[BioC] error installing KEGGSOAP

Steve Lianoglou mailinglist.honeypot at gmail.com
Thu Jan 17 20:42:32 CET 2013


Hi,

Just a random question re: the KEGG stuff.

Is the suggestion that the KEGG info using KEGGREST up to date? I get
the impression that this is what's being alluded to, but I thought
that all-things-related-to-KEGG were being either (1) cutoff entirely;
or (2) restricted behind some pay wall.

Am I wrong?

-steve


On Thu, Jan 17, 2013 at 2:28 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 1/17/2013 11:11 AM, array chip wrote:
>>
>> Thanks Martin for pointing this out.
>>
>> Does this mean other KEGG packages may not be up-to-date as well if they
>> depend
>> on KEGG.db? For example, I am interested in KEGGprofile package for
>> enrichment
>> analysis. Is KEGGprofile not up-to-date now?
>
>
> I have not used KEGGprofile so do not have a direct answer; perhaps the
> maintainer will respond (packageDescription("KEGGprofile")[["Maintainer"]]).
> From a brief look, e.g., download_KEGGfile and plot_pathway, the package
> allows retrieval of data from the KEGG web site so do not necessarily use
> the KEGG.db package. On the other hand, find_enriched_pathway does seem to
> use KEGG.db.
>
> Martin
>
>>
>> Thanks
>>
>> John
>>
>>
>>
>> --------------------------------------------------------------------------------
>> *From:* Martin Morgan <mtmorgan at fhcrc.org>
>> *To:* Dan Tenenbaum <dtenenba at fhcrc.org>
>> *Cc:* array chip <arrayprofile at yahoo.com>; "bioconductor at r-project.org"
>> <bioconductor at r-project.org>
>> *Sent:* Thursday, January 17, 2013 10:53 AM
>> *Subject:* Re: [BioC] error installing KEGGSOAP
>>
>>
>> On 1/17/2013 10:45 AM, Dan Tenenbaum wrote:
>>  > On Thu, Jan 17, 2013 at 10:08 AM, array chip <arrayprofile at yahoo.com
>> <mailto: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.
>>
>> Also, the KEGG.db package provides a now quite out-of-date version
>> (because of
>> changes in licensing requirements) of the KEGG data base.
>>
>>  > library(org.Hs.eg.db)
>>  > # discover the columns that can be queried, and the format of the
>> 'PATH' keys
>>  > cols(org.Hs.eg.db)
>>    [1] "ENTREZID"    "PFAM"        "IPI"          "PROSITE"      "ACCNUM"
>>    [6] "ALIAS"        "CHR"          "CHRLOC"      "CHRLOCEND"    "ENZYME"
>> [11] "MAP"          "PATH"        "PMID"        "REFSEQ"      "SYMBOL"
>> [16] "UNIGENE"      "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
>> "GENENAME"
>> [21] "UNIPROT"      "GO"          "EVIDENCE"    "ONTOLOGY"    "GOALL"
>> [26] "EVIDENCEALL"  "ONTOLOGYALL"  "OMIM"        "UCSCKG"
>>  > head(keys(org.Hs.eg.db, "PATH"))
>> [1] "04610" "00232" "00983" "01100" "00380" "00970"
>>  > head(select(org.Hs.eg.db, "00010", "ENTREZID", "PATH"))
>>      PATH ENTREZID
>> 1 00010      124
>> 2 00010      125
>> 3 00010      126
>> 4 00010      127
>> 5 00010      128
>> 6 00010      130
>> Warning message:
>> In .generateExtraRows(tab, keys, jointype) :
>>    'select' resulted in 1:many mapping between keys and return rows
>>
>> Note that on loading KEGG.db we see this:
>>
>> KEGG.db contains mappings based on older data because the original
>>    resource was removed from the the public domain before the most
>>    recent update was produced. This package should now be considered
>>    deprecated and future versions of Bioconductor may not have it
>>    available.  One possible alternative to consider is to look at the
>>    reactome.db package
>>
>>  >
>>  > Dan
>>  >
>>  >
>>  >
>>  >
>>  >> Many thanks for all your help,
>>  >>
>>  >> John
>>  >>
>>  >> ________________________________
>>  >> From: Dan Tenenbaum <dtenenba at fhcrc.org <mailto:dtenenba at fhcrc.org>>
>>  >> To: array chip <arrayprofile at yahoo.com
>> <mailto:arrayprofile at yahoo.com>>
>>  >> Cc: Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>;
>> "bioconductor at r-project.org <mailto:bioconductor at r-project.org>"
>>  >> <bioconductor at r-project.org <mailto: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
>> <mailto: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 <mailto:dtenenba at fhcrc.org>>
>>  >>> To: array chip <arrayprofile at yahoo.com
>> <mailto:arrayprofile at yahoo.com>>
>>  >>> Cc: Martin Morgan <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>;
>> "bioconductor at r-project.org <mailto:bioconductor at r-project.org>"
>>  >>> <bioconductor at r-project.org <mailto: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
>> <mailto:dtenenba at fhcrc.org>> wrote:
>>  >>>> On Wed, Jan 16, 2013 at 11:36 PM, array chip <arrayprofile at yahoo.com
>> <mailto: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
>> <mailto:mtmorgan at fhcrc.org>>
>>  >>>>>
>>  >>>>> Cc: "bioconductor at r-project.org
>> <mailto:bioconductor at r-project.org>"
>> <bioconductor at r-project.org <mailto:bioconductor at r-project.org>>;
>>  >>>>> "r-help at r-project.org <mailto:r-help at r-project.org>"
>> <r-help at r-project.org <mailto: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 <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'
>>
>> <http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/KEGGSOAP_1.32.0.zip%27>
>>
>>  >>>>>> 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   Â
>>  >>>>>> methodsÂ
>>  >>>>>>   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]]
>>  >>>>>>
>>  >>>>>>
>>  >>>>>>
>>  >>>>>> _______________________________________________
>>  >>>>>> Bioconductor mailing list
>>  >>>>>> Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>
>>  >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>  >>>>>> 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
>>  >>>>> Phone: (206) 667-2793
>>  >>>>>        [[alternative HTML version deleted]]
>>  >>>>>
>>  >>>>>
>>  >>>>> _______________________________________________
>>  >>>>> Bioconductor mailing list
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>>
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>>  >>>
>>  >>>
>>  >>
>>  >>
>>
>>
>> --
>> Dr. Martin Morgan, PhD
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>>
>
>
> --
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> _______________________________________________
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> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact



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