[BioC] Error installing package affy

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Fri May 14 17:44:12 CEST 2004


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 at 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'


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