Opened 7 years ago
Last modified 8 months ago
#16694 needs_info defect
Rscript is currently non-functional
Reported by: | charpent | Owned by: | |
---|---|---|---|
Priority: | minor | Milestone: | sage-6.4 |
Component: | packages: standard | Keywords: | r-project |
Cc: | kcrisman | Merged in: | |
Authors: | Emmanuel Charpentier | Reviewers: | |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description
Sage's Rscript accepts neither files nor arguments.
Compare
## System version charpent@SAP5057241:~/Dev/nloptr$ cat foo.R 2+2 charpent@SAP5057241:~/Dev/nloptr$ which Rscript /usr/bin/Rscript charpent@SAP5057241:~/Dev/nloptr$ Rscript foo.R [1] 4 charpent@SAP5057241:~/Dev/nloptr$ Rscript -e "2+3" [1] 5
with
## Sage's version charpent@SAP5057241:~/Dev/nloptr$ sage -sh Starting subshell with Sage environment variables set. Don't forget to exit when you are done. Beware: * Do not do anything with other copies of Sage on your system. * Do not use this for installing Sage packages using "sage -i" or for running "make" at Sage's root directory. These should be done outside the Sage shell. Bypassing shell configuration files... Note: SAGE_ROOT=/usr/local/sage-6.3.beta6-x86_64-Linux (sage-sh) charpent@SAP5057241:nloptr$ which Rscript /usr/local/sage-6.3.beta6-x86_64-Linux/local/bin/Rscript (sage-sh) charpent@SAP5057241:nloptr$ Rscript foo.R Rscript execution error: No such file or directory (sage-sh) charpent@SAP5057241:nloptr$ Rscript -e "2+3" Rscript execution error: No such file or directory
Consequence : some packages, which need Rscript for installation (because they try to download some library source tarballs) can no longer be installed in R. This include notoriously nloptr, on which lme4 (a mixed-model package ofextremely frequent use) and other often-used packages depend.
Consequence of this consequence : Sage no longer offers a *replacement* for system's R. Ouch !
Change History (8)
comment:1 Changed 7 years ago by
- Priority changed from major to minor
comment:2 Changed 7 years ago by
Pursuing an apparent bug with an (seemingly unrelated) R package, I came to the conclusion that the proble might be related to R initial configuration.
Since this has been extensively modified in order to accomodate Cygwin's whims, I'd like to suggest that authors of #14706 have a look at https://groups.google.com/forum/#!topic/stan-users/Qbkuu51QZvU and make suggestions about the possible solutions.
comment:3 Changed 7 years ago by
- Milestone changed from sage-6.3 to sage-6.4
comment:4 follow-up: ↓ 6 Changed 7 years ago by
Further experiences let me think that this bug might be an artefact of iterative sage building (typical git use) : I'm still unable to reproduce it after "make distclean ; make".
However, I won't close this ticket now.
comment:5 Changed 7 years ago by
- Cc kcrisman added
comment:6 in reply to: ↑ 4 Changed 5 years ago by
- Status changed from new to needs_info
Replying to charpent:
Further experiences let me think that this bug might be an artefact of iterative sage building (typical git use) : I'm still unable to reproduce it after "make distclean ; make".
However, I won't close this ticket now.
And two years later?
comment:7 follow-up: ↓ 8 Changed 8 months ago by
and 6 years later ? can we close as obsolete ?
comment:8 in reply to: ↑ 7 Changed 8 months ago by
and 6 years later ? can we close as obsolete ?
Probably based on charpent's comments and the time elapsed, yes.
Apparently, this is not constant.
The problem I reported was shown on a machine using a Sage tarball precompiled on a fast machine with SAGE_FAT_BINARY="yes".
On another machine, compiled without any other flag other than MAJE="make -j8", Rscript works as advertised.
I have other problems with Sage's R (notably, rstan doesn't install), but this another problem (in general Sage builds are brittle...).
Downgrading the priority of the defect to "minor"