[BioC] error installing KEGGSOAP

Thu Jan 17 19:45:46 CET 2013

On Thu, Jan 17, 2013 at 10:08 AM, array chip <arrayprofile at yahoo.com> wrote:
> 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?
>

>From a web browser you can do this to get the list of all pathways:
http://rest.kegg.jp/list/pathway
To restrict by organism, add the kegg organism code (in this case hsa
for human):
http://rest.kegg.jp/list/pathway/hsa

To get the genes per kegg pathway:
http://rest.kegg.jp/link/genes/path:hsa00010

Or just show all info about the pathway:
http://rest.kegg.jp/get/path:hsa00010

...and parse out the GENE section.
For both of these last two URLs you need to do a bit of parsing.
KEGGREST takes care of this for you.

Dan

> Many thanks for all your help,
>
> John
>
> ________________________________
> From: Dan Tenenbaum <dtenenba at fhcrc.org>
> To: array chip <arrayprofile at yahoo.com>
> Cc: Martin Morgan <mtmorgan at fhcrc.org>; "bioconductor at r-project.org"
> <bioconductor at r-project.org>
> Sent: Thursday, January 17, 2013 9:50 AM
>
> Subject: Re: [BioC] error installing KEGGSOAP
>
> On Thu, Jan 17, 2013 at 9:45 AM, array chip <arrayprofile at yahoo.com> wrote:
>> 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 at fhcrc.org>
>> To: array chip <arrayprofile at yahoo.com>
>> Cc: Martin Morgan <mtmorgan at fhcrc.org>; "bioconductor at r-project.org"
>> <bioconductor at 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 at fhcrc.org> wrote:
>>> On Wed, Jan 16, 2013 at 11:36 PM, array chip <arrayprofile at yahoo.com>
>>> 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 at fhcrc.org>
>>>>
>>>> Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>;
>>>> "r-help at r-project.org" <r-help at 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]]
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
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>>>>> Search the archives:
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>>>>>
>>>>
>>>>
>>>> --
>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N.
>>>> PO Box 19024 Seattle, WA 98109
>>>>
>>>> Location: Arnold Building M1 B861
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>>>>        [[alternative HTML version deleted]]
>>>>
>>>>
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>>
>>
>
>