affy devel fails to install with getBioC and Rbeta1.8.0
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@nicholas-lewin-koh-63
Last seen 9.6 years ago
Hi, Not sure if this is on my end or not. Using todays R-1.8.0 beta release and RH linux 9.0: > getBioC(relLevel = "devel",destdir="test/testlibs") ....... [1] "Attempting to download affy from http://www.bioconductor.org/repository/devel/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 -Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c getall_locations.c -o getall_locations.o gcc -Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c qnorm.c -o qnorm.o gcc -Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c read_cdffile.c -o read_cdffile.o gcc -Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma2.c -o rma2.o gcc --Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c rma_background2.c -o rma_background2.o gcc -Itest/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -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 read_cdffile.o rma2.o rma_background2.o rma_common.o -lz -L/test/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 [1] TRUE [1] TRUE [1] "Cdf" [1] "name.levels" [1] "name.levels" [1] "name.levels<-" [1] "name.levels<-" [1] "pbase" [1] "pbase" [1] "pbase<-" [1] "pbase<-" [1] "pbase.levels" [1] "pbase.levels" [1] "pbase.levels<-" [1] "pbase.levels<-" [1] "tbase" [1] "tbase" [1] "tbase<-" [1] "tbase<-" [1] "tbase.levels" [1] "tbase.levels" [1] "tbase.levels<-" [1] "tbase.levels<-" [1] "atom" [1] "atom" [1] "atom<-" [1] "atom<-" [1] "probeNames" [1] "probeNames" [1] "probeNames<-" [1] "probeNames<-" [1] "show" [1] "AffyBatch" [1] "intensity" [1] "intensity" [1] "intensity<-" [1] "intensity<-" [1] "length" [1] "ncol" [1] "ncol" [1] "nrow" [1] "nrow" [1] "getCdfInfo" [1] "getCdfInfo" Error in getMethodsForDispatch(f, fdef) : Trying to get slot ".Methods" from an object whose class ("genericMethods") is not defined Execution halted test/lib/R/bin/INSTALL: line 1: 15051 Broken pipe cat "test/testlibs/affy/R/affy" ERROR: execution of package source for 'affy' failed ** Removing 'test/testlibs/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 affycomp from http://www.bioconductor.org/repository/devel/package/Source" Note if some of the paths look funny I had to take them out becuase of company security. Nicholas
affy affycomp affy affycomp • 1.0k views
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@vincent-j-carey-jr-4
Last seen 16 days ago
United States
On Thu, 2 Oct 2003, Nicholas Lewin-Koh wrote: > Hi, > Not sure if this is on my end or not. Using todays R-1.8.0 beta release > and RH linux 9.0: > > > getBioC(relLevel = "devel",destdir="test/testlibs") > ....... FWIW I had no problem installing from the current CVS image of affy devel into today's R-1.8.0 beta (on an openmosix rh7.1).
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