Don't do anything yet. I may have found the problem by accident.
I tried to use the computer from something else, and it was being
drastically slowed down by some leftover processes, which turned out
to be xlhtml. That is something that converts Excel files. Apparently,
some excel files got into the libraries, and they were causing the
indexing to hang completely.
I am now running everything again, starting from scratch, and it might
work. (I'm doing it wrong, but it is 3/4 done. I will do it right
tomorrow, if it works overnight.)
Jon
On 09/07/16 16:53, Jonathan Baron wrote:
Spencer,
Thanks for the quick reply.
I am open to someone who knows Perl getting an account on my site and
trying to get it working. It will probably involve fixing more than
one thing, as mknmz depends on some perl modules that also generate
errors.
My main contribution is figuring out how to extract the html help
files and vignettes only, with some help from R developers and Fedora
maintainers. Here is the trick, for someone who wants to do it:
m0 <- rownames(installed.packages())
m1 <- m0[which(m0 %in% needed.packages)]
source("http://bioconductor.org/biocLite.R";)
update.packages(oldPkgs=m1,repos=biocinstallRepos())
update.packages(dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-load","
--no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--html
"),repos=biocinstallRepos(),ask=F)
m3 <- new.packages()
install.packages(m3,dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-loa
d","--no-R","--no-clean-on-error","--no-libs","--no-data","--no-demo","--no-exec","--
html"),repos=biocinstallRepos())
Note 1: The first 4 lines are designed to deal with a list of the
packages that you actually use. These can be eliminated if you don't
use R on the same machine. The last 3 lines are all you need.
Note 2: This works on Fedora, but I think that the Fedora maintainers
of R have set some defaults that are helpful.
Jon
On 09/07/16 15:41, Spencer Graves wrote:
Hello, All:
Jonathan Baron is "giving up" maintaining the RSiteSearch database.
This breaks three things: (1) The R Site Search web service that
Baron has maintained. (2) The RSiteSearch function in the utils
package. (3) The sos package, for which I'm the maintainer and lead
author.
Might someone else be willing to take these over?
For me, the "findFn" capability with "writeFindFn2xls" is the
fastest literature search for anything statistical. However, I don't
have the resources to take over the management of Baron's R Site Search
database.
He's provided a great service for the R community for many
years. I hope we can find a way to keep the system maintained. Failing
that, I could use help in adapting the sos package to another database.
Thanks,
Spencer Graves
-------- Forwarded Message --------
Subject: Re: RSiteSearch, sos, rdocumentation.org, ...?
Date: Wed, 7 Sep 2016 16:15:22 -0400
From: Jonathan Baron <ba...@psych.upenn.edu>
To: Spencer Graves <spencer.gra...@prodsyse.com>
CC: Jonathan Baron <ba...@psych.upenn.edu>, chris.is....@gmail.com,
i...@datacamp.com <i...@datacamp.com>, Sundar Dorai-Raj
<sdorai...@gmail.com>, webmaster@www.r-project-org
R site search has stopped working. The indexing scrip, mknmz, failed
to complete. It has been producing more and more errors and warnings,
since it has not been updated for 5 yeaers.
I am giving up on this site. I have too many other things to do aside
from find bugs in programs written in languages I don't know (Perl),
or set up an alternative search engine.
Please inform anyone else who needs to be informed.
I cannot find the email of the www.r-project.org webmaster, so I'm
taking a stab. There are several links to this site in those pages.
Jon
--
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page: http://www.sas.upenn.edu/~baron
Editor: Judgment and Decision Making (http://journal.sjdm.org)
--
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page: http://www.sas.upenn.edu/~baron
Editor: Judgment and Decision Making (http://journal.sjdm.org)
--
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page: http://www.sas.upenn.edu/~baron
Editor: Judgment and Decision Making (http://journal.sjdm.org)
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