[BioC] error installing KEGGSOAP
Martin Morgan
mtmorgan at fhcrc.org
Thu Jan 17 20:28:04 CET 2013
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 Also, the KEGG.db package provides a now quite out-of-date version (because of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
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> >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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> >>>>> 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
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