[sage-support] Re: upgrading R in sage ?

2013-01-25 Thread Emmanuel Charpentier
Patch uploaded, new spkg available here http://dl.free.fr/fVPIHKbzO. 
make ptestlong tells me that all test passed.  I think that trac#14008 
is ready for a review...

Thank you to all people who have guided my first steps in the sage 
contribution labyrinth.


   Emmanuel Charpentier

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[sage-support] Re: upgrading R in sage ?

2013-01-24 Thread Volker Braun
Search for r-project. We are trying to add that keyword to all R-related 
tickets. As you say, just searching for R is pointless ;-)



On Thursday, January 24, 2013 4:38:08 PM UTC, Emmanuel Charpentier wrote:

 Since a couple of versions ago, the package installation mechanism in R 
 has changed, and some packages are no longer installable. Case in point : 
 rjags, which needs code, whose installation fro CRAN packages will fail due 
 to different lazy loading management.

 Reading the SPKG file of the standard spkg for R makes me think that 
 installing a newer R version could be as simple as creating a newer branch, 
 installing the newer R source in that branch and recompiling. Is that 
 correct ?

 I tried to search relevant trac tickets, but this is not easy : R is not 
 a good target for trac searching...

 More general note : tghe R community is somewhat adamantine about 
 running an up-to-date R : perusing the r-help mailing list, one can often 
 see questions on older R version, almost always getting the standard answer 
 upgrade to current version  R. having at least an *optional* r-latest 
 spkg might be useful...

 Any advice ?


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[sage-support] Re: upgrading R in sage ?

2013-01-24 Thread Dima Pasechnik
On 2013-01-24, Emmanuel Charpentier emanuel.charpent...@gmail.com wrote:
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 Le jeudi 24 janvier 2013 21:01:33 UTC+1, Emmanuel Charpentier a =E9crit :

 [ Snip... ]
  Any advice ?=20

 Go for it!  Create a Trac ticket and post a new spkg.=20


 I will do that. But not immediately : RealLife(TM) has its exigences...

 [ Later ] almost done :
 dropping the new source code was a breeze. I had to delete the=20
 install_parallel patch, which does something already in the new source.=20
 Installation was uneventful, and the new code do fix my gripe : rjags and=
=20
 coda can be installed now, and seem functional.

 However, I have two ptestlong failures, (both expectable in hindsight...) :

these are trivial to fix: create a patch for 
$SAGE_ROOT/devel/sage/sage/interfaces/r.py
and upload it on the ticket

(no need to create a new branch or anything, as this is a very harmless
patch, which shouldn't break anything of importance in your Sage
installation)

 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.

 I do not (yet) know where to find these doctests and how to present the=20
 relevant patches. Any pointers ? My view of the sage development process is=
=20
 not yet absolutely clear...

   Emmanuel=
=20
 Charpentier

=20
=20

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 Le jeudi 24 janvier 2013 21:01:33 UTC+1, Emmanuel Charpentier a =E9critnbs=
 p;:brblockquote class=3Dgmail_quote style=3Dmargin: 0;margin-left: 0.=
 8ex;border-left: 1px #ccc solid;padding-left: 1ex;[ Snip... ]divgt; An=
 y advice ?nbsp;brblockquote class=3Dgmail_quote style=3Dmargin:0;mar=
 gin-left:0.8ex;border-left:1px #ccc solid;padding-left:1exGo for it! nbs=
 p;Create a Trac ticket and post a new spkg.
br/blockquotedivbr/divdivI will do that. But not immediately : =
 RealLife(TM) has its exigences.../div/divdivbr/div/blockquoted=
 iv[ Later ] almost done :/divdivdropping the new source code was a bre=
 eze. I had to delete the install_parallel patch, which does something alrea=
 dy in the new source. Installation was uneventful, and the new code do fix =
 my gripe : rjags and coda can be installed now, and seem functional./div=
 divbr/divdivHowever, I have two ptestlong failures, (both expectable=
  in hindsight...) :/divdivdivbr/divdivsage -t nbsp;--long -for=
 ce_lib devel/sage/sage/interfaces/r.py/divdiv**=
 /divdivFile /home/sage/sag=
 e-5.6/devel/sage-main/sage/interfaces/r.py, line 555:/divdivnbsp; nb=
 sp; sage: r.version()/divdivExpected:/divdivnbsp; nbsp; ((2, 14, =
 0), 'R version 2.14.0 (2011-10-31)')/divdivGot:/divdivnbsp; nbsp;=
  ((2, 15, 2), 'R version 2.15.2 (2012-10-26)')/divdiv**=
 /divdivFile /home/=
 sage/sage-5.6/devel/sage-main/sage/interfaces/r.py, line 2049:/divdiv=
 nbsp; nbsp; sage: r.version()/divdivExpected:/divdivnbsp; nbsp; =
 ((2, 14, 0), 'R version 2.14.0 (2011-10-31)')/divdivGot:/divdivnbs=
 p; nbsp; ((2, 15, 2), 'R version 2.15.2 (2012-10-26)')/divdiv*=
 */divdiv2 i=
 tems had failures:/divdivnbsp; nbsp;1 of nbsp; 4 in __main__.example=
 _16/divdivnbsp; nbsp;1 of nbsp; 4 in __main__.example_80/divdiv*=
 **Test Failed*** 2 failures./div/divdivbr/divdivI do not (yet) =
 know where to find these doctests and how to present the relevant patches. =
 Any pointers ? My view of the sage development process is not yet absolutel=
 y clear.../divdivbr/divblockquote class=3Dgmail_quote style=3Dm=
 argin: 0;margin-left: