[sage-devel] Re: Request for test of installing R packages
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:
[sage-devel] Re: Request for test of installing R packages
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
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[sage-devel] Re: Request for test of installing R packages
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
real0m11.704s
user0m7.979s
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.)
--
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[sage-devel] Re: Request for test of installing R packages
Thanks. What kind of computer did you try this on?
- kcrisman
On Dec 14, 2:35 pm, davidp dav...@reed.edu wrote:
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.)
--
To post to this group, send an email to sage-devel@googlegroups.com
To unsubscribe from this group, send an email to
sage-devel+unsubscr...@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sage-devel
URL: http://www.sagemath.org
