Thanks Dan. For some other reason, I can't use devel version of R and/or devel Bioconductor.... Is tere any other way of getting the list of genes per KEGG pathway, and a list of available KEGG pathways?


Many thanks for all your help,

John


________________________________
 From: Dan Tenenbaum <dtenenba@fhcrc.org>

Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" <bioconductor@r-project.org> 
Sent: Thursday, January 17, 2013 9:50 AM
Subject: Re: [BioC] error installing KEGGSOAP


> Thanks Dan. what package is keggLink() from?

It's from the KEGGREST package that Martin mentioned, which is only
available in the devel version of Bioconductor (the one that will be
installed if you use R-devel (aka R 3.0)).

Dan


>
> John
>
> ________________________________
> From: Dan Tenenbaum <dtenenba@fhcrc.org>

> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org"
> <bioconductor@r-project.org>
> Sent: Thursday, January 17, 2013 7:39 AM
>
> Subject: Re: [BioC] error installing KEGGSOAP
>
> On Thu, Jan 17, 2013 at 7:14 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

>> wrote:
>>> Thanks Martin. Is there a simple method to get a list of genes for a
>>> given pathway?
>>>
>>
>> This is how you would do it for human:
>> keggLink("hsa", "path:hsa00010")
>>
>
> Or more generally:
> keggLink("genes", "path:hsa00010")
>
> Dan
>
>
>> Dan
>>
>>
>>> John
>>>
>>>
>>> ________________________________
>>>  From: Martin Morgan <mtmorgan@fhcrc.org>
>>>
>>> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>;
>>> "r-help@r-project.org" <r-help@r-project.org>
>>> Sent: Wednesday, January 16, 2013 10:38 PM
>>> Subject: Re: [BioC] error installing KEGGSOAP
>>>
>>> On 01/16/2013 05:58 PM, array chip wrote:
>>>> Hi, I am new to bioconductor, trying to install KEGGSOAP package, but
>>>> got warnings() when installing and error message when trying to load the
>>>> package, can anyone suggest what went wrong?
>>>>
>>>> many thanks
>>>>
>>>> John
>>>>
>>>>
>>>>
>>>>> source("http://bioconductor.org/biocLite.R")
>>>> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>>>>> biocLite("KEGGSOAP")
>>>> BioC_mirror: http://bioconductor.org
>>>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>>>> Installing package(s) 'KEGGSOAP'
>>>> trying URL
>>>> 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/KEGGSOAP_1.32.0.zip'
>>>> Content type 'application/zip' length 69037 bytes (67 Kb)
>>>> opened URL
>>>> downloaded 67 Kb
>>>>
>>>> package â€˜KEGGSOAPâ€™ successfully unpacked and MD5 sums checked
>>>>
>>>> The downloaded binary packages are in
>>>> Â Â Â Â Â Â Â
>>>> C:\Users\yzhang\AppData\Local\Temp\RtmpawAjwx\downloaded_packages
>>>> Warning message:
>>>> installed directory not writable, cannot update packages 'acepack',
>>>> 'actuar', 'ada', 'ade4', 'ade4TkGUI',
>>>> Â  'agricolae', 'akima', 'ape', 'aplpack', 'arules', 'bitops', 'boot',
>>>> 'Cairo', 'car', 'caTools', 'cba',
>>>> Â  'chron', 'class', 'clue', 'cluster', 'coda', 'colorspace',
>>>> 'CompQuadForm', 'corpcor', 'DAAG', 'date',
>>>> Â  'deldir', 'descr', 'deSolve', 'devtools', 'digest', 'diptest',
>>>> 'doBy', 'DoE.wrapper', 'e1071', 'effects',
>>>> Â  'ENmisc', 'epiR', 'eRm', 'evaluate', 'evd', 'FactoMineR', 'fArma',
>>>> 'fAssets', 'fBasics', 'fdrtool',
>>>> Â  'fExoticOptions', 'fExtremes', 'fGarch', 'fields', 'flexclust',
>>>> 'fMultivar', 'fNonlinear', 'fOptions',
>>>> Â  'forecast', 'foreign', 'fpc', 'fracdiff', 'fRegression', 'FrF2',
>>>> 'FrF2.catlg128', 'fTrading',
>>>> Â  'fUnitRoots', 'gamlss', 'gamlss.data', 'gamlss.dist', 'gclus',
>>>> 'gdata', 'geoR', 'GGally', 'ggm',
>>>> Â  'ggplot2', 'gmodels', 'gridBase', 'gWidgets', 'gWidgetstcltk', 'HH',
>>>> 'Hmisc', 'httr', 'igraph',
>>>> Â  'igraph0', 'inline', 'ipred', 'isa2', 'JavaGD', 'JGR', 'kernlab',
>>>> 'KernSmoot [... truncated]
>>>>
>>>>
>>>>> library(KEGGSOAP)
>>>> Loading required package: BiocGenerics
>>>>
>>>> Attaching package: â€˜BiocGenericsâ€™
>>>>
>>>> The following object(s) are masked from â€˜package:statsâ€™:
>>>>
>>>> Â Â Â  xtabs
>>>>
>>>> The following object(s) are masked from â€˜package:baseâ€™:
>>>>
>>>> Â Â Â  anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>>>> get, intersect, lapply, Map, mapply, mget, order, paste,
>>>> Â Â Â  pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
>>>> rownames, sapply, setdiff, table, tapply, union, unique
>>>>
>>>> failed to load HTTP resource
>>>> Error : .onLoad failed in loadNamespace() for 'KEGGSOAP', details:
>>>> Â  call: NULL
>>>> Â  error: 1: failed to load HTTP resource
>>>>
>>>> Error: package/namespace load failed for â€˜KEGGSOAPâ€™
>>>
>>> KEGG's SOAP service has been discontinued; the package has been replaced
>>> by
>>> KEGGREST, but KEGGREST is only available if using the 'devel' version of
>>> R, e.g.,
>>>
>>>    http://cran.fhcrc.org/bin/windows/base/rdevel.html
>>>
>>> Martin
>>>
>>>>
>>>>
>>>>> sessionInfo()
>>>> R version 2.15.1 (2012-06-22)
>>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_United States.1252Â  LC_CTYPE=English_United
>>>> States.1252Â Â
>>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=CÂ Â Â Â Â Â Â Â Â
>>>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>>>> [5] LC_TIME=English_United States.1252Â Â Â
>>>>
>>>> attached base packages:
>>>> [1] statsÂ Â Â Â  graphicsÂ  grDevices datasetsÂ  utilsÂ Â Â Â  methodsÂ
>>>> Â  baseÂ Â Â Â
>>>>
>>>> other attached packages:
>>>> [1] BiocGenerics_0.4.0Â  BiocInstaller_1.8.3
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] codetools_0.2-8 RCurl_1.91-1.1Â  SSOAP_0.8-0Â Â Â Â  tools_2.15.1Â Â
>>>> Â  XML_3.9-4.1Â Â Â Â  XMLSchema_0.7-2
>>>>    [[alternative HTML version deleted]]
>>>>
>>>>
>>>>
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>>>>
>>>
>>>
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