[BioC] affy packages on Linux doesn't get installed

juliab at stat.berkeley.edu juliab at stat.berkeley.edu
Thu Nov 20 22:51:03 MET 2003


Hi,

I am having trouble getting packages in Bioconductor installed.  It looks
like affy is the one causing the trouble, and that's the one I actually
need, too...

I am working under Linux, with R 1.8.1 beta.  I copy the report of the
intallation below in this email.  Any help would be very much appreciated.

Thank you,
Julia

> source("http://www.bioconductor.org/getBioC.R")
> getBioC(relLevel="release", destdir="/var/tmp/juliab/RLibs",
libName="affy")
Running getBioC version 1.2.46....
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.


Synching your local package management information ...
Packages which have been removed:
        tkWidgets
        affy
        affyPLM


Note: You did not specify a download type.  Using a default value of:
Source
This will be fine for almost all users

[1] "Attempting to download tkWidgets from
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing tkWidgets"
* Installing *source* package 'tkWidgets' ...
** R
** inst
** save image
[1] TRUE
Error in setIs("character", "characterORMIAME", where = where) :
        Class "character" is sealed; new superclasses can not be defined,
except by setClassUnion
Error in firstlib(which.lib.loc, package) :
        cannot load DynDoc without Biobase
Error: Package DynDoc unavailable
Execution halted
ERROR: execution of package source for 'tkWidgets' failed
** Removing '/var/tmp/juliab/RLibs/tkWidgets'
Warning message:
Installation of package tkWidgets had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
[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   -D__NO_MATH_INLINES -mieee-fp
-fPIC  -g -O2 -c chipbackground.c -o chipbackground.o
gcc -I/usr/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/usr/lib/R/include -DHAVE_ZLIB=1   -D__NO_MATH_INLINES -mieee-fp
-fPIC  -g -O2 -c qnorm.c -o qnorm.o
gcc -I/usr/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/usr/lib/R/include -DHAVE_ZLIB=1   -D__NO_MATH_INLINES -mieee-fp
-fPIC  -g -O2 -c rma2.c -o rma2.o
gcc -I/usr/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/usr/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  -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
Error in setIs("character", "characterORMIAME", where = where) :
        Class "character" is sealed; new superclasses can not be defined,
except by setClassUnion
[1] FALSE
[1] TRUE
[1] TRUE
Error in getClass(Class, where = topenv(parent.frame())) :
        "MIAME" is not a defined class
Execution halted
ERROR: execution of package source for 'affy' failed
** Removing '/var/tmp/juliab/RLibs/affy'
Warning message:
Installation of package affy had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
[1] "Attempting to download affyPLM from
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing affyPLM"
* Installing *source* package 'affyPLM' ...
** libs
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c LESN.c -o LESN.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c SCAB.c -o SCAB.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c avg_log.c -o avg_log.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c biweight.c -o biweight.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c chipbackground.c -o chipbackground.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c do_PLMrlm.c -o do_PLMrlm.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c idealmismatch.c -o idealmismatch.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c lm.c -o lm.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c lm_threestep.c -o lm_threestep.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c log_avg.c -o log_avg.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c medianPM.c -o medianPM.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c median_logPM.c -o median_logPM.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c medianpolish.c -o medianpolish.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c nthLargestPM.c -o nthLargestPM.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c preprocess.c -o preprocess.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c psi_fns.c -o psi_fns.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c qnorm.c -o qnorm.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c qnorm_probeset.c -o qnorm_probeset.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c rlm.c -o rlm.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c rlm_PLM.c -o rlm_PLM.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c rlm_se.c -o rlm_se.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c rlm_threestep.c -o rlm_threestep.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c rma_background2.c -o rma_background2.ogcc -I/usr/lib/R/include
-D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g -O2 -c rma_common.c -o
rma_common.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c scaling.c -o scaling.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c threestep.c -o threestep.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c threestep_common.c -o threestep_common.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c threestep_summary.c -o threestep_summary.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c threestep_summary_methods.c -o threestep_summary_methods.o
gcc -I/usr/lib/R/include   -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC  -g
-O2 -c weightedkerneldensity.c -o weightedkerneldensity.o
gcc -shared  -o affyPLM.so LESN.o SCAB.o avg_log.o biweight.o
chipbackground.o do_PLMrlm.o idealmismatch.o lm.o lm_threestep.o log_avg.o
medianPM.o median_logPM.o medianpolish.o nthLargestPM.o preprocess.o
psi_fns.o qnorm.o qnorm_probeset.o rlm.o rlm_PLM.o rlm_se.o
rlm_threestep.o rma_background2.o rma_common.o scaling.o threestep.o
threestep_common.o threestep_summary.o threestep_summary_methods.o
weightedkerneldensity.o -L/usr/lib/R/bin -lRlapack -lblas
-L/usr/lib/R/bin -lR
** R
** inst
** save image
[1] TRUE
Error in setIs("character", "characterORMIAME", where = where) :
        Class "character" is sealed; new superclasses can not be defined,
except by setClassUnion
[1] FALSE
Error: package affy was built for  sparc-sun-solaris2.7
Execution halted
ERROR: execution of package source for 'affyPLM' failed
** Removing '/var/tmp/juliab/RLibs/affyPLM'
Warning message:
Installation of package affyPLM had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
>From URL:
http://www.bioconductor.org/repository/release1.3/package/Source
        tkWidgets version 1.3.0
        affy version 1.3.26
        affyPLM version 1.0.0

Packages that were not updated:
        Biobase
        annotate
        genefilter
        geneplotter
        edd
        ROC
        multtest
        pamr
        limma
        MAGEML
        siggenes
        globaltest
        vsn
        affycomp
        affydata
        annaffy
        matchprobes
        gcrma
        makecdfenv

>



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