[Bioc-devel] Install edgeR

[Martin Morgan]

On 02/08/2015 05:31 AM, def87 at gmx.de wrote:
>
>     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

Have you also

   sudo apt-get install r-base-dev

? This is needed to install packages from source and as as described at 
http://cran.r-project.org/bin/linux/ubuntu/.

>
>     $ R --version
>     R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"

this is unfortunately an old version of R, hence old version of Bioconductor / 
edgeR. Look instead for R version 3.1.2 which should be widely available from an 
appropriate repository, as described at http://cran.r-project.org/bin/linux/ubuntu/.


>
>     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" ... ?

These list R package dependencies, not operating system dependencies. If your R 
installation is complete, then the system dependencies you are missing will be 
satisfied.

Hope that helps,

Martin

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