00263"))
>> Error in .SOAP(KEGGserver, "mark_pathway_by_objects", .soapArgs =
>> list(pathway_id = pathway.id,  : Error occurred in the HTTP  
>> request: Failed
>> to access class (SOAP::KEGG): Can't locate File/Basename.pm in @INC  
>> (@INC
>> contains: /usr/local/WWW/pub/kegg/soap/cgi-bin
>> /usr/local/WWW/cgi/kegg/ligand-bin/PACKAGE
>> /usr/local/WWW/cgi/kegg/ligand-bin/DBIF
>> /usr/local/WWW/cgi/kegg/ssdb-bin/package/GFIT_DBIF
>> /usr/local/WWW/cgi/kegg/ssdb-bin/package/SS_DBIF
>> /usr/local/WWW/pub/kegg/soap) at /usr/local/WWW/pub/kegg/soap/SOAP/ 
>> KEGG.pm
>> line 14. BEGIN failed--compilation aborted at
>> /usr/local/WWW/pub/kegg/soap/SOAP/KEGG.pm line 14. Compilation  
>> failed in
>> require at (eval 89) line 3.
>
>I'am quite sure it used to work - any ideas ?
>Thanks
>
>Manuel Mayhaus
>Genopolis Consortium
>(+39) 02 6448 3530
>http://www.genopolis.it
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084