Hi everyone, I am trying to install the edgeR package on Linux Mint 17 Cinnamon 64-bit.
I have installed R the normal way via sudo apt-get install r-base $ R --version R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" So then I proceed according to the instructions at http://www.bioconductor.org/packages/release/bioc/html/edgeR.html and type: source("http://bioconductor.org/biocLite.R";) biocLite("edgeR") But then I get: > biocLite("edgeR") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. Installing package(s) 'edgeR' trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/edgeR_3.4.2.tar.gz' Content type 'application/x-gzip' length 1126311 bytes (1.1 Mb) opened URL ================================================== downloaded 1.1 Mb * installing *source* package ‘edgeR’ ... ** libs g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_loess_by_col.cpp -o R_loess_by_col.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_cr_adjust.cpp -o R_cr_adjust.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_levenberg.cpp -o R_levenberg.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_one_group.cpp -o R_one_group.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/adj_coxreid.cpp -o core/adj_coxreid.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/glm_levenberg.cpp -o core/glm_levenberg.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/glm_one_group.cpp -o core/glm_one_group.o g++ -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/interpolator.cpp -o core/interpolator.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./core -I. -fpic -O3 -pipe -g -c core/fmm_spline.c -o core/fmm_spline.o g++ -shared -o edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR /usr/bin/ld: cannot find -llapack /usr/bin/ld: cannot find -lblas /usr/bin/ld: cannot find -lgfortran collect2: error: ld returned 1 exit status make: *** [edgeR.so] Error 1 ERROR: compilation failed for package ‘edgeR’ * removing ‘/home/robert/R/x86_64-pc-linux-gnu-library/3.0/edgeR’ The downloaded source packages are in ‘/tmp/RtmpezIkbL/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘edgeR’ had non-zero exit status 2: installed directory not writable, cannot update packages 'cluster', 'KernSmooth', 'Matrix', 'mgcv', 'nlme' Which sudo apt-get install <tellme> do I have to perform in order to resolve the dependencies? Also: Why do they not write anything on the bioconductor homepage about this issue? It only states "Depends: R (>= 2.15.0), limma" ... ? _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
