tried but still no go. Thanks anyway. On 12/5/05, Benilton Carvalho wrote: > > It looks like affyPLM requires the BLAS library installed on your system. > > http://www.netlib.org/blas/ > > hph > > b. > > On Sun, 4 Dec 2005, Frank Duan wrote: > > > 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]]