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error installing KEGGSOAP
3 messages · array chip, Jeff Newmiller, Martin Morgan
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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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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]]
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