Linux Mint: Not playing nice with bioconductor/edgeR. Why?

[hyates]

I am running Linux Mint (a variant of Ubuntu basically). I get the following warning messages:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.1.
Warning message:
installed directory not writable, cannot update packages 'class', 'foreign',
  'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart', 'survival'

Worse still. I cannot install packages such as edgeR.

* 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/hlyates/R/x86_64-pc-linux-gnu-library/3.0/edgeR’

The downloaded source packages are in
	‘/tmp/Rtmpu5qpbt/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 'class', 'foreign',
  'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart', 'survival'

I never had this trouble on my OSX. Has anyone else had experience with problems like this? I tried updating my bioconductor package and that didn't fix it. Never saw this error before.

[rhinoceros]

installed directory not writable
..
installed directory not writable

There's your problem. Where does it try to install? You could probably do it the sudo way, or alternatively, chown -R the install dir..

[hyates]

> .libPaths()
[1] "/home/hlyates/R/x86_64-pc-linux-gnu-library/3.0"
[2] "/usr/local/lib/R/site-library"                  
[3] "/usr/lib/R/site-library"                        
[4] "/usr/lib/R/library"

So my guess is that I will have to see if this puppy below is writable right?

[1] "/home/hlyates/R/x86_64-pc-linux-gnu-library/3.0"

So I checked. I did the following chmod 777 /home/hlyates/R/x86_64-pc-linux-gnu-library/3.0

And it shows the following:
drwxrwxrwx

I am reinstalling the bioconductor package as we speak. And...it didn't work. I got

The downloaded source packages are in

‘/tmp/Rtmpu5qpbt/downloaded_packages’
Warning messages:
1: packages ‘base’, ‘compiler’, ‘datasets’, ‘graphics’, ‘grDevices’, ‘grid’, ‘methods’, ‘parallel’, ‘splines’, ‘stats’, ‘stats4’, ‘tcltk’, ‘tools’, ‘utils’ are not available (for R version 3.0.1)
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘cluster’ had non-zero exit status
3: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘KernSmooth’ had non-zero exit status
4: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Matrix’ had non-zero exit status
5: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘nlme’ had non-zero exit status
6: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘mgcv’ had non-zero exit status
7: installed directory not writable, cannot update packages 'class', 'foreign',
'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart', 'survival'

Why the heck is this even an issue?

So now when I get into R, I typed

sudo R

. Which probably will fix the issue. But in general. How can I make sure all my stuff is writable. Kind of weird that this happened in Linux given I am the admin. Maybe the lesson here is that whenever I want to install packages, I makes sure my R session is sudo?

[Richard Finney]

run these updates as root.

OR

Know how to run your own local, user copy of R which is just a little bit tricky.

[mtmorgan]

These lines

/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -lgfortran

indicate that more-or-less standard libraries liblapack, libblas, and libgfortran are not being found. Likely they _were_ found when you installed R, and you've done something to your system in the mean time. Use your system package manager to re-install these packages, or `ldconfig` with appropriate arguments to update the ld data base to include the paths where the libraries are located, or (temporarily) set LD_LIBRARY_PATH to the path(s) where the libraries are located (discovered using, e.g., `locate liblapack.so`). Searching for `[r] gfortran` on StackOverflow might lead to more extensive suggestions.

The warnings about 'installed directory not writeable' means that the listed R packages were installed in a directory that is not writeable, probably by a system administrator. This means that they cannot be updated (except by the administrator), but should not be causing problems with installation of edgeR.