#14008: Some R packages no longer can be installed
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Reporter: charpent | Owner: tbd
Type: enhancement | Status: needs_review
Priority: major | Milestone: sage-5.7
Component: packages | Resolution:
Keywords: r-project | Work issues:
Report Upstream: N/A | Reviewers:
Authors: Emmanuel Charpentier | Merged in:
Dependencies: | Stopgaps:
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Changes (by dimpase):
* status: new => needs_review
Old description:
> (At least) some R packages can no longer be installed.
>
> This is due to upstream's change of management of "lazy loading" : some
> packages version available through default repositories now expect to use
> this new mecaism, which is not available in R 2.14.0.
>
> The best solution is probably to update the R version shipping with Sage.
> I have packaged and tested it, but my solution is not yet complete :
> "make ptestlong" gives me two (expectable failures) :
>
> {{{
> sage -t --long -force_lib devel/sage/sage/interfaces/r.py
> **********************************************************************
> File "/home/sage/sage-5.6/devel/sage-main/sage/interfaces/r.py", line
> 555:
> sage: r.version()
> Expected:
> ((2, 14, 0), 'R version 2.14.0 (2011-10-31)')
> Got:
> ((2, 15, 2), 'R version 2.15.2 (2012-10-26)')
> **********************************************************************
> File "/home/sage/sage-5.6/devel/sage-main/sage/interfaces/r.py", line
> 2049:
> sage: r.version()
> Expected:
> ((2, 14, 0), 'R version 2.14.0 (2011-10-31)')
> Got:
> ((2, 15, 2), 'R version 2.15.2 (2012-10-26)')
> **********************************************************************
> 2 items had failures:
> 1 of 4 in __main__.example_16
> 1 of 4 in __main__.example_80
> ***Test Failed*** 2 failures.
> }}}
>
> which I do not know (yet) how to fix, because they involve patching
> doctests for r.py. Any pointer would be appreciated.
New description:
(At least) some R packages can no longer be installed.
This is due to upstream's change of management of "lazy loading" : some
packages version available through default repositories now expect to use
this new mecaism, which is not available in R 2.14.0.
The best solution is probably to update the R version shipping with Sage.
I have packaged and tested it, but my solution is not yet complete :
"make ptestlong" gives me two (expectable failures) :
{{{
sage -t --long -force_lib devel/sage/sage/interfaces/r.py
**********************************************************************
File "/home/sage/sage-5.6/devel/sage-main/sage/interfaces/r.py", line 555:
sage: r.version()
Expected:
((2, 14, 0), 'R version 2.14.0 (2011-10-31)')
Got:
((2, 15, 2), 'R version 2.15.2 (2012-10-26)')
**********************************************************************
File "/home/sage/sage-5.6/devel/sage-main/sage/interfaces/r.py", line
2049:
sage: r.version()
Expected:
((2, 14, 0), 'R version 2.14.0 (2011-10-31)')
Got:
((2, 15, 2), 'R version 2.15.2 (2012-10-26)')
**********************************************************************
2 items had failures:
1 of 4 in __main__.example_16
1 of 4 in __main__.example_80
***Test Failed*** 2 failures.
}}}
Install the spkg from
http://boxen.math.washington.edu/home/dima/packages/r-2.15.2.p0.spkg
and apply the [http://trac.sagemath.org/sage_trac/raw-
attachment/ticket/14008/trac-14008.patch patch]
--
Comment:
Replying to [comment:12 charpent]:
> spkg-upload is out of commission (my email to get upload credentials
bounced).
try {{{[email protected]}}}
I have but it there :
https://docs.google.com/file/d/0B1gfn4_V_wm3bHVqN3dMbzF4SGs/edit .
This kind of URL won't do as the parameter of {{{sage -f}}}
I've uploaded your file to the following location:
http://boxen.math.washington.edu/home/dima/packages/r-2.15.2.p0.spkg
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/14008#comment:13>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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