kcrisman wrote:
> Dear sage-devel,
>
> It's time to fix our R stuff. I have some suspicions on some issues,
> so I would appreciate if people on a wide variety of machines could
> try the following and reply to this thread.
>
> sage: r.install_packages('aaMI')
> # hopefully a happy result
> sage: r.console()
>> install.packages('abind')
> # you'll be asked to pick a mirror using a Tcl/Tk thingie>
> # hopefully a happy result
>
> I have already done OSX 10.5 on Macintel, where it works fine, as well
> as on sage.math (some kind of Linux, I guess), where it doesn't for
> some reason (see #4959 for details), though only for the second
> package which seems to require something unusual. Reports would help
> a lot with figuring out what is going on with #4959 and #5246. Please
> note that these packages don't depend on anything else, so the
> problems from #6532 or #2198 should not occur.
This is on x86 64-bit Ubuntu Karmic, sage 4.3.rc0.
Thanks,
Jason
% sage
----------------------------------------------------------------------
| Sage Version 4.3.rc0, Release Date: 2009-12-10 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
**********************************************************************
* *
* Warning: this is a prerelease version, and it may be unstable. *
* *
**********************************************************************
sage: r.install_packages('aaMI')
0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+214minor)pagefaults 0swaps
R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> options(repos="http://cran.r-project.org/";); install.packages("aaMI")
trying URL 'http://cran.r-project.org/src/contrib/aaMI_1.0-1.tar.gz'
Content type 'application/x-gzip' length 3487 bytes
opened URL
==================================================
downloaded 3487 bytes
* Installing *source* package ‘aaMI’ ...
** R
** preparing package for lazy loading
Error in if (file.info(codeFile)["size"] ==
file.info(loaderFile)["size"]) warning("package seems to be using lazy
loading already") else { :
missing value where TRUE/FALSE needed
ERROR: lazy loading failed for package ‘aaMI’
* Removing ‘/home/grout/sage-4.3.rc0/local/lib/R/library/aaMI’
The downloaded packages are in
‘/tmp/RtmpxzBKKg/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("aaMI") :
installation of package 'aaMI' had non-zero exit status
2: In file.create(f.tg) :
cannot create file
'/dev/shm/sage-4.3.rc0/local/lib/R/doc/html/packages.html', reason 'No
such file or directory'
3: In tools:::unix.packages.html(.Library) :
cannot create HTML package index
>
Please restart Sage or restart the R interface (via r.restart()) in
order to use 'aaMI'.
sage:
Exiting SAGE (CPU time 0m0.03s, Wall time 0m20.52s).
% sage
----------------------------------------------------------------------
| Sage Version 4.3.rc0, Release Date: 2009-12-10 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
**********************************************************************
* *
* Warning: this is a prerelease version, and it may be unstable. *
* *
**********************************************************************
sage: r.console()
R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages('abind')
--- Please select a CRAN mirror for use in this session ---
CRAN mirror
1: Argentina (Buenos Aires) 2: Australia
3: Austria 4: Belarus
5: Belgium 6: Brazil (PR)
7: Brazil (RJ) 8: Brazil (SP 1)
9: Brazil (SP 2) 10: Canada (BC)
11: Canada (ON) 12: Canada (QC)
13: Chile 14: China (Beijing 1)
15: China (Beijing 2) 16: China (Hong Kong)
17: Colombia 18: Denmark
19: France (Toulouse) 20: France (Lyon)
21: France (Paris) 22: Germany (Berlin)
23: Germany (Goettingen) 24: Germany (Hannover)
25: Germany (Muenchen) 26: Germany (Wiesbaden)
27: Iran 28: Ireland
29: Italy (Milano) 30: Italy (Padua)
31: Italy (Palermo) 32: Japan (Aizu)
33: Japan (Hyogo) 34: Japan (Tokyo)
35: Japan (Tsukuba) 36: Korea
37: Netherlands 38: New Zealand
39: Norway 40: Poland (Oswiecim)
41: Poland (Wroclaw) 42: Portugal
43: Russia 44: Singapore 1
45: Singapore 2 46: Slovakia
47: South Africa 48: Spain (Madrid)
49: Sweden 50: Switzerland
51: Taiwan (Taichung) 52: Taiwan (Taipeh)
53: Thailand 54: UK (Bristol)
55: UK (London) 56: USA (AZ)
57: USA (CA 1) 58: USA (CA 2)
59: USA (IA) 60: USA (MA)
61: USA (MD) 62: USA (MI)
63: USA (MO) 64: USA (NC)
65: USA (OH) 66: USA (PA 1)
67: USA (PA 2) 68: USA (TN)
69: USA (TX 1) 70: USA (TX 3)
71: USA (WA)
Selection: 65
trying URL 'http://cran.case.edu/src/contrib/abind_1.1-0.tar.gz'
Content type 'application/x-gzip' length 10280 bytes (10 Kb)
opened URL
==================================================
downloaded 10 Kb
* Installing *source* package ‘abind’ ...
** R
** preparing package for lazy loading
Error in if (file.info(codeFile)["size"] ==
file.info(loaderFile)["size"]) warning("package seems to be using lazy
loading already") else { :
missing value where TRUE/FALSE needed
ERROR: lazy loading failed for package ‘abind’
* Removing ‘/home/grout/sage-4.3.rc0/local/lib/R/library/abind’
The downloaded packages are in
‘/tmp/RtmpumN13m/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("abind") :
installation of package 'abind' had non-zero exit status
2: In file.create(f.tg) :
cannot create file
'/dev/shm/sage-4.3.rc0/local/lib/R/doc/html/packages.html', reason 'No
such file or directory'
3: In tools:::unix.packages.html(.Library) :
cannot create HTML package index
>
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