Dear madame, dear sir, upon installation of bioconductor package affy I receive the error message which I have attached. I would be grateful for your assistance. Thank you very much Armin Schmitt -- Dr. Armin Schmitt INW-LGF Humboldt-Universit?t zu Berlin Invalidenstra?e 42 D-10115 Berlin Tel.: ++49-30-2093-9074 -------------- next part -------------- > source("http://www.bioconductor.org/getBioC.R") > getBioC("affy") Running getBioC version 1.2.54.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Loading required package: reposTools Synching your local package management information ... Synching your local package management information ... Warning messages: 1: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") 2: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") Note: NA does not seem to have a valid repository, skipping [1] "Attempting to download affy from http://www.bioconductor.org/repository/release1.3/package/Source" [1] "Download complete." [1] "Installing affy" * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c chipbackground.c -o chipbackground.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c getall_locations.c -o getall_locations.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c qnorm.c -o qnorm.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c read_abatch.c -o read_abatch.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c rma2.c -o rma2.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c rma_background2.c -o rma_background2.o gcc -I/usr/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I/opt/gnome/include -D__NO_MATH_INLINES -mieee-fp -fPIC -c rma_common.c -o rma_common.o gcc -shared -L/usr/local/lib -L/opt/gnome/lib -o affy.so chipbackground.o getall_locations.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o -lz -L/usr/lib/R/bin -lR ** R ** data ** demo ** inst ** save image Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. [1] TRUE Warning message: 'package.description' is deprecated. Use 'packageDescription' instead. See help("Deprecated") [1] TRUE Warning message: package 'modreg' has been merged into 'stats' [1] TRUE Warning message: package 'eda' has been merged into 'stats' [1] "AffyBatch" [1] "cdfName" [1] "cdfName" [1] "intensity" [1] "intensity" [1] "intensity<-" [1] "intensity<-" [1] "length" [1] "ncol" [1] "ncol" [1] "nrow" [1] "nrow" [1] "geneNames" [1] "show" [1] "indexProbes" [1] "indexProbes" [1] "pmindex" [1] "pmindex" [1] "mmindex" [1] "mmindex" [1] "probeNames" [1] "probeNames" [1] "probes" [1] "probes" [1] "pm" [1] "pm" [1] "pm<-" [1] "pm<-" [1] "mm" [1] "mm" [1] "mm<-" [1] "mm<-" [1] "probeset" [1] "probeset" [1] "[" [1] "[<-" [1] "bg.correct" [1] "bg.correct" [1] "normalize.methods" [1] "normalize.methods" [1] "normalize" [1] "normalize" [1] "computeExprSet" [1] "computeExprSet" [1] "image" [1] "image" [1] "boxplot" [1] "boxplot" [1] "hist" [1] "hist" [1] "mas5calls" [1] "mas5calls" [1] "ProbeSet" [1] "show" [1] "colnames" [1] "sampleNames" [1] "colnames" [1] "pm" [1] "pm<-" [1] "mm" [1] "mm<-" [1] "express.summary.stat" [1] "express.summary.stat" [1] "barplot" [1] "barplot" [1] "mas5calls" ** help >>> Building/Updating help pages for package 'affy' Formats: text html latex example .setAffyOptions text html latex example AffyBatch-class text html latex example AffyRNAdeg text html latex example ProbeSet-class text html latex example SpikeIn text html latex affy-options text html latex example affy.scalevalue.exprSet text html latex affybatch.example text html latex barplot.ProbeSet text html latex example bg.adjust text html latex bgc text html latex example cdfFromBioC text html latex example cdfenv.example text html latex cleancdfname text html latex example debug.affy123 text html latex expresso text html latex example expressoWidget text html latex example fit.li.wong text html latex example generateExprSet-methods text html latex example generateExprVal-methods text html latex example generateExprVal.method.avgdiff text html latex example generateExprVal.method.playerout text html latex hlog text html latex justrma text html latex example list.celfiles text html latex example loess.normalize text html latex maffy.normalise text html latex example maffy.subset text html latex example mas5 text html latex example mas5calls text html latex example merge.AffyBatch text html latex example multiloess text html latex mva.pairs text html latex example normalize-methods text html latex example normalize text html latex normalize.constant text html latex normalize.contrast text html latex example normalize.invariantset text html latex ERROR: command (e.g. \url) inside \link ERROR: building help failed for package 'affy' ** Removing '/usr/lib/R/library/affy' >From URL: http://www.bioconductor.org/repository/release1.3/package/Source affy version 1.3.28 Packages that were not updated: Biobase annotate genefilter geneplotter edd ROC multtest pamr limma MAGEML siggenes globaltest vsn affydata annaffy affyPLM matchprobes gcrma makecdfenv Warning messages: 1: Failed to read replisting at NA in: getReplisting(repURL, repFile) 2: Installation of package affy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > library("affy") Error in library("affy") : There is no package called 'affy'