Opened 8 years ago
Closed 8 years ago
#14008 closed enhancement (fixed)
Some R packages no longer can be installed
Reported by: | charpent | Owned by: | tbd |
---|---|---|---|
Priority: | major | Milestone: | sage-5.7 |
Component: | packages: standard | Keywords: | r-project |
Cc: | kcrisman | Merged in: | sage-5.7.beta2 |
Authors: | Emmanuel Charpentier | Reviewers: | Dmitrii Pasechnik |
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
(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 mechanism, 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 Install the spkg from http://boxen.math.washington.edu/home/dima/packages/r-2.15.2.p0.spkg and apply the patch
Attachments (2)
Change History (25)
comment:1 follow-up: ↓ 2 Changed 8 years ago by
comment:2 in reply to: ↑ 1 Changed 8 years ago by
Replying to jason:
(Brief pointer; post if this doesn't make sense...)
Update the tests in SAGE_ROOT/devel/sage/sage/interfaces/r.py and then run
sage -hg commit
and thensage -hg export tip > trac-14008.patch
and attach the resulting file.
Thanks. This make sense and I will do that, but I'll first have to create a branch... Not until tomorrow (RealLife?(TM) again...).
comment:3 follow-up: ↓ 5 Changed 8 years ago by
You don't have to create a branch if you don't want.
comment:4 Changed 8 years ago by
- Cc kcrisman added
reoved
?
Also, maybe the formatting of SPKG.txt is just slightly off...
So ... it sounds like even with this r.install_package()
wouldn't work for all packages? (Or any?) Or am I misunderstanding things?
comment:5 in reply to: ↑ 3 Changed 8 years ago by
comment:6 follow-up: ↓ 8 Changed 8 years ago by
And where is the new spkg? Can you upload it somewhere? Thanks!
comment:7 Changed 8 years ago by
- Component changed from misc to packages
- Owner changed from jason to tbd
- Priority changed from minor to major
- Type changed from defect to enhancement
comment:8 in reply to: ↑ 6 Changed 8 years ago by
Replying to dimpase:
And where is the new spkg? Can you upload it somewhere? Thanks!
Try http://dl.free.fr/fVPIHKbzO .
Sorry for the inconvenience : I didn't know that the trac server did not accept large files, and I had to jury-rig this a bit quickly...
A formal patch is on its way (I botched my first attempt by recompiling my modified sage too early, and I have to go back...).
comment:9 Changed 8 years ago by
comment:10 follow-up: ↓ 11 Changed 8 years ago by
Patch uploaded. With the new spkg (to be found at http://dl.free.fr/fVPIHKbzO), this should go to "needs review", no ? Should I do this status change ?
comment:11 in reply to: ↑ 10 Changed 8 years ago by
Replying to charpent:
Patch uploaded. With the new spkg (to be found at http://dl.free.fr/fVPIHKbzO), this should go to "needs review", no ? Should I do this status change ?
I tried to download the spkg, but I keep getting a corrupt file (and it goes veeeery slow too). Could you upload it to a more reasonable hosting place?
- One option is to use http://code.google.com/p/spkg-upload/
- Another option is to ask for an account on the UW sage cluster (write directly to William).
- You might also try Dropbox or Google Drive, I think they are much faster than free.fr...
comment:12 follow-ups: ↓ 13 ↓ 14 Changed 8 years ago by
spkg-upload is out of commission (my email to get upload credentials bounced). I have but it there : https://docs.google.com/file/d/0B1gfn4_V_wm3bHVqN3dMbzF4SGs/edit .
Hoping that this will be more efficient...
comment:13 in reply to: ↑ 12 Changed 8 years ago by
- Description modified (diff)
- Status changed from new to needs_review
Replying to charpent:
spkg-upload is out of commission (my email to get upload credentials bounced).
try mvngu dot name СОБАКА(as we call this symbol in Russian) gmail dot com
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
comment:14 in reply to: ↑ 12 Changed 8 years ago by
Replying to charpent:
spkg-upload is out of commission (my email to get upload credentials bounced).
just got a reply from the maintainer of http://code.google.com/p/spkg-upload/ He's updated the email there (to the one I gave here already :))
comment:15 follow-up: ↓ 16 Changed 8 years ago by
- Description modified (diff)
Could you provide examples related to R packages which this is supposed to fix? (Even better, doctests, perhaps optional)
comment:16 in reply to: ↑ 15 ; follow-up: ↓ 18 Changed 8 years ago by
Replying to dimpase:
Could you provide examples related to R packages which this is supposed to fix? (Even better, doctests, perhaps optional)
An example is easy (but dangerous, see below), a doctest is not : installing an R package is supposed to have a permanent effect on the state of the installed system (an installed package stays installed between sessions). This, as far as I can tell, cannot be checked in a doctest.
Furthermore, a newly installed R package needs a restart of Sage to be usable (or so says the final message given by r.install.packages()).
An example is trivial : take example given for r.install_package(, which installs the R aami package). But :
- the side effect is to have the R package aami permanently installed, which is not necessarily a Good Thing(TM).
- if aami is already installed in the user's system, the example will fail.
One could implement the following pseudocode :
if (aami is installed) { uninstall it demonstrate the uninstallation reinstall it demonstrate the installation } else { install it demonstrate the installation uninstall it demonstrate the uninstallation }
But this might be a bit contrived for an example, no ?
An example which demonstrates the usefulness of this newer R version is to install the R package coda, I couldn't do that with sage 5.6 and R 2.14.0, I can do that with sage 5.6 and R 2.15.2.
HTH,
comment:18 in reply to: ↑ 16 ; follow-up: ↓ 20 Changed 8 years ago by
Furthermore, a newly installed R package needs a restart of Sage to be usable (or so says the final message given by r.install.packages()).
Somewhere I have a new doctest or something... some ticket talks about this. I have tried many times, and I am convinced the restart is not necessary and we just added that message "to be sure".
comment:19 Changed 8 years ago by
Thanks to all people who guided my first (stumbling) steps in Sage maintenance and coped with somewhat stupid-in-hinsight questions.
comment:20 in reply to: ↑ 18 Changed 8 years ago by
Replying to kcrisman:
Furthermore, a newly installed R package needs a restart of Sage to be usable (or so says the final message given by r.install.packages()).
Somewhere I have a new doctest or something... some ticket talks about this. I have tried many times, and I am convinced the restart is not necessary and we just added that message "to be sure".
This is consonant with my (limited) trials in Sage and my (somewhat more extensive) R experience. In less busy times, I'll have a look into this... But I have other fishes to fry first.
comment:21 Changed 8 years ago by
- Reviewers set to Dmitrii Pasechnik
- Status changed from positive_review to needs_work
There are a few administrative issues with your package:
SPKG.txt
mentions the deleted patchinstall_parallel.patch
in the section "Special Update/Build Instructions
", simply remove that item.- The Changelog header should be
=== r-2.15.2.p0 (Emmanuel Charpentier, 25 January 2013) ===
- You should commit (
hg rm patches/install_parallel.patch
andhg commit
) the changes,hg status
now reportsM SPKG.txt ! patches/install_parallel.patch
when it should report nothing.
comment:22 Changed 8 years ago by
- Status changed from needs_work to positive_review
updated the spkg to take care of the admin issues.
comment:23 Changed 8 years ago by
- Merged in set to sage-5.7.beta2
- Resolution set to fixed
- Status changed from positive_review to closed
(Brief pointer; post if this doesn't make sense...)
Update the tests in SAGE_ROOT/devel/sage/sage/interfaces/r.py and then run
sage -hg commit
and thensage -hg export tip > trac-14008.patch
and attach the resulting file.