Hi folks,
I want to install an optional R package from source that I've
downloaded from CRAN, say the package /home/mvngu/sna_1.5.tar.gz.
Here's my first attempt on Sage 3.2.3:
<begin-error-message>
sage: r.install_packages("/home/mvngu/sna_1.5.tar.gz")
R version 2.6.1 (2007-11-26)
Copyright (C) 2007 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.
Natural language support but running in an English locale
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("/home/mvngu/sna_1.5.tar.gz")
Warning: unable to access index for repository
http://cran.r-project.org/src/contrib
Warning message:
In install.packages("/home/mvngu/sna_1.5.tar.gz") :
package '/home/mvngu/sna_1.5.tar.gz' is not available
>
real 0m1.147s
user 0m0.952s
sys 0m0.036s
Please restart Sage or restart the R interface (via r.restart()) in
order to use '/home/mvngu/sna_1.5.tar.gz'.
<end-error-message>
All I understand from the above error message is that I need an
Internet connection, especially to
http://cran.r-project.org/src/contrib. But the machine I'm using
doesn't have Internet connection. OK, no problem. I looked into the
Sage <----> R interface file
sage-3.2.3/local/lib/python2.5/site-packages/sage/interfaces/r.py
and modified the function install_packages() to be as follows:
<begin-modified-r.py>
def install_packages(self, package_name):
"""
Install an R package into Sage's R installation.
EXAMPLES:
sage: r.install_package('Hmisc') #optional requires
internet
[1] 4 5 6
"""
if UNAME == "Darwin":
warn = "** You are using OS X. Unfortunately, the R
optional package system currently doesn't support OS X
very well. We are working on this. **"
else:
warn = None
if warn is not None: print warn
cmd = """options(repos="%s");
# install.packages("%s")"""%(RRepositoryURL, package_name)
# os.system("time echo '%s' | R --vanilla"%cmd)
os.system("/home/mvngu/usr/bin/sage-3.2.3/local/lib/R/bin/R
CMD INSTALL /home/mvngu/sna_1.5.tar.gz")
print "Please restart Sage or restart the R interface (via
r.restart()) in order to use '%s'."%package_name
if warn is not None: print warn
#s = r.eval('install.packages("%s")'%package_name)
#print s
<end-modified-r.py>
Notice that I uncommented out these lines:
install.packages("%s")"""%(RRepositoryURL, package_name)
os.system("time echo '%s' | R --vanilla"%cmd)
and added the following quick-and-dirty fix:
os.system("/home/mvngu/usr/bin/sage-3.2.3/local/lib/R/bin/R CMD
INSTALL /home/mvngu/sna_1.5.tar.gz")
I exited Sage and issued a re-build of modified Sage library files with
$ sage -br main
Then I loaded Sage again for another attempt at installing sna_1.5.tar.gz:
<begin-error-message>
sage: r.install_packages("abc doesn't matter what name you put here!")
* Installing to library
'/home/mvngu/usr/bin/sage-3.2.3/local/lib/R//library'
WARNING: ignoring environment value of R_HOME
* Installing *source* package 'sna' ...
** libs
gcc -std=gnu99 -I/home/mvngu/usr/bin/sage-3.2.3/local/lib/R/include
-I/home/mvngu/usr/bin/sage-3.2.3/local/lib/R/include
-I/home/mvngu/usr/bin/sage-3.2.3/local/inlcude WARNING: ignoring
environment value of R_HOME -fpic
-I/home/mvngu/usr/bin/sage-3.2.3/local/include
-L/home/mvngu/usr/bin/sage-3.2.3/local/lib/ -c components.c -o
components.o
gcc: WARNING:: No such file or directory
gcc: ignoring: No such file or directory
gcc: environment: No such file or directory
gcc: value: No such file or directory
gcc: of: No such file or directory
gcc: R_HOME: No such file or directory
make: *** [components.o] Error 1
ERROR: compilation failed for package 'sna'
** Removing '/home/mvngu/usr/bin/sage-3.2.3/local/lib/R/library/sna'
Please restart Sage or restart the R interface (via r.restart()) in
order to use 'abc'.
<end-error-message>
The closest problems to mine that I can locate are
http://groups.google.com/group/sage-support/browse_thread/thread/2c0ef9eb24e8dd53/2c559b00b3585b18
in sage-devel and this one in sage-support:
http://groups.google.com/group/sage-support/browse_thread/thread/881b23030c56f48d/4d28b33aa01bfb63
But they don't seem to have any work around I can use, especially when
the tickets #4959 and #1476 they spawned as yet either haven't been
resolved or closed as "worksforme".
Does anyone have a suggestion I can try to install sna_1.5.tar.gz?
--
Regards
Minh Van Nguyen
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