Installation fails with R
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Dear authors/developers,
I am attempting to install nonpareil on my cluster environment. Therefore, I do not have any root access.
However, I keep failing on the R package getting a "Permission denied" error, despite the R package install path belonging to me.
$ make prefix=/mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil R=/mnt/nfs/projects/ecosystem_biology/local_tools/R-ESB install
if [ ! -d /mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil/bin ] ; then mkdir -p /mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil/bin ; fi
if [ ! -d /mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil/man/man1 ] ; then mkdir -p /mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil/man/man1 ; fi
if [ -e nonpareil ] ; then install -m 0755 nonpareil /mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil/bin/ ; fi
if [ -e nonpareil-mpi ] ; then install -m 0755 nonpareil-mpi /mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil/bin/ ; fi
cp docs/_build/man/nonpareil.1 /mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil/man/man1/nonpareil.1
/mnt/nfs/projects/ecosystem_biology/local_tools/R-ESB CMD INSTALL utils/Nonpareil
make: execvp: /mnt/nfs/projects/ecosystem_biology/local_tools/R-ESB: Permission denied
Makefile:44: recipe for target 'install' failed
make: *** [install] Error 127
I attempted the same by giving my $HOME/R
as the path with the same outcome.
To further check, I also tried installing the packages outside make install
like so:
$ R CMD INSTALL -l /mnt/nfs/projects/ecosystem_biology/local_tools/R-ESB utils/Nonpareil
* installing *source* package ‘Nonpareil’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (Nonpareil)
Despite the packages already installed, make install
still attempts to install R.
Any idea why this is happening and if there is a fix for it?
I look forward to your reply.
Best regards,
Shaman
Hello @shaman-narayanasamy ,
The R package installation is the last step of make install
, so you have successfully installed it by manually running the R CMD INSTALL
.
However, if you want make
to succeed (e.g., if you're automating the installation and want to check exit code, or if you just like clean runs) the way to control the R library is by passing the R library variable. The R
variable you're passing to make install
is not the library folder, but the actual R command or the path to the binary. In your case, you can run it like this:
make install \
R_LIBS_USER=/mnt/nfs/projects/ecosystem_biology/local_tools/R-ESB \
prefix=/mnt/nfs/projects/ecosystem_biology/local_tools/nonpareil
Please feel free to reopen if it fails.