Jonathan Baron
2016-Sep-08 02:06 UTC
[Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
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 <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)
Jonathan Baron
2016-Sep-08 10:01 UTC
[Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
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 <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)-- 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)
Michael Dewey
2016-Sep-08 11:00 UTC
[Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
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 <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) >-- Michael http://www.dewey.myzen.co.uk/home.html
Dirk Eddelbuettel
2016-Sep-08 11:36 UTC
[Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
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 -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Spencer Graves
2016-Sep-08 13:32 UTC
[Rd] Fwd: Re: 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) >
Jonathan Baron
2016-Sep-08 14:31 UTC
[Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
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)
Kevin Coombes
2016-Sep-08 14:51 UTC
[Rd] Fwd: Re: RSiteSearch, sos, rdocumentation.org, ...?
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--- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus
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