Background: some CRAN or Bioconductor packages contain native code that needs to be compiled and then linked against a system library. Some of those libraries are not part of a standard Ubuntu installation and need to be installed explicitly (sudo apt-get install <somelib>-dev). In the case of preprocessCore, the output below suggests that it needs to be linked against the BLAS and LAPACK libraries. Not sure but I think those are part of a default R installation unless R has been configured with --with-blas and --with-lapack which might be your case. Not sure what's going on. Just a couple of suggestions: - Make sure you have Ubuntu pkg r-base-dev - Try to install KernSmooth (recommended pkg) from source: > install.packages('KernSmooth') This will replace the one you got when you installed Ubuntu pkg r-cran-kernsmooth KernSmooth also needs to be linked against BLAS so if this fails then it means something is wrong with your R installation (in that case R-help might be a better place to ask for help). H. Tiandao Li wrote: > Thanks, Vincent. I installed XML. However, I still can't install > preprocessCore or other standard packages from BioC. > > > biocLite("preprocessCore") > Running biocinstall version 2.3.9 with R version 2.8.0 > Your version of R requires version 2.3 of Bioconductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using '/usr/local/lib/R/site-library' > trying URL > 'http://bioconductor.org/packages/2.3/bioc/src/contrib/preprocessCor e_1.4.0.tar.gz' > Content type 'application/x-gzip' length 109921 bytes (107 Kb) > opened URL > ================================================== > downloaded 107 Kb > > * Installing *source* package 'preprocessCore' ... > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking for pthread_create in -lpthread... yes > checking if we can use pthreads... yes > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c avg.c -o avg.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c avg_log.c -o avg_log.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c biweight.c -o biweight.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c init_package.c -o init_package.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c lm.c -o lm.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c log_avg.c -o log_avg.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c log_median.c -o log_median.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c matrix_functions.c -o matrix_functions.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c median.c -o median.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c median_log.c -o median_log.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c medianpolish.c -o medianpolish.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c plmd.c -o plmd.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c plmr.c -o plmr.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c psi_fns.c -o psi_fns.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c qnorm.c -o qnorm.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c R_colSummarize.c -o R_colSummarize.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c rlm_anova.c -o rlm_anova.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c rlm.c -o rlm.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c rlm_se.c -o rlm_se.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c rma_background4.c -o rma_background4.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c rma_common.c -o rma_common.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c R_subColSummarize.c -o R_subColSummarize.o > gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" > -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" > -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g > -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o > gcc -std=gnu99 -shared -o preprocessCore.so avg.o avg_log.o biweight.o > init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o > median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o > R_colSummarize.o rlm_anova.o rlm.o rlm_se.o rma_background4.o > rma_common.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o > R_subColSummarize.o weightedkerneldensity.o -lpthread -lpthread > -lgfortran -lm -llapack -lf77blas -latlas -L/usr/lib/R/lib -lR > /usr/bin/ld: cannot find -lf77blas > collect2: ld returned 1 exit status > make: *** [preprocessCore.so] Error 1 > chmod: cannot access > `/usr/local/lib/R/site-library/preprocessCore/libs/*': No such file or > directory > ERROR: compilation failed for package 'preprocessCore' > ** Removing '/usr/local/lib/R/site-library/preprocessCore' > > The downloaded packages are in > /tmp/RtmpqCLrkQ/downloaded_packages > Warning message: > In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'preprocessCore' had non-zero exit status > > > > > > On Mon, Dec 1, 2008 at 2:34 PM, Vincent Goulet > <vincent.goulet at="" act.ulaval.ca="" <mailto:vincent.goulet="" at="" act.ulaval.ca="">> wrote: > > Tiandao, > > According to > > http://packages.ubuntu.com/ > > the file xml2-config is in the Ubuntu package libxml2-dev. I'd try > installing this package and then retry installing XML. > > HTH Vincent > > Le lun. 1 d?c. ? 15:53, Tiandao Li a ?crit : > > I always followed http://cran.r-project.org/bin/linux/ubuntu/ to > install R > on Ubuntu 8.1. I had no errors before! > > install.packages("XML") > > Warning in install.packages("XML") : > argument 'lib' is missing: using '/usr/local/lib/R/site- library' > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.98-1.tar.gz' > Content type 'application/x-gzip' length 648274 bytes (633 Kb) > opened URL > ================================================== > downloaded 633 Kb > > * Installing *source* package 'XML' ... > checking for gcc... gcc > checking for C compiler default output file name... a.out > checking whether the C compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -E > checking for sed... /bin/sed > checking for xml2-config... no > Cannot find xml2-config > ERROR: configuration failed for package 'XML' > ** Removing '/usr/local/lib/R/site-library/XML' > > The downloaded packages are in > /tmp/RtmpqCLrkQ/downloaded_packages > Warning message: > In install.packages("XML") : > installation of package 'XML' had non-zero exit status > > > > > > On Mon, Dec 1, 2008 at 1:42 PM, Hervé Pagès <hpages at="" fhcrc.org=""> <mailto:hpages at="" fhcrc.org="">> wrote: > > Hi Tiandao, > > What OS do you have? How did you install R? It looks like > you cannot > install an R package with native code at all. Please try > > install.packages("XML") > > > and show us the complete output. > You could also try the R-help mailing list > (r-help at r-project.org <mailto:r-help at="" r-project.org="">) > since your problem doesn't seem to be Bioconductor- specific. > > Cheers, > H. > > > Tiandao Li wrote: > > Hello, > > I tried to install BioC 2.3 on a new laptop (HP AMD > Turion x2). However I > constantly had the following warnings, I tried several > times for the last > few days. I never had this kind of errors before. > > sudo R > > source("http://bioconductor.org/biocLite.R") > > > > biocLite() > > > > warnings() > > > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'Matrix' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'preprocessCore' had non- zero > exit status > 3: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'IRanges' had non-zero exit status > 4: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'affy' had non-zero exit status > 5: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'affydata' had non-zero exit status > 6: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'Biostrings' had non-zero exit > status > 7: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'matchprobes' had non-zero exit > status > 8: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'vsn' had non-zero exit status > 9: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'gcrma' had non-zero exit status > 10: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'simpleaffy' had non-zero exit > status > 11: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'affyPLM' had non-zero exit status > 12: In install.packages(pkgs = pkgs, repos = repos, > dependencies = > dependencies, ... : > installation of package 'affyQCReport' had non-zero exit > status > > sessionInfo() > > > R version 2.8.0 (2008-10-20) > i486-pc-linux-gnu > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF- 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPE R=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_ US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.8.0 tools_2.8.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org <mailto:hpages at="" fhcrc.org=""> > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org <mailto:r-help at="" r-project.org=""> mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

On Mon, Dec 1, 2008 at 3:42 PM, Hervé Pagès <hpages@fhcrc.org> wrote: > Background: some CRAN or Bioconductor packages contain native code > that needs to be compiled and then linked against a system library. > Some of those libraries are not part of a standard Ubuntu installation > and need to be installed explicitly (sudo apt-get install > <somelib>-dev). > > In the case of preprocessCore, the output below suggests that it > needs to be linked against the BLAS and LAPACK libraries. Not sure > but I think those are part of a default R installation unless R has > been configured with --with-blas and --with-lapack which might be > your case. > > Not sure what's going on. Just a couple of suggestions: > > - Make sure you have Ubuntu pkg r-base-dev DONE! > > - Try to install KernSmooth (recommended pkg) from source: > > > install.packages('KernSmooth') > > This will replace the one you got when you installed > Ubuntu pkg r-cran-kernsmooth > KernSmooth also needs to be linked against BLAS so if > this fails then it means something is wrong with your > R installation (in that case R-help might be a better place > to ask for help). > > H. > > library() Packages in library '/usr/local/lib/R/site-library': affyio Tools for parsing Affymetrix data files annaffy Annotation tools for Affymetrix biological metadata annotate Annotation for microarrays AnnotationDbi Annotation Database Interface Biobase Biobase: Base functions for Bioconductor DBI R Database Interface DynDoc Dynamic document tools genefilter genefilter: methods for filtering genes from microarray experiments geneplotter Grapics related functions for Bioconductor GO.db A set of annotation maps describing the entire Gene Ontology hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) KEGG.db A set of annotation maps for KEGG limma Linear Models for Microarray Data marray Exploratory analysis for two-color spotted microarray data multtest Resampling-based multiple hypothesis testing RColorBrewer ColorBrewer palettes ROC utilities for ROC, with uarray focus RSQLite SQLite interface for R XML Tools for parsing and generating XML within R and S-Plus. xtable Export tables to LaTeX or HTML Packages in library '/usr/lib/R/library': base The R Base Package boot Bootstrap R (S-Plus) Functions (Canty) class Functions for Classification cluster Cluster Analysis Extended Rousseeuw et al. codetools Code Analysis Tools for R datasets The R Datasets Package foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, dBase, ... graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours and Fonts grid The Grid Graphics Package KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graphics MASS Main Package of Venables and Ripley's MASS methods Formal Methods and Classes mgcv GAMs with GCV smoothness estimation and GAMMs by REML/PQL nlme Linear and Nonlinear Mixed Effects Models nnet Feed-forward Neural Networks and Multinomial Log-Linear Models rpart Recursive Partitioning spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes stats The R Stats Package stats4 Statistical Functions using S4 Classes survival Survival analysis, including penalised likelihood. tcltk Tcl/Tk Interface tools Tools for Package Development utils The R Utils Package (END) > Tiandao Li wrote: > >> Thanks, Vincent. I installed XML. However, I still can't install >> preprocessCore or other standard packages from BioC. >> >> > biocLite("preprocessCore") >> Running biocinstall version 2.3.9 with R version 2.8.0 Your version of R >> requires version 2.3 of Bioconductor. >> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, : >> argument 'lib' is missing: using '/usr/local/lib/R/site-library' >> trying URL ' >> http://bioconductor.org/packages/2.3/bioc/src/contrib/preprocessCor e_1.4.0.tar.gz >> ' >> Content type 'application/x-gzip' length 109921 bytes (107 Kb) >> opened URL >> ================================================== >> downloaded 107 Kb >> >> * Installing *source* package 'preprocessCore' ... >> checking for gcc... gcc >> checking for C compiler default output file name... a.out >> checking whether the C compiler works... yes >> checking whether we are cross compiling... no >> checking for suffix of executables... checking for suffix of object >> files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ISO C89... none needed >> checking for pthread_create in -lpthread... yes >> checking if we can use pthreads... yes >> configure: creating ./config.status >> config.status: creating src/Makevars >> ** libs >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c avg.c -o avg.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c avg_log.c -o avg_log.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c biweight.c -o biweight.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c init_package.c -o init_package.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c lm.c -o lm.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c log_avg.c -o log_avg.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c log_median.c -o log_median.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c matrix_functions.c -o matrix_functions.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c median.c -o median.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c median_log.c -o median_log.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c medianpolish.c -o medianpolish.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c plmd.c -o plmd.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c plmr.c -o plmr.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c psi_fns.c -o psi_fns.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c qnorm.c -o qnorm.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c R_colSummarize.c -o R_colSummarize.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c rlm_anova.c -o rlm_anova.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c rlm.c -o rlm.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c rlm_se.c -o rlm_se.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c rma_background4.c -o rma_background4.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c rma_common.c -o rma_common.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c R_plmd_interfaces.c -o R_plmd_interfaces.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c R_plmr_interfaces.c -o R_plmr_interfaces.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c R_rlm_interfaces.c -o R_rlm_interfaces.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c R_subColSummarize.c -o R_subColSummarize.o >> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" >> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g -O2 >> -c weightedkerneldensity.c -o weightedkerneldensity.o >> gcc -std=gnu99 -shared -o preprocessCore.so avg.o avg_log.o biweight.o >> init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o >> median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o R_colSummarize.o >> rlm_anova.o rlm.o rlm_se.o rma_background4.o rma_common.o >> R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o >> R_subColSummarize.o weightedkerneldensity.o -lpthread -lpthread -lgfortran >> -lm -llapack -lf77blas -latlas -L/usr/lib/R/lib -lR >> /usr/bin/ld: cannot find -lf77blas >> collect2: ld returned 1 exit status >> make: *** [preprocessCore.so] Error 1 >> chmod: cannot access >> `/usr/local/lib/R/site-library/preprocessCore/libs/*': No such file or >> directory >> ERROR: compilation failed for package 'preprocessCore' >> ** Removing '/usr/local/lib/R/site-library/preprocessCore' >> >> The downloaded packages are in >> /tmp/RtmpqCLrkQ/downloaded_packages >> Warning message: >> In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, : >> installation of package 'preprocessCore' had non-zero exit status >> > >> >> >> On Mon, Dec 1, 2008 at 2:34 PM, Vincent Goulet < >> vincent.goulet@act.ulaval.ca <mailto:vincent.goulet@act.ulaval.ca>> >> wrote: >> >> Tiandao, >> >> According to >> >> http://packages.ubuntu.com/ >> >> the file xml2-config is in the Ubuntu package libxml2-dev. I'd try >> installing this package and then retry installing XML. >> >> HTH Vincent >> >> Le lun. 1 déc. à 15:53, Tiandao Li a écrit : >> >> I always followed http://cran.r-project.org/bin/linux/ubuntu/ to >> install R >> on Ubuntu 8.1. I had no errors before! >> >> install.packages("XML") >> >> Warning in install.packages("XML") : >> argument 'lib' is missing: using '/usr/local/lib/R/site- library' >> --- Please select a CRAN mirror for use in this session --- >> Loading Tcl/Tk interface ... done >> trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.98-1.tar.gz' >> Content type 'application/x-gzip' length 648274 bytes (633 Kb) >> opened URL >> ================================================== >> downloaded 633 Kb >> >> * Installing *source* package 'XML' ... >> checking for gcc... gcc >> checking for C compiler default output file name... a.out >> checking whether the C compiler works... yes >> checking whether we are cross compiling... no >> checking for suffix of executables... >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ANSI C... none needed >> checking how to run the C preprocessor... gcc -E >> checking for sed... /bin/sed >> checking for xml2-config... no >> Cannot find xml2-config >> ERROR: configuration failed for package 'XML' >> ** Removing '/usr/local/lib/R/site-library/XML' >> >> The downloaded packages are in >> /tmp/RtmpqCLrkQ/downloaded_packages >> Warning message: >> In install.packages("XML") : >> installation of package 'XML' had non-zero exit status >> >> >> >> >> >> On Mon, Dec 1, 2008 at 1:42 PM, Hervé Pagès <hpages@fhcrc.org>> <mailto:hpages@fhcrc.org>> wrote: >> >> Hi Tiandao, >> >> What OS do you have? How did you install R? It looks like >> you cannot >> install an R package with native code at all. Please try >> >> install.packages("XML") >> >> >> and show us the complete output. >> You could also try the R-help mailing list >> (r-help@r-project.org <mailto:r-help@r-project.org>) >> since your problem doesn't seem to be Bioconductor- specific. >> >> Cheers, >> H. >> >> >> Tiandao Li wrote: >> >> Hello, >> >> I tried to install BioC 2.3 on a new laptop (HP AMD >> Turion x2). However I >> constantly had the following warnings, I tried several >> times for the last >> few days. I never had this kind of errors before. >> >> sudo R >> >> source("http://bioconductor.org/biocLite.R") >> >> >> >> biocLite() >> >> >> >> warnings() >> >> >> Warning messages: >> 1: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'Matrix' had non-zero exit status >> 2: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'preprocessCore' had non- zero >> exit status >> 3: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'IRanges' had non-zero exit status >> 4: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'affy' had non-zero exit status >> 5: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'affydata' had non-zero exit status >> 6: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'Biostrings' had non-zero exit >> status >> 7: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'matchprobes' had non-zero exit >> status >> 8: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'vsn' had non-zero exit status >> 9: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'gcrma' had non-zero exit status >> 10: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'simpleaffy' had non-zero exit >> status >> 11: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'affyPLM' had non-zero exit status >> 12: In install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, ... : >> installation of package 'affyQCReport' had non-zero exit >> status >> >> sessionInfo() >> >> >> R version 2.8.0 (2008-10-20) >> i486-pc-linux-gnu >> >> locale: >> >> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID ENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tcltk_2.8.0 tools_2.8.0 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages@fhcrc.org <mailto:hpages@fhcrc.org> >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org <mailto:r-help@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]

[back to the lists] So it seems that r-base-dev forgets to depend on libatlas-base-dev You can fix this by installing libatlas-base-dev manually: apt-get install libatlas-base-dev This should solve the compilation/linking problem with KernSmooth, preprocessCore and any other package that needs to be linked against the BLAS/ATLAS/LAPACK libraries on Ubuntu 8.10 (Intrepid Ibex). Note that this problem only affects people that get their R-2.8 from r-base + r-base-dev Cheers, H. Tiandao Li wrote: > This is my installation: > > > install.packages("KernSmooth") > Warning in install.packages("KernSmooth") : > argument 'lib' is missing: using '/usr/local/lib/R/site-library' > trying URL 'http://cran.fhcrc.org/src/contrib/KernSmooth_2.22-22.tar.gz' > Content type 'application/x-gzip' length 28422 bytes (27 Kb) > opened URL > ================================================== > downloaded 27 Kb > > * Installing *source* package 'KernSmooth' ... > ** libs > gfortran -fpic -g -O2 -c blkest.f -o blkest.o > gfortran -fpic -g -O2 -c cp.f -o cp.o > gfortran -fpic -g -O2 -c dgedi.f -o dgedi.o > gfortran -fpic -g -O2 -c dgefa.f -o dgefa.o > gfortran -fpic -g -O2 -c dgesl.f -o dgesl.o > gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o > gfortran -fpic -g -O2 -c linbin2D.f -o linbin2D.o > gfortran -fpic -g -O2 -c linbin.f -o linbin.o > gfortran -fpic -g -O2 -c locpoly.f -o locpoly.o > gfortran -fpic -g -O2 -c rlbin.f -o rlbin.o > gfortran -fpic -g -O2 -c sdiag.f -o sdiag.o > gfortran -fpic -g -O2 -c sstdiag.f -o sstdiag.o > gcc -std=gnu99 -shared -o KernSmooth.so blkest.o cp.o dgedi.o dgefa.o > dgesl.o init.o linbin2D.o linbin.o locpoly.o rlbin.o sdiag.o sstdiag.o > -lf77blas -latlas -lgfortran -lm -lgfortran -lm -L/usr/lib/R/lib -lR > /usr/bin/ld: cannot find -lf77blas > collect2: ld returned 1 exit status > make: *** [KernSmooth.so] Error 1 > ERROR: compilation failed for package 'KernSmooth' > ** Removing '/usr/local/lib/R/site-library/KernSmooth' > > The downloaded packages are in > /tmp/RtmpqCLrkQ/downloaded_packages > Warning message: > In install.packages("KernSmooth") : > installation of package 'KernSmooth' had non-zero exit status > > > > On Mon, Dec 1, 2008 at 4:05 PM, Hervé Pagès <hpages at="" fhcrc.org=""> <mailto:hpages at="" fhcrc.org="">> wrote: > > I'm taking this off-list for now. > > Tiandao Li wrote: > [...] > > library() > > [...] > > KernSmooth Functions for kernel smoothing for Wand & Jones > (1995) > > > yes this shows that you have KernSmooth but my suggestion was that you > try to install it *from source*. I don't know how you got this > KernSmooth, maybe you installed the Ubuntu pkg r-cran- kernsmooth, > which is a binary package (precompiled), so the fact that you were > able to install it doesn't tell me anything useful... > > Thanks! > H. > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319