From spencer.graves at prodsyse.com  Thu Sep  8 15:32:16 2016
From: spencer.graves at prodsyse.com (Spencer Graves)
Date: Thu, 8 Sep 2016 08:32:16 -0500
Subject: [Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
In-Reply-To: <20160908100100.GA30732@psych.upenn.edu>
References: <20160907201522.GA12554@psych.upenn.edu>
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	<20160907205321.GB24417@psych.upenn.edu>
	<20160908020657.GA27642@psych.upenn.edu>
	<20160908100100.GA30732@psych.upenn.edu>
Message-ID: <b7e7da04-0154-3dcb-fda9-be1d0dc13929@prodsyse.com>



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)
>



[Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
Spencer Graves