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:

Status badges

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 charpent

  • Priority changed from major to minor

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"

comment:2 Changed 7 years ago by charpent

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 vbraun_spam

  • Milestone changed from sage-6.3 to sage-6.4

comment:4 follow-up: Changed 7 years ago by 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.

comment:5 Changed 7 years ago by kcrisman

  • Cc kcrisman added

comment:6 in reply to: ↑ 4 Changed 5 years ago by leif

  • 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: Changed 8 months ago by chapoton

and 6 years later ? can we close as obsolete ?

comment:8 in reply to: ↑ 7 Changed 8 months ago by kcrisman

and 6 years later ? can we close as obsolete ?

Probably based on charpent's comments and the time elapsed, yes.

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