[Bioc-devel] Install edgeR

[def87 at gmx.de]

   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" ... ?