[R] error installing KEGGSOAP

Jeff Newmiller jdnewmil at dcn.davis.CA.us
Thu Jan 17 03:06:34 CET 2013

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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
>> 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
>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
>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)
>[1] LC_COLLATE=English_United States.1252�� LC_CTYPE=English_United
>[3] LC_MONETARY=English_United States.1252
>[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
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>R-help at r-project.org mailing list
>PLEASE do read the posting guide
>and provide commented, minimal, self-contained, reproducible code.

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