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 <bcarvalh at="" jhsph.edu=""> 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 <tliu at="" fhcrc.org=""> 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 at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >>>> >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> >