Hi all, I think what Martin said is exact. The primary function of KEGGprofile package is plot_pathway, which uses the latest files in the KEGG website. So the final result figure which represents the gene expression in each pathway is up-to-date. Because find_enriched_pathway needs a list with genes for every pathway, which is only provided by KEGG.db, it is not up-to-date. An alternative solution is generating the list from KEGG website every time when running the function. But I think it would take too much time. Any suggestion for improving this function is welcome. Shilin 2013/1/18 array chip <arrayprofile at="" yahoo.com="">: > Thanks Martin. > > John > > ________________________________ > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > To: array chip <arrayprofile at="" yahoo.com=""> > Cc: Dan Tenenbaum <dtenenba at="" fhcrc.org="">; "bioconductor at r-project.org" > <bioconductor at="" r-project.org="">; zhaoshilin at gmail.com > Sent: Thursday, January 17, 2013 11:28 AM > > Subject: Re: [BioC] error installing KEGGSOAP > > 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/2.1 5/KEGGSOAP_1.32.0.zip' >> >> <http: bioconductor.org="" packages="" 2.11="" bioc="" bin="" windows="" contrib="" 2.1="" 5="" 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 >> >>>>>> ? ? ? ? ? ? ? >> >>>>>> C:\Users\yzhang\AppData\Local\Temp\RtmpawAjwx\downloaded_packages >> >>>>>> Warning message: >> >>>>>> installed directory not writable, cannot update packages >> 'acepack', >> >>>>>> 'actuar', 'ada', 'ade4', 'ade4TkGUI', >> >>>>>> ? 'agricolae', 'akima', 'ape', 'aplpack', 'arules', 'bitops', >> 'boot', >> >>>>>> 'Cairo', 'car', 'caTools', 'cba', >> >>>>>> ? 'chron', 'class', 'clue', 'cluster', 'coda', 'colorspace', >> >>>>>> 'CompQuadForm', 'corpcor', 'DAAG', 'date', >> >>>>>> ? 'deldir', 'descr', 'deSolve', 'devtools', 'digest', 'diptest', >> >>>>>> 'doBy', 'DoE.wrapper', 'e1071', 'effects', >> >>>>>> ? 'ENmisc', 'epiR', 'eRm', 'evaluate', 'evd', 'FactoMineR', >> 'fArma', >> >>>>>> 'fAssets', 'fBasics', 'fdrtool', >> >>>>>> ? 'fExoticOptions', 'fExtremes', 'fGarch', 'fields', 'flexclust', >> >>>>>> 'fMultivar', 'fNonlinear', 'fOptions', >> >>>>>> ? 'forecast', 'foreign', 'fpc', 'fracdiff', 'fRegression', >> 'FrF2', >> >>>>>> 'FrF2.catlg128', 'fTrading', >> >>>>>> ? 'fUnitRoots', 'gamlss', 'gamlss.data', 'gamlss.dist', 'gclus', >> >>>>>> 'gdata', 'geoR', 'GGally', 'ggm', >> >>>>>> ? 'ggplot2', 'gmodels', 'gridBase', 'gWidgets', 'gWidgetstcltk', >> 'HH', >> >>>>>> 'Hmisc', 'httr', 'igraph', >> >>>>>> ? '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???: >> >>>>>> >> >>>>>> ? ? ? xtabs >> >>>>>> >> >>>>>> The following object(s) are masked from ???package:base???: >> >>>>>> >> >>>>>> ? ? ? anyDuplicated, cbind, colnames, duplicated, eval, Filter, >> Find, >> >>>>>> get, intersect, lapply, Map, mapply, mget, order, paste, >> >>>>>> ? ? ? 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: >> >>>>>> ? call: NULL >> >>>>>> ? 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.1252? >> LC_CTYPE=English_United >> >>>>>> States.1252? ? >> >>>>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C? ? ? ? ? ? >> ? ? >> >>>>>> ? >> >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >> >>>>>> [5] LC_TIME=English_United States.1252? ? ? >> >>>>>> >> >>>>>> attached base packages: >> >>>>>> [1] stats? ? ? ? graphics? grDevices datasets? utils? ? ? ? >> >>>>>> methods? >> >>>>>> ? base? ? ? ? >> >>>>>> >> >>>>>> other attached packages: >> >>>>>> [1] BiocGenerics_0.4.0? BiocInstaller_1.8.3 >> >>>>>> >> >>>>>> loaded via a namespace (and not attached): >> >>>>>> [1] codetools_0.2-8 RCurl_1.91-1.1? SSOAP_0.8-0? ? ? ? >> tools_2.15.1? >> >>>>>> ? >> >>>>>> ? XML_3.9-4.1? ? ? ? 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 > >

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 >>> >>>>>> ? ? ? ? ? ? ? >>> >>>>>> C:\Users\yzhang\AppData\Local\Temp\RtmpawAjwx\downloaded_packages >>> >>>>>> Warning message: >>> >>>>>> installed directory not writable, cannot update packages >>> 'acepack', >>> >>>>>> 'actuar', 'ada', 'ade4', 'ade4TkGUI', >>> >>>>>> ? 'agricolae', 'akima', 'ape', 'aplpack', 'arules', 'bitops', >>> 'boot', >>> >>>>>> 'Cairo', 'car', 'caTools', 'cba', >>> >>>>>> ? 'chron', 'class', 'clue', 'cluster', 'coda', 'colorspace', >>> >>>>>> 'CompQuadForm', 'corpcor', 'DAAG', 'date', >>> >>>>>> ? 'deldir', 'descr', 'deSolve', 'devtools', 'digest', 'diptest', >>> >>>>>> 'doBy', 'DoE.wrapper', 'e1071', 'effects', >>> >>>>>> ? 'ENmisc', 'epiR', 'eRm', 'evaluate', 'evd', 'FactoMineR', >>> 'fArma', >>> >>>>>> 'fAssets', 'fBasics', 'fdrtool', >>> >>>>>> ? 'fExoticOptions', 'fExtremes', 'fGarch', 'fields', 'flexclust', >>> >>>>>> 'fMultivar', 'fNonlinear', 'fOptions', >>> >>>>>> ? 'forecast', 'foreign', 'fpc', 'fracdiff', 'fRegression', >>> 'FrF2', >>> >>>>>> 'FrF2.catlg128', 'fTrading', >>> >>>>>> ? 'fUnitRoots', 'gamlss', 'gamlss.data', 'gamlss.dist', 'gclus', >>> >>>>>> 'gdata', 'geoR', 'GGally', 'ggm', >>> >>>>>> ? 'ggplot2', 'gmodels', 'gridBase', 'gWidgets', 'gWidgetstcltk', >>> 'HH', >>> >>>>>> 'Hmisc', 'httr', 'igraph', >>> >>>>>> ? '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???: >>> >>>>>> >>> >>>>>> ? ? ? xtabs >>> >>>>>> >>> >>>>>> The following object(s) are masked from ???package:base???: >>> >>>>>> >>> >>>>>> ? ? ? anyDuplicated, cbind, colnames, duplicated, eval, Filter, >>> Find, >>> >>>>>> get, intersect, lapply, Map, mapply, mget, order, paste, >>> >>>>>> ? ? ? 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: >>> >>>>>> ? call: NULL >>> >>>>>> ? 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.1252? >>> LC_CTYPE=English_United >>> >>>>>> States.1252? ? >>> >>>>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C? ? ? ? ? ? >>> ? ? >>> >>>>>> ? >>> >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >>> >>>>>> [5] LC_TIME=English_United States.1252? ? ? >>> >>>>>> >>> >>>>>> attached base packages: >>> >>>>>> [1] stats? ? ? ? graphics? grDevices datasets? utils? ? ? ? >>> >>>>>> methods? >>> >>>>>> ? base? ? ? ? >>> >>>>>> >>> >>>>>> other attached packages: >>> >>>>>> [1] BiocGenerics_0.4.0? BiocInstaller_1.8.3 >>> >>>>>> >>> >>>>>> loaded via a namespace (and not attached): >>> >>>>>> [1] codetools_0.2-8 RCurl_1.91-1.1? SSOAP_0.8-0? ? ? ? >>> tools_2.15.1? >>> >>>>>> ? >>> >>>>>> ? XML_3.9-4.1? ? ? ? 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 >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor