Add R package in Sage folder

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Hi,

Simple question (I think) but have not found anything. I want to add package in R like GGPLOT2 and use it in IDE/command line for sage (not note book). I am using Ubuntu Lucid and have r working on its own.

So.

  1. Is it better to use the R in the Sage folder and add packages to that folder? If so how, as in Ubuntu everything goes to the main R installation.

  2. Or is there an easy way to just point RPy to the main R installation when using SAGE.

asked Apr 11 '12

mcm3 gravatar image mcm3
13 1 6

updated Apr 11 '12

3 Answers:

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Not sure why Niles thinks you need to do this... this was built in early on by the Sage-R interface.

sage: r.install_packages('ggplot2')

I've even done this live in talks I've given. Naturally, make sure you have an internet connection and that the package you want is supported by the version of R in Sage.

link

posted Apr 11 '12

kcrisman gravatar image kcrisman
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Ha! Because Niles isn't really familiar with R -- sorry for the confusion.

niles (Apr 11 '12)
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You could switch to a shell with the same environment variable settings that Sage uses. sage -sh starts such a shell for you, and then package installation might work on sage's copy of R instead of the system copy. More details are described for a similar question here:

http://ask.sagemath.org/question/1252/using-psycopg2-and-other-libraries-in-sage

link

posted Apr 11 '12

niles gravatar image niles
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http://nilesjohnson.net/

updated Apr 11 '12

This definitely should work. I'm putting yet another way of thinking of this below.

kcrisman (Apr 11 '12)

OK after reinstalling using sage -f r this works for 1. sage -sh 2. sage - R 3. install.packages('orloca'). Thanks for all the help.

mcm3 (Apr 12 '12)
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Or you could do

$ sage -R
<snip lots of stuff>
> install.packages('orloca')

and you will probably get some popup or some menu about choosing a CRAN mirror.

link

posted Apr 11 '12

kcrisman gravatar image kcrisman
7802 20 78 170

updated Apr 11 '12

This almost works but has not installed anything correctly yet. I have tried orloca, ggplot2, and maptools so far. I will put a big list of output below just FYI. Systems info: Sage 4.7, ubuntu lucid. Other aspects of SAGE are working fine for me.

mcm3 (Apr 11 '12)

This is some output FYI. matthew@matthew-laptop:~$ sage -R 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 ‘proto’ * removing ‘/opt/sage-4.8-linux-32bit-ubuntu_10.04_lts-i686-Linux/local/lib/R/library/proto’ ERROR: dependency ‘plyr’ is not available for package ‘stringr’ * removing ‘/opt/sage-4.8-linux-32bit-ubuntu_10.04_lts-i686-Linux/local/lib/R/library/stringr’ ERROR: dependency ‘colorspace’ is not available for package ‘munsell’ * removing ‘/opt/sage-4.8-linux-32bit-ubuntu_10.04_lts-i686-Linux/local/lib/R/library/munsell’ ERROR: dependency ‘digest’ is not available for package ‘memoise’ * removing ‘/opt/sage-4.8-li

mcm3 (Apr 11 '12)

for maptools error looks like thismake: /home/wstein/build/sage-4.8/local/lib/R/share/make/shlib.mk: No such file or directory make: * No rule to make target `/home/wstein/build/sage-4.8/local/lib/R/share/make/shlib.mk'. Stop. ERROR: compilation failed for package ‘sp’ * removing ‘/opt/sage-4.8-linux-32bit-ubuntu_10.04_lts-i686-Linux/local/lib/R/library/sp’ ERROR: dependency ‘sp’ is not available for package ‘maptools’ * removing ‘/opt/sage-4.8-linux-32bit-ubuntu_10.04_lts-i686-Linux/local/lib/R/library/maptools’

The downloaded packages are in ‘/tmp/RtmpzrpYpN/downloaded_packages’ Warning messages: 1: In install.packages("maptools") : installation of package ‘sp’ had non-zero exit status 2: In install.packages("maptools") : installation of package ‘maptools’ had non-zero exit stat

mcm3 (Apr 11 '12)

Hmm, that is puzzling. What happens if you use the "within Sage" option? I think that at least part of the problem is that there are some "hardcoded" parts - see the wstein bits, that shouldn't be there. If it persists, I would try doing sage -f r, assuming you have the right dependencies like fortran on your system, and then doing all of this again.

kcrisman (Apr 11 '12)

Or you could just build Sage from scratch :)

kcrisman (Apr 11 '12)
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Asked: Apr 11 '12

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