[BioC] error installing KEGGSOAP
Dan Tenenbaum
dtenenba at fhcrc.org
Thu Jan 17 20:46:39 CET 2013
On Thu, Jan 17, 2013 at 11:42 AM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> 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.
>
Two things happened at KEGG:
1) They started charging money (or requiring a license) for ftp access.
2) They shut off the SOAP server and replaced it with a REST server.
These two things are not related in any practical way as far as I can tell.
See this page, especially the second post, for more:
http://www.genome.jp/kegg/docs/plea.html
Dan
> 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:
>>> >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> >>>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>> --
>>> >>>>> 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
>>> >>>>> Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>>>
>>> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> >>>>> Search the archives:
>>> >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> >>>
>>> >>>
>>> >>
>>> >>
>>>
>>>
>>> --
>>> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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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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