[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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