Dear all, I received the following error (full output attached) when I tried to install the affy package and there does not seem to be mentioned in the mail archives recently. ERROR: command (e.g. \url) inside \link ERROR: building help failed for package 'affy' R-version : 1.9.0 Bioconductor : Release 1.3 (today) System : Linux 2.4.18-27.8.0 gcc-version : gcc (GCC) 3.2 Can anyone please help ? Thank you. -- Adaikalavan Ramasamy <ramasamy@cancer.org.uk> Cancer Research UK -------------- next part -------------- > R CMD INSTALL affy_1.3.28.tar.gz * 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/home/msl/ramasa01/R/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -I/home/msl/ramasa01/R/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c getall_locations.c -o getall_locations.o gcc -I/home/msl/ramasa01/R/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c qnorm.c -o qnorm.o gcc -I/home/msl/ramasa01/R/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -I/home/msl/ramasa01/R/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma2.c -o rma2.o gcc -I/home/msl/ramasa01/R/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma_background2.c -o rma_background2.o gcc -I/home/msl/ramasa01/R/lib/R/include -DHAVE_ZLIB=1 -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma_common.c -o rma_common.o gcc -shared -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o -lz ** 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'