RSiteSearch, sos, rdocumentation.org, ...?
On 9/8/2016 5:01 AM, Jonathan Baron wrote:
OK. It is sort of fixed and sort of works. We'll keep it for now, but this is not going to work forever. When namazu fails completely I will not have the time to install a new search engine. One option is to use google. For a site like this, I think they will want some money, but I'm not sure, and I do not have the time to deal with it. We have over 10,000 packages now. I wonder if searching all help files is really helpful anymore.
The fastest way I know to do a literature search for anything
statistical uses the sos package as follows:
1. docPages <- findFn('search string') or findFn('{search
string}')
2. installPackages(docPages) # this installs packages to
enable a more complete package summary
3. writeFindFn2xls(docPages) # this creates an Excel file
with 3 sheets: a package summary, the findFn table, and the call.
4. Then I open the Excel file, and review the package
summary sheet. I prioritize my search from there based on the number
and strength of matches, how close it sounds to what I want, the date of
the last update, whether it has a vignette, and the authors and
maintainers.
There may be a better way to do this using Google or something
else. I'd be pleased if someone else could enlighten me. I admit to
being biased: I'm the lead author and maintainer of "sos". However, I
don't want to perpetuate a tool that has outlived its usefulness, and
I'm too blind to see that!
Spencer
Jon On 09/07/16 22:06, Jonathan Baron wrote:
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","--htm
l
"),repos=biocinstallRepos(),ask=F)
m3 <- new.packages()
install.packages(m3,dependencies=FALSE,INSTALL_opts=c("--no-configure","--no-test-lo
a
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 <baron at psych.upenn.edu>
To: Spencer Graves <spencer.graves at prodsyse.com>
CC: Jonathan Baron <baron at psych.upenn.edu>,
chris.is.fun at gmail.com, info at datacamp.com <info at datacamp.com>,
Sundar Dorai-Raj <sdorairaj at gmail.com>, webmaster at 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)