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

2016-12-22 Thread Jonathan Baron 

The site is working again, although for some reason it did not
download any vignettes. I think that is OK.

On 12/21/16 18:22, Jonathan Baron wrote:

Unfortunately, I am unable to get this search site working again. (The
message below explains why I had to rebuild it.)


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

2016-12-21 Thread Jonathan Baron 

Unfortunately, I am unable to get this search site working again. (The
message below explains why I had to rebuild it.)

The computer worked for the better part of a day downloading and
installing all the help files from all CRAN packages. Somehow it
failed to get the vignettes this time. But I pushed ahead and ran the
part of namazu that makes the search indices: mknmz. And you can see
the results if you go to finzi.psych.upenn.edu. The search works, but
then you can't get the actual help pages.

The problem seems to be that namazu search is ignoring the "Replace"
rules in the configuration file, namazurc. I have tried 4 versions of
that file, in combination with 3 versions of namazu-cgi, and nothing
works. Note that the last version of namzu was about 2009, the result
of some fixes by linux distribution maintainers, not by the original
creators, who gave up a few years before.

If someone wants to replace namazu with a different search engine, let
me know. I do have a server with all the help files.

And I can tell you how I made them if you want to do this somewhere
else. The trick is:

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)

and

install.packages(m3,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())

This works as is in the fedora version of R, which I think is modified
(for my benefit, about 10 years ago) from the distribution version,
and I think I know what the modification is. The first is for packages
I already have. The second can be used to build the site.

(I use the bioconductor repository because most of the time it doesn't
matter, but there were once a few packages that were only there, ones
that I used myself, like multtest.)

Of course, if there is a human being who reads this and wants to
fiddle with namazu, he or she should contact me.

Jon

On 12/17/16 15:32, Jonathan Baron wrote:

Spencer and others.

I am going to have to take down the server for RSiteSearch, which is
finzi.psych.upenn.edu, for at least a couple of days starting Sunday
morning. It has been hacked. And I have another server that has also
been hacked, which is higher priority (sjdm.org). On Monday, I will
probably have time to rebuild that one, but I may not have time to
rebuild finzi for another week. I will try to get it all done in one
day, but I don't know if I can.

Sorry about this.

I thought that there was an alternative to this site, namely
http://rdocumentation.org/
but, as bad is my site is, that one, I think, is worse.

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)

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

2016-12-17 Thread Jonathan Baron 

Spencer and others.

I am going to have to take down the server for RSiteSearch, which is
finzi.psych.upenn.edu, for at least a couple of days starting Sunday
morning. It has been hacked. And I have another server that has also
been hacked, which is higher priority (sjdm.org). On Monday, I will
probably have time to rebuild that one, but I may not have time to
rebuild finzi for another week. I will try to get it all done in one
day, but I don't know if I can.

Sorry about this.

I thought that there was an alternative to this site, namely
http://rdocumentation.org/
but, as bad is my site is, that one, I think, is worse.

Jon

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

2016-12-17 Thread Spencer Graves 

Hi, Jonathan:


  Thanks for letting us know.  I can't imagine that the 
unavailability of RSiteSearch would be more than an inconvenience.



  When you get time, I'd like to know more about what you know 
about how it was hacked, the host operating system, any anti-virus / 
Internet protection software that failed and anything you think might 
reduce the risk of a repeat in the future.



  Best Wishes,
  Spencer Graves


On 12/17/2016 2:32 PM, Jonathan Baron wrote:

Spencer and others.

I am going to have to take down the server for RSiteSearch, which is
finzi.psych.upenn.edu, for at least a couple of days starting Sunday
morning. It has been hacked. And I have another server that has also
been hacked, which is higher priority (sjdm.org). On Monday, I will
probably have time to rebuild that one, but I may not have time to
rebuild finzi for another week. I will try to get it all done in one
day, but I don't know if I can.

Sorry about this.

I thought that there was an alternative to this site, namely
http://rdocumentation.org/
but, as bad is my site is, that one, I think, is worse.

Jon


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

2016-09-08 Thread John Merrill 
That would work, although it would entail standing up a server to front the
elasticsearch module.  The strikes me a huge investment of time which
would, in addition, recreate the current key man risk.

On Thu, Sep 8, 2016 at 7:51 AM, Kevin Coombes 
wrote:

> Would it make sense to recreate the "searchable R help pages" by feeding
> them all into elasticsearch, which will automatically index them and also
> provides an extensive (HTTP+JSON-based) API to perform complex searches?
>
> On 9/8/2016 10:31 AM, Jonathan Baron wrote:
>
>> On 09/08/16 07:09, John Merrill wrote:
>>
>>> Given Google's commitment to R, I don't think that they'd be at all
>>> averse
>>> to supporting a custom search box on the package page. It might well be a
>>> good thing for "someone" to examine the API for setting up such a page
>>> and
>>> to investigate how to mark the main CRAN page as searchable.
>>>
>>
>> The main CRAN page is not ideal. We need to be able to search the help
>> files. My site has only the html help files for each package (except
>> the ones I use, which are fully installed), so someone should
>> re-create that. The CRAN page has a "Reference manual" in pdf for
>> every package, but the individual functions are not separated.
>>
>> But, yes, Google would work, even for my page. And the sos package
>> would have to be modified for that. As I said, I'm not going to do
>> this. But I would welcome it.
>>
>> Jon
>>
>
>
> ---
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Re: [Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?

2016-09-08 Thread Kevin Coombes 
Would it make sense to recreate the "searchable R help pages" by feeding 
them all into elasticsearch, which will automatically index them and 
also provides an extensive (HTTP+JSON-based) API to perform complex 
searches?


On 9/8/2016 10:31 AM, Jonathan Baron wrote:

On 09/08/16 07:09, John Merrill wrote:
Given Google's commitment to R, I don't think that they'd be at all 
averse
to supporting a custom search box on the package page. It might well 
be a
good thing for "someone" to examine the API for setting up such a 
page and

to investigate how to mark the main CRAN page as searchable.


The main CRAN page is not ideal. We need to be able to search the help
files. My site has only the html help files for each package (except
the ones I use, which are fully installed), so someone should
re-create that. The CRAN page has a "Reference manual" in pdf for
every package, but the individual functions are not separated.

But, yes, Google would work, even for my page. And the sos package
would have to be modified for that. As I said, I'm not going to do
this. But I would welcome it.

Jon



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

2016-09-08 Thread Dirk Eddelbuettel 

Jonathan,

FWIW I mentored a Google Summer of Code student (who was more than highly
self-sufficient and needed next to no help, apart from some small R packaging
tricks) as part of the Xapian project in order to write RXapian:

   https://github.com/amandaJayanetti/RXapian

which is an R interface to the Xapian index engine.

I don't know much about these indice generators, but Xapian [1] appears to be
free, open-source, current, maintained, powerful, and used.  From what I
gather you are still betting on an older (and as I seem to recall,
deprecated) technology. There may be more teers ahead.

The other tip would be to get in touch with Gabor who as part of r-hub has
indices for just about anything, and 9as he his a generation younger than
Spencer, you or me) also provides current (ie JSON over REST) interfaces.

Dirk

[1] https://xapian.org/

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

2016-09-08 Thread Jonathan Baron 

On 09/08/16 07:09, John Merrill wrote:

Given Google's commitment to R, I don't think that they'd be at all averse
to supporting a custom search box on the package page. It might well be a
good thing for "someone" to examine the API for setting up such a page and
to investigate how to mark the main CRAN page as searchable.


The main CRAN page is not ideal. We need to be able to search the help
files. My site has only the html help files for each package (except
the ones I use, which are fully installed), so someone should
re-create that. The CRAN page has a "Reference manual" in pdf for
every package, but the individual functions are not separated.

But, yes, Google would work, even for my page. And the sos package
would have to be modified for that. As I said, I'm not going to do
this. But I would welcome it.

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)

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

2016-09-08 Thread Jonathan Baron 

I looked at rdocumentation.org. At first I thought it was a superior
replacement for namazu, but after I tried a few things I decided that
it wasn't. I could not find any documentation about how to search, and
the various things I tried seemed to yield very strange responses,
e.g., a search for "Hayes mediation bootstrap" gave me mostly
functions that had nothing to do with the search except for the word
"bootstrap".

So I managed to fix the major Perl module errors (one of which was
quite bothersome although not fatal ... yet). And I figured out a new
way to create the indices that namazu uses; the new way is more
selective. And things seem to work now. Aside from the problems I just
fixed, this is not hard to maintain, so I will continue.

It also seems that someone IS sort of maintaining namazu,
sporadically. There is a Fedora rpm for it. That was how I found out
how to fix the Perl module.

But I did end up spending a few hours on this on a day when I am
behind writing action letters, etc. etc. And ultimately I cannot do
this forever and would love it if someone else took it over, or at
least helped, with an account on my server.

Jon

On 09/08/16 06:36, Dirk Eddelbuettel wrote:


On 8 September 2016 at 06:01, Jonathan Baron wrote:
| We have over 10,000 packages now. I wonder if searching all help files
| is really helpful anymore.

Yes it is. I go to http://rdocumentation.org a lot for quick look-ups.

So thanks to Datacamp for running that.  


Dirk

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

2016-09-08 Thread Spencer Graves 



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 
To: Spencer Graves 
CC: Jonathan Baron , 
chris.is@gmail.com, i...@datacamp.com , 
Sundar Dorai-Raj , webmaster@www.r-project-org




R site search has stopped working. The indexing scrip, mknmz, failed
to

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

2016-09-08 Thread Spencer Graves 


On 9/8/2016 3:30 AM, Joris Meys wrote:
>
> Hi Jonathan,
>
> I have neither the resources nor the skills to take over, but whatever 
> happens I want to thank you for all the work. Too often people forget 
> that all these nice tools keep working due to the devotion of people 
> like you.
>
> So thank you!
>


   I concur.  People all over the world live better today, because R 
made it easier for others to solve problems -- and Jon made a 
substantive contribution to that.  Spencer


> Cheers
> Joris
>
>
> On 8 Sep 2016 04:08, "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","--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  >
> To: Spencer Graves  >
> CC: Jonathan Baron  >, chris.is@gmail.com
> , i...@datacamp.com
>   >, Sundar Dorai-Raj
>

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

2016-09-08 Thread Dirk Eddelbuettel 

On 8 September 2016 at 06:01, Jonathan Baron wrote:
| We have over 10,000 packages now. I wonder if searching all help files
| is really helpful anymore.

Yes it is. I go to http://rdocumentation.org a lot for quick look-ups.

So thanks to Datacamp for running that.  

Dirk

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

2016-09-08 Thread Michael Dewey 
I have mixed feelings about this. I used to find the sos package very 
useful when I first started using it but as the number of packages has 
grown I now find it gives me a huge list which takes a lot of time to 
digest. This may of course reflect my rudimentary search term selection 
skills.


Michael

On 08/09/2016 11:01, 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.

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 
To: Spencer Graves 
CC: Jonathan Baron ,
chris.is@gmail.com, i...@datacamp.com ,
Sundar Dorai-Raj , 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

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

2016-09-08 Thread Jonathan Baron 

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.

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 
To: Spencer Graves 
CC: 	Jonathan Baron , chris.is@gmail.com, 
i...@datacamp.com , Sundar Dorai-Raj 
, 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)


--
Jonathan Baron, Professor of Psychology, University of Pennsylvania
Home page: http://www.sas.upenn.edu/~baron
Editor:

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

2016-09-07 Thread Jonathan Baron 

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 
To: Spencer Graves 
CC: 	Jonathan Baron , chris.is@gmail.com, 
i...@datacamp.com , Sundar Dorai-Raj 
, 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)

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

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

2016-09-07 Thread Jonathan Baron 

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-load","--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 
To: Spencer Graves 
CC: 	Jonathan Baron , chris.is@gmail.com, 
i...@datacamp.com , Sundar Dorai-Raj 
, 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)

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel