Request for test of installing R packages

[kcrisman]

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.

Thanks,
- kcrisman

[Jason Grout]

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
>

[John Cremona]

2009/12/14 kcrisman <kcri...@gmail.com>:

This worked ok for me both on 64-bit ubuntu (the dialog for choosing a
mirror appeared in the command-line window) and on 32-bit Suse (where
it popped up a separate window which took me a few minutes to notice,
but which worked).

I could not test R afterwards since I have never used it.

The only thing which did not work as it apparently should is that
after the first r.install_packages('aaMI') it says that r.restart()
should work, but it gives an error message (sage0 not found).
Quitting Sage and then restarting is ok though.

John

>
> Thanks,
> - kcrisman
>
> --
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> URL: http://www.sagemath.org
>

[kcrisman]

>
> I could not test R afterwards since I have never used it.

That's ok - just trying to see one thing at a time.

>
> The only thing which did not work as it apparently should is that
> after the first r.install_packages('aaMI') it says that r.restart()
> should work, but it gives an error message (sage0 not found).
> Quitting Sage and then restarting is ok though.

I've noticed this in the past as well, not sure what to do about it.

Thanks for the report!
- kcrisman

[davidp]

sage: r.install_packages('aaMI')

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 ‘/usr/local/sage-4.2/local/lib/R/library/aaMI’

The downloaded packages are in

‘/tmp/Rtmpr0HuZc/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 '/home/davidp/download/sage-4.2/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
>

real 0m11.704s
user 0m7.979s
sys 0m0.148s

Please restart Sage or restart the R interface (via r.restart()) in
order to use 'aaMI'.
sage:

sage: sage: r.restart()
Error: object 'sage0' not found
sage: r.restart()
Error: object 'sage1' not found

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 ---

Loading Tcl/Tk interface ... done

trying URL 'http://cran.fhcrc.org/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 ‘/usr/local/sage-4.2/local/lib/R/library/abind’

The downloaded packages are in

‘/tmp/RtmpSImocY/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 '/home/davidp/download/sage-4.2/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

(I chose USA WA from the Tcl/Tk interface.)

[kcrisman]

Thanks. What kind of computer did you try this on?

- kcrisman

[François Bissey]

Same results in sage-4.2.1 on my gentoo x86 box. It worked but r.restart()
give the same error message.

Francois

[kcrisman]

Okay, looks like the spkg at #6532 fixes the issues, thanks to the
Fortran fix recently merged in 4.3.1. Installing packages works in
various ways on both sage.math and my Macintel with that spkg now, and
all tests pass when installing it with SAGE_CHECK=yes, so we might be
able to close 7 tickets with this spkg, depending on how things shake
out.

- kcrisman

> > 2009/12/14 kcrisman <kcris...@gmail.com>: