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Question: KEGGSOAP
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gravatar for Dr.Mayhaus Manuel
11.7 years ago by
Dr.Mayhaus Manuel30 wrote:
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
ADD COMMENTlink modified 11.7 years ago by Seth Falcon7.4k • written 11.7 years ago by Dr.Mayhaus Manuel30
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gravatar for Seth Falcon
11.7 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Hi, I'm able to reproduce the error message with the devel version of KEGGSOAP. We will look into it. Seems that something changed on the server side. + seth
ADD COMMENTlink written 11.7 years ago by Seth Falcon7.4k
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gravatar for John Zhang
11.7 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
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
ADD COMMENTlink written 11.7 years ago by John Zhang2.9k
0
gravatar for Nianhua Li
11.7 years ago by
Nianhua Li870
Nianhua Li870 wrote:
Dear Dr. Mayhaus Manuel, The problem is due to an update at KEGG server. They modified the port url from "http://soap.genome.ad.jp/keggapi/request.cgi" into "http://soap.genome.ad.jp/keggapi/request_v5.0.cgi". You could check out an updated version of KEGGSOAP from devel repository or you could update the KEGGserver object: > library(KEGGSOAP) Loading required package: XML Loading required package: SSOAP Loading required package: RCurl Loading required package: RCurl > get.pathways.by.genes(c("eco:b0077", "eco:b0078")) Error in .SOAP(KEGGserver, "get_pathways_by_genes", .soapArgs = list(genes_id_list= genes.id.list), : 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. > > KEGGserver An object of class "HTTPSOAPServer" Slot "host": [1] "soap.genome.ad.jp" Slot "port": [1] NA Slot "url": [1] "/keggapi/request.cgi" > KEGGserver at url <- "/keggapi/request_v5.0.cgi" > get.pathways.by.genes(c("eco:b0077", "eco:b0078")) [1] "path:eco00290" "path:eco00650" "path:eco00660" "path:eco00770" > mark.pathway.by.objects ("path:eco00260", c("eco:b0002", "eco:c00263")) [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api29687/eco00260.gif" thanks nianhua Program in Computational Biology Fred Hutchinson Cancer Research Center
ADD COMMENTlink written 11.7 years ago by Nianhua Li870
Thanks Nianhua, I had been trying the devel-version as well ... with no results. Now having changed the URL it works ! best Manuel Mayhaus Genopolis Consortium (+39) 02 6448 3530 http://www.genopolis.it On Mar 20, 2006, at 8:42 PM, Nianhua Li wrote: > Dear Dr. Mayhaus Manuel, > > The problem is due to an update at KEGG server. They modified the port > url from "http://soap.genome.ad.jp/keggapi/request.cgi" into > "http://soap.genome.ad.jp/keggapi/request_v5.0.cgi". You could > check out > an updated version of KEGGSOAP from devel repository or you could > update > the KEGGserver object: > >> library(KEGGSOAP) > Loading required package: XML > Loading required package: SSOAP > Loading required package: RCurl > Loading required package: RCurl >> get.pathways.by.genes(c("eco:b0077", "eco:b0078")) > Error in .SOAP(KEGGserver, "get_pathways_by_genes", .soapArgs = > list(genes_id_list= genes.id.list), : > 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. >> >> KEGGserver > An object of class "HTTPSOAPServer" > Slot "host": > [1] "soap.genome.ad.jp" > > Slot "port": > [1] NA > > Slot "url": > [1] "/keggapi/request.cgi" > >> KEGGserver at url <- "/keggapi/request_v5.0.cgi" > >> get.pathways.by.genes(c("eco:b0077", "eco:b0078")) > [1] "path:eco00290" "path:eco00650" "path:eco00660" "path:eco00770" >> mark.pathway.by.objects ("path:eco00260", c("eco:b0002", >> "eco:c00263")) > [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api29687/ > eco00260.gif" > > thanks > > nianhua > Program in Computational Biology > Fred Hutchinson Cancer Research Center > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD REPLYlink written 11.7 years ago by Dr.Mayhaus Manuel30
0
gravatar for Seth Falcon
11.7 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"michael watson (IAH-C)" <michael.watson at="" bbsrc.ac.uk=""> writes: > I have been trying to repeat the steps in this thread on Windows, but I > can't find the SSOAP package for windows. Is it available? We have it in the Bioconductor package repositories. Please try: source("http://bioconductor.org/biocLite.R") biocLite("KEGGSOAP") or, if you just want SSOAP, biocLite("SSOAP") + seth
ADD COMMENTlink written 11.7 years ago by Seth Falcon7.4k
0
gravatar for michael watson IAH-C
11.7 years ago by
michael watson IAH-C3.4k wrote:
Hi I have been trying to repeat the steps in this thread on Windows, but I can't find the SSOAP package for windows. Is it available? Thanks Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dr.Mayhaus Manuel Sent: 21 March 2006 08:21 To: Nianhua Li Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] KEGGSOAP Thanks Nianhua, I had been trying the devel-version as well ... with no results. Now having changed the URL it works ! best Manuel Mayhaus Genopolis Consortium (+39) 02 6448 3530 http://www.genopolis.it On Mar 20, 2006, at 8:42 PM, Nianhua Li wrote: > Dear Dr. Mayhaus Manuel, > > The problem is due to an update at KEGG server. They modified the port > url from "http://soap.genome.ad.jp/keggapi/request.cgi" into > "http://soap.genome.ad.jp/keggapi/request_v5.0.cgi". You could check > out an updated version of KEGGSOAP from devel repository or you could > update the KEGGserver object: > >> library(KEGGSOAP) > Loading required package: XML > Loading required package: SSOAP > Loading required package: RCurl > Loading required package: RCurl >> get.pathways.by.genes(c("eco:b0077", "eco:b0078")) > Error in .SOAP(KEGGserver, "get_pathways_by_genes", .soapArgs = > list(genes_id_list= genes.id.list), : > 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. >> >> KEGGserver > An object of class "HTTPSOAPServer" > Slot "host": > [1] "soap.genome.ad.jp" > > Slot "port": > [1] NA > > Slot "url": > [1] "/keggapi/request.cgi" > >> KEGGserver at url <- "/keggapi/request_v5.0.cgi" > >> get.pathways.by.genes(c("eco:b0077", "eco:b0078")) > [1] "path:eco00290" "path:eco00650" "path:eco00660" "path:eco00770" >> mark.pathway.by.objects ("path:eco00260", c("eco:b0002", >> "eco:c00263")) > [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api29687/ > eco00260.gif" > > thanks > > nianhua > Program in Computational Biology > Fred Hutchinson Cancer Research Center > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 11.7 years ago by michael watson IAH-C3.4k
0
gravatar for Seth Falcon
11.7 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
>> Is it possible to get the zip file for SSOAP for windows rather than >> use biocLite? Some people I want to give access to don't have access >> to the internet. I looked on bioconductor.org and couldn't find the >> zip file .... > > When you use biocLite, you also get the zip file - note the second to > last line in this R session: You can also specify a 'destdir' argument and the package should get downloaded there (and not deleted when you quit R). The SSOAP package is provided by the Omegahat project (http://www.omegahat.org) and you may be able to browse for a download there. + seth
ADD COMMENTlink written 11.7 years ago by Seth Falcon7.4k
0
gravatar for michael watson IAH-C
11.7 years ago by
michael watson IAH-C3.4k wrote:
Hi Seth Is it possible to get the zip file for SSOAP for windows rather than use biocLite? Some people I want to give access to don't have access to the internet. I looked on bioconductor.org and couldn't find the zip file .... Mick ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Seth Falcon Sent: Tue 21/03/2006 2:05 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] KEGGSOAP "michael watson (IAH-C)" <michael.watson at="" bbsrc.ac.uk=""> writes: > I have been trying to repeat the steps in this thread on Windows, but I > can't find the SSOAP package for windows. Is it available? We have it in the Bioconductor package repositories. Please try: source("http://bioconductor.org/biocLite.R") biocLite("KEGGSOAP") or, if you just want SSOAP, biocLite("SSOAP") + seth _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 11.7 years ago by michael watson IAH-C3.4k
Hi Mick, michael watson (IAH-C) wrote: > Hi Seth > > Is it possible to get the zip file for SSOAP for windows rather than > use biocLite? Some people I want to give access to don't have access > to the internet. I looked on bioconductor.org and couldn't find the > zip file .... When you use biocLite, you also get the zip file - note the second to last line in this R session: > source("http://www.bioconductor.org/biocLite.R") > biocLite("SSOAP") Running bioCLite version 0.1 with R version 2.3.0 Running biocinstall version 1.3 with R version 2.3.0 trying URL 'http://www.bioconductor.org/packages/omegahat/1.8/bin/windows/contrib /2.3/SSOAP_0.2-2.zip' Content type 'application/zip' length 209039 bytes opened URL downloaded 204Kb package 'SSOAP' successfully unpacked and MD5 sums checked The downloaded packages are in C:\WINDOWS\Temp\RtmpG4dwpb\downloaded_packages updating HTML package descriptions Also note that this file will be removed when you quit R, so you have to retrieve it first. Best, Jim > > Mick > > ________________________________ > > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Seth Falcon > Sent: Tue 21/03/2006 2:05 PM To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] KEGGSOAP > > > > "michael watson (IAH-C)" <michael.watson at="" bbsrc.ac.uk=""> writes: > >> I have been trying to repeat the steps in this thread on Windows, >> but I can't find the SSOAP package for windows. Is it available? > > > We have it in the Bioconductor package repositories. Please try: > > source("http://bioconductor.org/biocLite.R") biocLite("KEGGSOAP") > > or, if you just want SSOAP, biocLite("SSOAP") > > + seth > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 11.7 years ago by James W. MacDonald45k
0
gravatar for Seth Falcon
11.7 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Sean Davis <sdavis2 at="" mail.nih.gov=""> writes: > Mick, > > I think Jim pointed out that when you do an install, it tells you from where > it is getting the file. From his previous email, it looks like this is what > you want: > > http://www.bioconductor.org/packages/omegahat/1.8/bin/windows/contri b/2.3/SS > OAP_0.2-2.zip Using biocLite as detailed earlier in this thread has the benefit that you will get the correct version for your R. The above package is for the devel version of R and may not work with the current release (but it might). + seth
ADD COMMENTlink written 11.7 years ago by Seth Falcon7.4k
0
gravatar for michael watson IAH-C
11.7 years ago by
michael watson IAH-C3.4k wrote:
Thanks Seth and Jim. I browsed omegahat but I could only find the .tar.gz package for SSOAP ATB Mick ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Seth Falcon Sent: Wed 22/03/2006 2:44 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] KEGGSOAP >> Is it possible to get the zip file for SSOAP for windows rather than >> use biocLite? Some people I want to give access to don't have access >> to the internet. I looked on bioconductor.org and couldn't find the >> zip file .... > > When you use biocLite, you also get the zip file - note the second to > last line in this R session: You can also specify a 'destdir' argument and the package should get downloaded there (and not deleted when you quit R). The SSOAP package is provided by the Omegahat project (http://www.omegahat.org) and you may be able to browse for a download there. + seth _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 11.7 years ago by michael watson IAH-C3.4k
Mick, I think Jim pointed out that when you do an install, it tells you from where it is getting the file. From his previous email, it looks like this is what you want: http://www.bioconductor.org/packages/omegahat/1.8/bin/windows/contrib/ 2.3/SS OAP_0.2-2.zip Sean On 3/23/06 9:28 AM, "michael watson (IAH-C)" <michael.watson at="" bbsrc.ac.uk=""> wrote: > Thanks Seth and Jim. I browsed omegahat but I could only find the .tar.gz > package for SSOAP > > ATB > Mick > > ________________________________ > > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Seth Falcon > Sent: Wed 22/03/2006 2:44 PM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] KEGGSOAP > > > >>> Is it possible to get the zip file for SSOAP for windows rather than >>> use biocLite? Some people I want to give access to don't have access >>> to the internet. I looked on bioconductor.org and couldn't find the >>> zip file .... >> >> When you use biocLite, you also get the zip file - note the second to >> last line in this R session: > > You can also specify a 'destdir' argument and the package should get > downloaded there (and not deleted when you quit R). > > The SSOAP package is provided by the Omegahat project > (http://www.omegahat.org) and you may be able to browse for a download > there. > > + seth > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 11.7 years ago by Sean Davis21k
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