Laurent,
> Interval does matter. The R server will timeout if it is too long. Try
> lowering it. The documentation will have a note about that
> (http://bitbucket.org/lgautier/rpy2/changeset/73bc2a415ba3/).
Thanks for that... I seem to have (partially) solved the issue, in
that I was having issues with proxy settings here at work.
However, I can now get the html help files to work, but *not*
help.start() and the help index.html page. The following is the exact
code that I am testing with:
import rpy2.robjects as robs
import time
import threading
def r_refresh(interval=0.02):
while True:
robs.rinterface.process_revents()
time.sleep(interval)
t = threading.Timer(0.02, r_refresh)
print robs.r("""help.start()""")
print robs.r("""help(help_type="html")""")
t.start()
Note that I start the timer after I call help.start() to avoid
congruent access to R errors. The first call "help.start()" attempts
to access http://127.0.0.1:22689/doc/html/index.html, and simply
returns:
"URL /doc/html/index.html was not found"
The second call "help(help_type="html")" attempts to access
http://127.0.0.1:22689/library/utils/html/help.html and works just
fine, including all the hyperlinks. This leads me to believe that the
server is running, but that for some reason the index.html page is not
being generated? The odd things is that if this is called from R, it
all works fine every time. There are some R environment variables that
are set somewhere that appear to adjust where R searches for the
relevant information to generate index.html.
>>> print robs.r("""R.home("doc")""")
[1] "/usr/lib64/R/doc"
> R.home("doc")
[1] "/usr/share/R/doc"
> R.home
function (component = "home")
{
rh <- .Internal(R.home())
switch(component, home = rh, share = if (nzchar(p <-
as.vector(Sys.getenv("R_SHARE_DIR"))))
p
else file.path(rh, component), doc = if (nzchar(p <-
as.vector(Sys.getenv("R_DOC_DIR"))))
p
else file.path(rh, component), include = if (nzchar(p <-
as.vector(Sys.getenv("R_INCLUDE_DIR"))))
p
else file.path(rh, component), file.path(rh, component))
}
and "R_DOC_DIR" is obviously set by R when run, but not by Rpy2
(probably for good reason). In fact, R_DOC_DIR is set in /usr/bin/R.
Is there any way I can access these environment variables from within
Rpy2, as I think I could probably get help.start() to work properly if
these environment variables were properly set?
Carson
--
Carson J. Q. Farmer
ISSP Doctoral Fellow
National Centre for Geocomputation
National University of Ireland, Maynooth,
http://www.carsonfarmer.com/
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