#9906: Move the RPy package outside of the R package
-----------------------------------+----------------------------------------
Reporter: mpatel | Owner: leif
Type: defect | Status: needs_review
Priority: major | Milestone: sage-4.7.2
Component: packages | Keywords:
Work_issues: | Upstream: N/A
Reviewer: Karl-Dieter Crisman | Author: Leif Leonhardy
Merged: | Dependencies:
-----------------------------------+----------------------------------------
Old description:
> We include the RPy spkg in the R spkg and install the former from the
> latter. It would be less potentially confusing to move RPy outside of R
> but make it depend on R and any other prerequisites in
> `spkg/standard/deps`.
>
> The necessary changes to `spkg/install` and `spkg/standard/deps` are
> already there, but currently commented out. Apply the following patch
> '''to the Sage root repository''' to activate them:
>
> [attachment:trac_9906-Activate_separate_RPy_spkg.root-repo.patch]
>
> ----
>
> '''New R spkg: http://spkg-
> upload.googlecode.com/files/r-2.10.1.p5.spkg'''
>
> '''md5sum:''' `5c47527326872143563b31317e2d044c r-2.10.1.p5.spkg`
>
> === r-2.10.1.p5 (Leif Leonhardy, September 26th 2010) ===
> * #9906: Move the RPy spkg out of R's.
> * Unset R_PROFILE in both spkg-install and spkg-check since this caused
> trouble when pointing to system-wide / site-specific installations
> (cf. #9847).
> * Clean up spkg-install and spkg-check.
> * Only delete old installations if the build succeeded.
> * Disable parallel make install properly.
> * Use $MAKE in spkg-check.
> * Use CFLAG64 if defined rather than hardcoded -m64.
> * Don't override user-specified flags unless necessary.
> * Disable optimization if SAGE_DEBUG=yes, add debug symbols by default.
> * Also respect SAGE_FAT_BINARY in second attempt to configure.
> * Add more error checks.
> * Add further dependencies, "Patches" section in SPKG.txt.
> * Remove some garbage from src/ (see Special Update/Build Instructions).
>
> '''New Rpy spkg: http://spkg-
> upload.googlecode.com/files/rpy2-2.0.8.p1.spkg'''
>
> '''md5sum:''' `e171d3641feaf1d3993c0a972675e1f7 rpy2-2.0.8.p1.spkg`
>
> === rpy2-2.0.8.p1 (Leif Leonhardy, September 26th 2010) ===
> * #9906: Moved the spkg out of R's. Since setup.py is patched, the
> previous version in Sage should have been 2.0.8.p0.
> * Added usual sanity check to spkg-install, changed #!/bin/sh
> to #!/usr/bin/env bash.
> * Renamed patches/setup.patch to patches/setup.py.patch.
> * Updated SPKG.txt, added dependencies.
>
> ----
>
> Related: #3086 (closed as duplicate).
>
> See also #8274, #9668 and #10967 for what could or should be addressed,
> too.
>
> Other related (R) tickets: #9847 (see comments below; can IMHO be closed
> as duplicate when this ticket gets merged)
New description:
We include the RPy spkg in the R spkg and install the former from the
latter. It would be less potentially confusing to move RPy outside of R
but make it depend on R and any other prerequisites in
`spkg/standard/deps`.
The necessary changes to `spkg/install` and `spkg/standard/deps` are
already there, but currently commented out. Apply the following patch
'''to the Sage root repository''' to activate them:
[attachment:trac_9906-Activate_separate_RPy_spkg.root-repo.patch]
----
'''New R spkg: http://spkg-upload.googlecode.com/files/r-2.10.1.p5.spkg'''
'''md5sum:''' `5c47527326872143563b31317e2d044c r-2.10.1.p5.spkg`
=== r-2.10.1.p5 (Leif Leonhardy, September 26th 2010) ===
* #9906: Move the RPy spkg out of R's.
* Unset R_PROFILE in both spkg-install and spkg-check since this caused
trouble when pointing to system-wide / site-specific installations
(cf. #9847).
* Clean up spkg-install and spkg-check.
* Only delete old installations if the build succeeded.
* Disable parallel make install properly.
* Use $MAKE in spkg-check.
* Use CFLAG64 if defined rather than hardcoded -m64.
* Don't override user-specified flags unless necessary.
* Disable optimization if SAGE_DEBUG=yes, add debug symbols by default.
* Also respect SAGE_FAT_BINARY in second attempt to configure.
* Add more error checks.
* Add further dependencies, "Patches" section in SPKG.txt.
* Remove some garbage from src/ (see Special Update/Build Instructions).
'''New Rpy spkg: http://spkg-
upload.googlecode.com/files/rpy2-2.0.8.p1.spkg'''
'''md5sum:''' `e171d3641feaf1d3993c0a972675e1f7 rpy2-2.0.8.p1.spkg`
=== rpy2-2.0.8.p1 (Leif Leonhardy, September 26th 2010) ===
* #9906: Moved the spkg out of R's. Since setup.py is patched, the
previous version in Sage should have been 2.0.8.p0.
* Added usual sanity check to spkg-install, changed #!/bin/sh
to #!/usr/bin/env bash.
* Renamed patches/setup.patch to patches/setup.py.patch.
* Updated SPKG.txt, added dependencies.
----
Related: #3086 (closed as duplicate).
See also #8274, #9668 and #10967 for what could or should be addressed,
too. #9668 will now function as a follow-up ticket, providing an R
2.10.1.p6 spkg, also fixing #10967.
Other related (R) tickets: #9847 (see comments below; can IMHO be closed
as duplicate when this ticket gets merged)
--
Comment(by leif):
Replying to [comment:20 kcrisman]:
> Here is another somewhat related ticket - #10967. I don't think that
is fixed, at least not in the same way, by this p5.
For the record: #10967 will be addressed at #9668, by an R 2.10.1.p6 spkg
there, so I've made the former ticket depend on the latter, and changed
its milestone to ''"duplicate/invalid/won't fix"''.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/9906#comment:22>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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