Many thanks, Benilton. After installed (gcc, g++, make, etc.), I finally got "Biobase" work. However, I met a new problem when I use "biocLite.R" to install "affyPLM". The compilation failed at the last step. Any suggestions are very welcomed and thanks ahead. Here is the problem. ............................... gcc -I/usr/lib/R/include -fPIC -g -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -shared -o affyPLM.so LESN.o PLM_modelmatrix.o SCAB.o avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm.o lm_threestep.o log_avg.o matrix_functions.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_anova.o rlm_se.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_background2.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o weightedkerneldensity.o -L/usr/lib/R/lib -lRlapack -lblas-3 -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -lblas-3 collect2: ld returned 1 exit status make: *** [affyPLM.so] Error 1 ERROR: compilation failed for package 'affyPLM' ** Removing '/usr/local/lib/R/site-library/affyPLM' The downloaded packages are in /tmp/Rtmpu89nBJ/downloaded_packages Warning message: installation of package 'affyPLM' had non-zero exit status in: install.packages(pkgs = "affyPLM", repos = c(" http://www.bioconductor.org/packages/bioc/1.7")) On 12/4/05, Benilton Carvalho wrote: > > i'd guess you don't have the C compiler installed on your machine... > > install GCC and try it again. > > b. > > On Sun, 4 Dec 2005, Frank Duan wrote: > > > Hi Anjia and Hi Ting-Yuan, > > > > It's nice to see this topic has been discussed here. I have the similar > (or > > the same) problem as Anjia's even after installing R 2.2.0 on my ubuntu > > linux. Here are the details. > > > > The error under R 2.2.0 is: > > > >> source("http://www.bioconductor.org/biocLite.R") > >> biocLite("Biobase") > > > > Running bioCLite version 0.1 with R version 2.2.0 > > > > Running biocinstall version 1.1 with R version 2.2.0 > > trying URL > > ' > > > http://www.bioconductor.org/packages/bioc/1.7/src/contrib/Biobase_1.8.0.tar.gz > > ' > > Content type 'application/x-gzip' length 1285566 bytes > > opened URL > > ================================================== > > downloaded 1255Kb > > > > * Installing *source* package 'Biobase' ... > > ** libs > > /usr/lib/R/bin/SHLIB: line 102: make: command not found > > ERROR: compilation failed for package 'Biobase' > > ** Removing '/usr/local/lib/R/site-library/Biobase' > > > > The downloaded packages are in > > /tmp/RtmpuiBzwp/downloaded_packages > > Warning message: > > installation of package 'Biobase' had non-zero exit status in: > > install.packages(pkgs = "Biobase", repos = > > c("http://www.bioconductor.org/packages/bioc/1.7", > > > > (Then I opened "/usr/lib/R/bin/SHLIB" and found the line 102) > > > > eval ${MAKE} ${makefiles} ${makeargs} ${makeobjs} > > > > > > I am a green hand to both Linux and C and can't fix the problem. My > guess is > > this is a problem specific to Linux Ubuntu Breezy Badger. > > > > Can anyone help me with it? Thanks ahead. > > > > Frank > > > > > > On 11/28/05, Ting-Yuan Liu wrote: > >> > >> > >> Hi Anja, > >> > >> If you are using R 2.1.1, could you upgrade to R 2.2.0, which is the > >> latest versionof R, please? > >> > >> After you upgrade to R 2.2.0, you can use the biocLite script to > install > >> BioConductor for you. In an R command window, type the following: > >> > >> source("http://www.bioconductor.org/biocLite.R") > >> biocLite() > >> > >> Please refer to the "Install - How To" page on the BioConductor > official > >> website. > >> > >> If you still have trouble in installing BioConductor, please report the > >> error/warning messages and the result of sessionInfo() to the list > again. > >> > >> HTH, > >> Ting-Yuan > >> > >> ______________________________________ > >> Ting-Yuan Liu > >> Program in Computational Biology > >> Division of Public Health Sciences > >> Fred Hutchinson Cancer Research Center > >> Seattle, WA, USA > >> ______________________________________ > >> > >> On Sat, 26 Nov 2005, Anja Schiel wrote: > >> > >>> I have downloaded R version 2.1.1 via apt-get and have now a running R > >> under Ubuntu Breezy Badger. But now I would like to use the > Bioconductor > >> packages and tried to install with BioC(). > >> No matter if I use the root account or my personal login, I always end > >> up with at least 11 to 14 warnings and always the problem that all > >> packages dependent on the Biobase package can not be installed. > >> > >> I should mention that I gave myself permission to all libraries and > >> anyhow, other libraries such as limma are not affected. > >> > >> Warning messages: > >> 1: installation of package 'Biobase' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 2: installation of package 'Biostrings' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 3: installation of package 'pamr' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 4: installation of package 'affy' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 5: installation of package 'annaffy' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 6: installation of package 'edd' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 7: installation of package 'genefilter' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 8: installation of package 'multtest' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 9: installation of package 'vsn' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 10: installation of package 'geneplotter' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 11: installation of package 'makecdfenv' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 12: installation of package 'matchprobes' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 13: installation of package 'gcrma' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> 14: installation of package 'affyPLM' had non-zero exit status in: > >> install.packages(pkgs = c("affy", "affydata", "affyPLM", > >> "annaffy", ... > >> > >> So when I try to open affy the following error message appears. > >> > >>> library(affy) > >> Loading required package: Biobase > >> Error in library.dynam(lib, package, package.lib) : > >> shared library 'Biobase' not found > >> In addition: Warning messages: > >> 1: package 'Biobase' contains no R code in: loadNamespace(package, > >> c(which.lib.loc, lib.loc)) > >> 2: S3 method 'as.data.frame.exprSet' was declared in NAMESPACE but not > >> found > >> Error: package 'Biobase' could not be loaded > >> > >> I used the woody URL to apt-get install, but I guess that should not > >> make a difference. > >> > >> I checked the mail archive, but somehow this particular problem was not > >> discussed. It seems that something goes wrong during compiling the > >> Biobase package. > >> Any suggestions would be very welcome, I am not necessarily an expert > on > >> Linux. > >> > >> Greetings and thanks in advance, > >> Anja Schiel > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > [[alternative HTML version deleted]]