How to specify lib directory when installing development version R Packages from github repository

Question

In Ubuntu, I am installing all the R packages in the directory, /usr/lib/R/site-library by specifying lib option in install.packages().

But when I try to install the development version of the R packages using, install_github(), it always installs in a local repository of the system user.

.libPaths() has 4 directories including the local repository. So, I have 2 questions,

Will it install in any of the other 3 repositories if i remove the local repository from .libPaths()?
Is there any way to specify installation library path in install_github()?

I am using Ubuntu 12.04 64bit and R 3.0.1

----------------------UPDATE--------------------------------

Unable to remove the local repository from .libPaths()
If I try to install using install_github() in RStudio, it installs in the local repository since lib is not specified.
If I try to install using install_github() as non-root user, it installs in the local repository since lib is not specified.
If I try to install using install_github() as root user, it installs in the /usr/local/lib/R/site-library since lib is not specified.

Is there any to specify installation lib?

Manoj G · Accepted Answer · 2014-07-10T04:39:54.990

55

To add specified library paths in devtools, we need to use with_libpaths()

Arguments for with_libpaths() are, with_libpaths(new, code)

Following is an example for using with_libpaths(),

library(devtools)
with_libpaths(new = "/usr/lib/R/site-library/", install_github('rCharts', 'ramnathv'))

Courtesy: Hadley, here :)

And other than with_libpaths(), there are more options for in devtools::with_something()

in_dir: working directory
with_collate: collation order
with_envvar: environmental variables
with_libpaths: library paths, replacing current libpaths
with_lib: library paths, prepending to current libpaths
with_locale: any locale setting
with_options: options
with_path: PATH environment variable
with_par: graphics parameters

More explanations here

edited Jul 10 '14 at 04:39

answered Jul 10 '14 at 04:34

Manoj G

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`devtools::with_libpaths()` is deprecated. Use `withr::with_libpaths()`. See `help("devtools-deprecated")`. – swihart May 13 '16 at 01:35
This gives me `install: cannot create regular file ‘/usr/lib64/R/lib/libs3.so.2.0’: Permission denied make[1]: *** [install] Error 1 make[1]: Leaving directory `/mnt/tmp/RtmpShKPQi/devtools15aa419a91f09/AnalyticalFlavorSystems-RS3-536f287/src/libs3' make: *** [libs3.so] Error 2 ERROR: compilation failed for package ‘RS3’ * removing ‘/home/hadoop/git/threat-odin/lib/R/RS3’ Error: Command failed (1)` – d8aninja Apr 01 '17 at 00:03
As indicated above (but not explicitly stated), the correct syntax is `withr::with_libpaths(new=libPath, devtools::install_github('/') )` – mikemtnbikes Jul 21 '21 at 17:49
This works now: `remotes::install_github("/", lib="")`. – Alan Oct 27 '22 at 11:48

jdharrison · Answer 2 · 2014-07-09T10:03:46.283

install_github takes a ... argument that passes to devtools::install. devtools::install has an args argument.

args
An optional character vector of additional command line arguments to be passed to R CMD install. This defaults to the value of the option "devtools.install.args".

R CMD install takes a library argument

 Options:
  -h, --help            print short help message and exit
  -v, --version         print INSTALL version info and exit
  -c, --clean           remove files created during installation
      --preclean        remove files created during a previous run
  -d, --debug           turn on debugging messages
                        and build a debug DLL
  -l, --library=LIB     install packages to library tree LIB

So the following should work:

devtools::install_github("repo", args = c('--library="./mypath/gdfgdg/"'))

however it doesnt appear to be replacing the call to R CMD install

"C:/PROGRA~1/R/R-31~1.0/bin/x64/R" --vanilla CMD INSTALL  \
  "C:\Users\john\AppData\Local\Temp\RtmpucrXMD/RSelenium_1.3.2.tar.gz"  \
  --library="C:/Users/john/Documents/R/win-library/3.1" --install-tests  \
  --library="C:/Users/john/Desktop/"

@ManojG have you checked whether this works or not. It seems to work for me on my setup. — jdharrison, Jul 09 '14 at 10:04
I tested out. I'm getting same kind of output as in ur answer. But still its not installing in the specified directory, but installs in local directory. — Manoj G, Jul 09 '14 at 10:20
try `args = '-l "./mypath/gdfgdg/"'` and see if it makes any difference — jdharrison, Jul 09 '14 at 10:22
This did not work, but the `with_libpaths()` answer did work for me. — Mark Lakata, Nov 30 '16 at 00:42

score 2 · Answer 3 · answered Jul 10 '14 at 02:08

2

This is more of a workaround, but I found a way using the command-line version of R.

Starting from Ubuntu:

sudo -i R

the trick (I found) is to use -i option

Then from R:

.libPaths()

my local R directory does not appear; the default directory is the one that I want.

Then, I install.packages() or install_github() with impunity.

Hope this helps,

Ian

answered Jul 10 '14 at 02:08

Ian Lyttle

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@lanLyttle: Thank you. But it still removes only local directory from `.libPaths()` and not there are 3 more directories. Same as running R as root user. – Manoj G Jul 10 '14 at 04:15

How to specify lib directory when installing development version R Packages from github repository

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