[BioC] Installation of package affy failed

Armin Schmitt armin.schmitt at agrar.hu-berlin.de
Thu Apr 29 12:12:38 CEST 2004


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-Universität zu Berlin
Invalidenstraße 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 at 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'


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