On 02/08/2015 05:31 AM, de...@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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