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Question: error installing KEGGSOAP
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gravatar for array chip
4.8 years ago by
array chip340
array chip340 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/con trib/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        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’ > 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]]
ADD COMMENTlink modified 4.8 years ago by Martin Morgan ♦♦ 20k • written 4.8 years ago by array chip340
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gravatar for Martin Morgan
4.8 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
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/c ontrib/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 > ? ? ? ? ? ? ? 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 > 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
ADD COMMENTlink written 4.8 years ago by Martin Morgan ♦♦ 20k
Thanks Martin. Is there a simple method to get a list of genes for a given pathway? John ________________________________ From: Martin Morgan <mtmorgan@fhcrc.org> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>; "r-help@r-project.org" <r-help@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/c ontrib/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 >        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@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]]
ADD REPLYlink written 4.8 years ago by array chip340
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") 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 >> ? ? ? ? ? ? ? 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 >> 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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 >>> ? ? ? ? ? ? ? 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 >>> 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 >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k
Thanks Dan. what package is keggLink() from? John ________________________________ From: Dan Tenenbaum <dtenenba@fhcrc.org> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" <bioconductor@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@fhcrc.org> wrote: te: >> 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@fhcrc.org> >> >> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>; "r-help@r-project.org" <r-help@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 >>>        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@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@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by array chip340
On Thu, Jan 17, 2013 at 9:45 AM, array chip <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=""> > To: array chip <arrayprofile at="" yahoo.com=""> > Cc: Martin Morgan <mtmorgan at="" fhcrc.org="">; "bioconductor at r-project.org" > <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=""> 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 >>>> ? ? ? ? ? ? ? >>>> 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 >>>> 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 >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD REPLYlink written 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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? Many thanks for all your help, John ________________________________ From: Dan Tenenbaum <dtenenba@fhcrc.org> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Thursday, January 17, 2013 9:50 AM Subject: Re: [BioC] error installing KEGGSOAP > 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@fhcrc.org> > Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" > <bioconductor@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@fhcrc.org> wrote: >> 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@fhcrc.org> >>> >>> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>; >>> "r-help@r-project.org" <r-help@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 >>>>        >>>> 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@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@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by array chip340
On Thu, Jan 17, 2013 at 10:08 AM, array chip <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. Dan > Many thanks for all your help, > > John > > ________________________________ > From: Dan Tenenbaum <dtenenba at="" fhcrc.org=""> > To: array chip <arrayprofile at="" yahoo.com=""> > Cc: Martin Morgan <mtmorgan at="" fhcrc.org="">; "bioconductor at r-project.org" > <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=""> 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=""> >> To: array chip <arrayprofile at="" yahoo.com=""> >> Cc: Martin Morgan <mtmorgan at="" fhcrc.org="">; "bioconductor at r-project.org" >> <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=""> 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 >>>>> ? ? ? ? ? ? ? >>>>> 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 >>>>> 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 >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >
ADD REPLYlink written 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k
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=""> 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=""> >> To: array chip <arrayprofile at="" yahoo.com=""> >> Cc: Martin Morgan <mtmorgan at="" fhcrc.org="">; "bioconductor at r-project.org" >> <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=""> 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=""> >>> To: array chip <arrayprofile at="" yahoo.com=""> >>> Cc: Martin Morgan <mtmorgan at="" fhcrc.org="">; "bioconductor at r-project.org" >>> <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=""> 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 >>>>>> ? ? ? ? ? ? ? >>>>>> 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 >>>>>> 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 >>>>> 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
ADD REPLYlink written 4.8 years ago by Martin Morgan ♦♦ 20k
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? Thanks John ________________________________ From: Martin Morgan <mtmorgan@fhcrc.org> To: Dan Tenenbaum <dtenenba@fhcrc.org> onductor@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: te: >> 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@fhcrc.org> >> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" >> <bioconductor@r-project.org> >> Sent: Thursday, January 17, 2013 9:50 AM >> >> Subject: Re: [BioC] error installing KEGGSOAP >> te: >>> 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@fhcrc.org> >>> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" >>> <bioconductor@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@fhcrc.org> wrote: >>>> 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@fhcrc.org> >>>>> >>>>> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>; >>>>> "r-help@r-project.org" <r-help@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 >>>>>>        >>>>>> 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@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@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 [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by array chip340
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
ADD REPLYlink written 4.8 years ago by Martin Morgan ♦♦ 20k
Thanks Martin. John ________________________________ From: Martin Morgan <mtmorgan@fhcrc.org> Cc: Dan Tenenbaum <dtenenba@fhcrc.org>; "bioconductor@r-project.org" <bioconductor@r-project.org>; zhaoshilin@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@fhcrc.org> > *To:* Dan Tenenbaum <dtenenba@fhcrc.org> > <bioconductor@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@yahoo.com>  >> 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@fhcrc.org <mailto:dtenenba@fhcrc.org="">> o.com>> >  >> Cc: Martin Morgan <mtmorgan@fhcrc.org <mailto:mtmorgan@fhcrc.org="">>; > "bioconductor@r-project.org <mailto:bioconductor@r-project.org>" >  >> <bioconductor@r-project.org <mailto:bioconductor@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@yahoo.com>  >>> 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@fhcrc.org <mailto:dtenenba@fhcrc.org="">> oo.com>> >  >>> Cc: Martin Morgan <mtmorgan@fhcrc.org <mailto:mtmorgan@fhcrc.org="">>; > "bioconductor@r-project.org <mailto:bioconductor@r-project.org>" >  >>> <bioconductor@r-project.org <mailto:bioconductor@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@fhcrc.org> <mailto:dtenenba@fhcrc.org>> wrote: >  >>>> On Wed, Jan 16, 2013 at 11:36 PM, array chip <arrayprofile@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@fhcrc.org <mailto:mtmorgan@fhcrc.org="">> >  >>>>> >  >>>>> Cc: "bioconductor@r-project.org <mailto:bioconductor@r-project.org>" > <bioconductor@r-project.org <mailto:bioconductor@r-project.org="">>; >  >>>>> "r-help@r-project.org <mailto:r-help@r-project.org>" > <r-help@r-project.org <mailto:r-help@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@r-project.org <mailto:bioconductor@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@r-project.org <mailto:bioconductor@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 [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by array chip340
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 > >
ADD REPLYlink written 4.8 years ago by zhao shilin60
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/2.1 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 > > _______________________________________________ > 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
ADD REPLYlink written 4.8 years ago by Steve Lianoglou12k
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
ADD REPLYlink written 4.8 years ago by Dan Tenenbaum ♦♦ 8.2k
Thank you Dan. This is great information. John ________________________________ From: Dan Tenenbaum <dtenenba@fhcrc.org> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Thursday, January 17, 2013 10:45 AM Subject: Re: [BioC] error installing KEGGSOAP > 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. Dan > Many thanks for all your help, > > John > > ________________________________ > From: Dan Tenenbaum <dtenenba@fhcrc.org> > Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" > <bioconductor@r-project.org> > Sent: Thursday, January 17, 2013 9:50 AM > > Subject: Re: [BioC] error installing KEGGSOAP > e: >> 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@fhcrc.org> >> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org" >> <bioconductor@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@fhcrc.org> wrote: >>> 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@fhcrc.org> >>>> >>>> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>; >>>> "r-help@r-project.org" <r-help@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 >>>>>        >>>>> 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@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@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by array chip340
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