Opened 4 years ago
Last modified 22 months ago
#25503 closed defect
Allow the use of system's R installation — at Version 5
Reported by: | tmonteil | Owned by: | |
---|---|---|---|
Priority: | major | Milestone: | sage-duplicate/invalid/wontfix |
Component: | packages: standard | Keywords: | R, sdl |
Cc: | charpent, embray, fbissey, kcrisman, slelievre, gh-timokau, mjo | Merged in: | |
Authors: | Thierry Monteil | Reviewers: | |
Report Upstream: | N/A | Work issues: | |
Branch: | u/tmonteil/allow_the_use_of_system_s_r_installation (Commits, GitHub, GitLab) | Commit: | eed2ea352af29fa6e6fb65d274c2e0078a7c07a6 |
Dependencies: | Stopgaps: |
Description (last modified by )
The aim of this ticket is to allow Sage to use the system's R
, instead of building its own.
It should work for:
sage -R
command- Sage's
r
interface - Sage's
rpy2
Python package - Sage's jupyter
IRkernel
Similarly to the way one can decide to use the system ATLAS when building Sage,
on the user side, building Sage so that it uses the system R is achieved by setting
the SAGE_R_LIB
environment variable.
To test this ticket, you should at least:
- install
R
on your system (e.g.sudo apt install r-base
) - reinstall
r
andrpy2
withSAGE_R_LIB
set:export SAGE_R_LIB=/usr/lib/R/ sage -f r sage -f rpy2 make build
- test Sage
R
command (this should/might show a different version than 3.4.4):sage -R
- test Sage's
R
interface:sage -t --long src/sage/interfaces/r.py
- test
rpy2
:sage -t --long src/sage/stats/r.py
Change History (5)
comment:1 Changed 4 years ago by
- Branch set to u/tmonteil/allow_the_use_of_system_s_r_installation
comment:2 Changed 4 years ago by
- Cc charpent embray added
- Commit set to eed2ea352af29fa6e6fb65d274c2e0078a7c07a6
- Description modified (diff)
- Status changed from new to needs_review
comment:3 Changed 4 years ago by
- Description modified (diff)
comment:4 Changed 4 years ago by
We should probably also update sage-env
script, which explicitly unset R
-related variables that the user could set in relation with system-wide install.
comment:5 Changed 4 years ago by
- Cc fbissey kcrisman slelievre added
- Description modified (diff)
- Keywords R added
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New commits:
#25503 : do not build R if SAGE_R_LIB is set
#25503 : let rpy2 use SAGE_R_LIB for its RHOMES variable
#25503 : fix issue between R interface and readline 7
#25503 : document the SAGE_R_LIB variable in the install guide