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’> 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]]
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array chip <arrayprofile at yahoo.com> 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???
>
>
>> 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]]
>
>
>
>------------------------------------------------------------------------
>
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>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
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