[BioC] error installing KEGGSOAP

[Dan Tenenbaum]

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 ‘KEGGSOAP’ 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: ‘BiocGenerics’
>>>
>>> The following object(s) are masked from ‘package:stats’:
>>>
>>> Â Â Â  xtabs
>>>
>>> The following object(s) are masked from ‘package:base’:
>>>
>>> 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 ‘KEGGSOAP’
>>
>> 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] stats     graphics  grDevices datasets  utils     methods   base   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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