[Rd] R CMD CHECK --run-donttest ignored
Dear R developers, As far as I can see R CMD CHECK --run-donttest does not test the \donttest examples. By contrast, --run-dontrun appears to run the \dontrun examples as expected. I have prepared a minimal package archive for illustrating this bug, which I can send to anyone interested (but I am not sure it is appropriate to attach it to this mail). I have formally tested this problem on = >sessionInfo() R Under development (unstable) (2014-11-06 r66943) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.0 = F.R. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] organisation of packages & CRAN
Hi, I’ve been using R on and off for a couple of years. I think R is pretty great but one thing I’d like to see improved is the way packages are organised. Instead of CRAN being a long list of packages having a short & usually unintelligible name I ‘d like to see packages organised in a hierarchical way with that path acting as a hierarchical namespace just like you have in many other languages like Java, C#,Scala,… The names of the (sub)packages should also be clear and unambiguous & packages should be organised according to their functionality and not just for example be code for a whole book thrown together and given a cryptic name. Next to that it would be nice to have extra metadata in the packages to allow for another more loose flat multi-class class-action like in tagging blog systems & other metadata to allow for for automatically generating something like task views. Due to the large number of packages it’s hard to see the forest from the trees so a recommendation system for CRAN based on popularity (download statistics) , ratings & other data like related packages from package metadata would be most welcome. Finally the number of packages in CRAN is exponentially growing but there is also a large partial overlap in functionality between packages & so many packages make it hard to find what you are looking for. So maybe there less is more and there should be a system of removing hardly used/low quality packages on a regular basis. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
Hi, I think much of this is simply impossible to do. CRAN packages are written and maintained by thousands of people, how are you planning to convince them to reorganize their packages? Or even just rename them? This obviously won't happen. Btw. did you see 'CRAN Task Views'? That is one organizations of packages into topics. Personally, I don't think organization is the solution here. It is too costly (i.e. too much work) to maintain, impossible to enforce. I think, however, that a good search engine would definitely help. FWIW there is a simple search engine here: http://metacran.github.io/search/ This ranks packages according to the number of reverse dependencies (among other things), i.e. packages more often used by other packages will be higher up in the list. Ranking them according to downloads is also possible, but AFAIK only one CRAN mirror gives out statistics about downloads, so you don't really have the complete numbers there. Disclaimer: I built the search engine above. There are obviously other alternatives as well, e.g. http://rdocumentation.org, and http://mran.revolutionanalytics.com/packages/ are the two I know. Gabor On Sun, Nov 9, 2014 at 11:24 AM, Steven Sagaert wrote: > Hi, > I’ve been using R on and off for a couple of years. I think R is pretty great > but one thing I’d like to see improved is the way packages are organised. > Instead of CRAN being a long list of packages having a short & usually > unintelligible name I ‘d like to see packages organised in a hierarchical way > with that path acting as a hierarchical namespace just like you have in many > other languages like Java, C#,Scala,… The names of the (sub)packages should > also be clear and unambiguous & packages should be organised according to > their functionality and not just for example be code for a whole book thrown > together and given a cryptic name. > > Next to that it would be nice to have extra metadata in the packages to allow > for another more loose flat multi-class class-action like in tagging blog > systems & other metadata to allow for for automatically generating something > like task views. > > Due to the large number of packages it’s hard to see the forest from the > trees so a recommendation system for CRAN based on popularity (download > statistics) , ratings & other data like related packages from package > metadata would be most welcome. > > Finally the number of packages in CRAN is exponentially growing but there is > also a large partial overlap in functionality between packages & so many > packages make it hard to find what you are looking for. So maybe there less > is more and there should be a system of removing hardly used/low quality > packages on a regular basis. > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
Gábor Csárdi gmail.com> writes: > > Hi, > > I think much of this is simply impossible to do. CRAN packages are > written and maintained by thousands of people, how are you planning to > convince them to reorganize their packages? Or even just rename them? > This obviously won't happen. > > Btw. did you see 'CRAN Task Views'? That is one organizations of > packages into topics. > > Personally, I don't think organization is the solution here. It is too > costly (i.e. too much work) to maintain, impossible to enforce. I > think, however, that a good search engine would definitely help. > > FWIW there is a simple search engine here: http://metacran.github.io/search/ > This ranks packages according to the number of reverse dependencies > (among other things), i.e. packages more often used by other packages > will be higher up in the list. > > Ranking them according to downloads is also possible, but AFAIK only > one CRAN mirror gives out statistics about downloads, so you don't > really have the complete numbers there. > > Disclaimer: I built the search engine above. There are obviously other > alternatives as well, e.g. http://rdocumentation.org, and > http://mran.revolutionanalytics.com/packages/ are the two I know. > > Gabor A few more thoughts: * similar topics have been discussed _many_ times over the years on the R mailing lists (sorry, I can't point you to any specific threads). So far the R core/CRAN team have not indicated any interest in making changes in the directions you suggest, so it's up to the community to implement the things it would like to see. There's nothing stopping you from mirroring CRAN packages in any way you'd like (e.g. see Revolution R's 'MRAN': http://mran.revolutionanalytics.com/ , which among other things allows you to sort packages by task view). In addition to the Task Views pointed out by Gabor (you may enjoy this version: http://www.maths.lancs.ac.uk/~rowlings/R/TaskViews/ ), there have been a variety of individual/community attempts to provide more package information: * CRANberries http://dirk.eddelbuettel.com/cranberries/ gives a feed about package changes * CRANtastic http://crantastic.org/ attempted to set up a community site for package rating/voting (never got a lot of traction though). * download information _is_ available, unofficially, from some mirrors other than the RStudio mirror: see http://www.rpubs.com/bbolker/3750 Questions: * how would you propose to enforce package naming? (One of the great things about packaging code R is the relatively *low* barriers to entry ... but that has obvious disadvantages ...) * who's going to enforce and curate the metadata? * who's going to decide on the criteria for CRAN package removal (i.e. how to determine quality, or how to decide on a threshold for removal?) There's some filtering based on packages failing their automated checks and being archived as R advances ... > On Sun, Nov 9, 2014 at 11:24 AM, Steven Sagaert > gmail.com> wrote: > > Hi, > > I’ve been using R on and off for a couple of years. I think R is > pretty great but one thing I’d like to see improved is the way > packages are organised. Instead of CRAN being a long list of > packages having a short & usually unintelligible name I ‘d like to > see packages organised in a hierarchical way with that path acting > as a hierarchical namespace just like you have in many other > languages like Java, C#,Scala,… The names of the (sub)packages > should also be clear and unambiguous & packages should be organised > according to their functionality and not just for example be code > for a whole book thrown together and given a cryptic name. > Next to that it would be nice to have extra metadata in the > packages to allow for another more loose flat multi-class > class-action like in tagging blog systems & other metadata to allow > for for automatically generating something like task views. > > Due to the large number of packages it’s hard to see the forest > from the trees so a recommendation system for CRAN based on > popularity (download statistics) , ratings & other data like related > packages from package metadata would be most welcome. > Finally the number of packages in CRAN is exponentially growing but > there is also a large partial overlap in functionality between > packages & so many packages make it hard to find what you are > looking for. So maybe there less is more and there should be a > system of removing hardly used/low quality packages on a regular > basis. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
Hi Ben. I agree with most of your points and questions, but just wanted to nitpick one little point, inline below: On 09/11/2014, 3:26 PM, Ben Bolker wrote: > Gábor Csárdi gmail.com> writes: > >> >> Hi, >> >> I think much of this is simply impossible to do. CRAN packages are >> written and maintained by thousands of people, how are you planning to >> convince them to reorganize their packages? Or even just rename them? >> This obviously won't happen. >> >> Btw. did you see 'CRAN Task Views'? That is one organizations of >> packages into topics. >> >> Personally, I don't think organization is the solution here. It is too >> costly (i.e. too much work) to maintain, impossible to enforce. I >> think, however, that a good search engine would definitely help. >> >> FWIW there is a simple search engine here: http://metacran.github.io/search/ >> This ranks packages according to the number of reverse dependencies >> (among other things), i.e. packages more often used by other packages >> will be higher up in the list. >> >> Ranking them according to downloads is also possible, but AFAIK only >> one CRAN mirror gives out statistics about downloads, so you don't >> really have the complete numbers there. >> >> Disclaimer: I built the search engine above. There are obviously other >> alternatives as well, e.g. http://rdocumentation.org, and >> http://mran.revolutionanalytics.com/packages/ are the two I know. >> >> Gabor > > A few more thoughts: > > * similar topics have been discussed _many_ times over the years on > the R mailing lists (sorry, I can't point you to any specific > threads). So far the R core/CRAN team have not indicated any interest "team" should be plural here. Though there is overlap in membership, CRAN is a separate entity from the R Core team. Duncan Murdoch > in making changes in the directions you suggest, so it's up to > the community to implement the things it would like to see. There's > nothing stopping you from mirroring CRAN packages in any way you'd > like (e.g. see Revolution R's 'MRAN': http://mran.revolutionanalytics.com/ , > which among other things allows you to sort packages by task view). > > In addition to the Task Views pointed out by Gabor (you may enjoy > this version: http://www.maths.lancs.ac.uk/~rowlings/R/TaskViews/ ), > there have been a variety of individual/community attempts to provide > more package information: > > * CRANberries http://dirk.eddelbuettel.com/cranberries/ gives a feed > about package changes > * CRANtastic http://crantastic.org/ attempted to set up a community > site for package rating/voting (never got a lot of traction though). > * download information _is_ available, unofficially, from some > mirrors other than the RStudio mirror: see > http://www.rpubs.com/bbolker/3750 > > Questions: > > * how would you propose to enforce package naming? (One of the > great things about packaging code R is the relatively *low* > barriers to entry ... but that has obvious disadvantages ...) > * who's going to enforce and curate the metadata? > * who's going to decide on the criteria for CRAN package removal > (i.e. how to determine quality, or how to decide on a threshold > for removal?) There's some filtering based on packages failing > their automated checks and being archived as R advances ... > >> On Sun, Nov 9, 2014 at 11:24 AM, Steven Sagaert >> gmail.com> wrote: >>> Hi, > >>> I’ve been using R on and off for a couple of years. I think R is >> pretty great but one thing I’d like to see improved is the way >> packages are organised. Instead of CRAN being a long list of >> packages having a short & usually unintelligible name I ‘d like to >> see packages organised in a hierarchical way with that path acting >> as a hierarchical namespace just like you have in many other >> languages like Java, C#,Scala,… The names of the (sub)packages >> should also be clear and unambiguous & packages should be organised >> according to their functionality and not just for example be code >> for a whole book thrown together and given a cryptic name. > >> Next to that it would be nice to have extra metadata in the >> packages to allow for another more loose flat multi-class >> class-action like in tagging blog systems & other metadata to allow >> for for automatically generating something like task views. > >>> Due to the large number of packages it’s hard to see the forest >> from the trees so a recommendation system for CRAN based on >> popularity (download statistics) , ratings & other data like related >> packages from package metadata would be most welcome. > > >> Finally the number of packages in CRAN is exponentially growing but >> there is also a large partial overlap in functionality between >> packages & so many packages make it hard to find what you are >> looking for. So maybe there less is more and there should be a >> system of removing hardly used/low quality packages on a regular >> basis. > >
Re: [Rd] organisation of packages & CRAN
On Sun, Nov 9, 2014 at 3:26 PM, Ben Bolker wrote: [...] > * download information _is_ available, unofficially, from some > mirrors other than the RStudio mirror: see > http://www.rpubs.com/bbolker/3750 You mean the report_cran.html file? According to my quick check it is indeed available on some mirrors, but it also seems to be the same file, so it is probably mirrored from cran.r-project.org. Why does it show the (almost) last 56 days, btw.? How often is it updated? Can you have daily values? Older data? In general, do you know any documentation about this? G. [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
On Sun, Nov 9, 2014 at 4:37 PM, Duncan Murdoch wrote: > Hi Ben. I agree with most of your points and questions, but just wanted > to nitpick one little point, inline below: > You're right -- I was being sloppy, that's worth clarifying. I think I originally meant to write "R core/the CRAN team" (i.e. referring to "R core" and "the CRAN team" as separate entities), but my fingers slipped ... Ben > On 09/11/2014, 3:26 PM, Ben Bolker wrote: > > Gábor Csárdi gmail.com> writes: > > > >> > >> Hi, > >> > >> I think much of this is simply impossible to do. CRAN packages are > >> written and maintained by thousands of people, how are you planning to > >> convince them to reorganize their packages? Or even just rename them? > >> This obviously won't happen. > >> > >> Btw. did you see 'CRAN Task Views'? That is one organizations of > >> packages into topics. > >> > >> Personally, I don't think organization is the solution here. It is too > >> costly (i.e. too much work) to maintain, impossible to enforce. I > >> think, however, that a good search engine would definitely help. > >> > >> FWIW there is a simple search engine here: > http://metacran.github.io/search/ > >> This ranks packages according to the number of reverse dependencies > >> (among other things), i.e. packages more often used by other packages > >> will be higher up in the list. > >> > >> Ranking them according to downloads is also possible, but AFAIK only > >> one CRAN mirror gives out statistics about downloads, so you don't > >> really have the complete numbers there. > >> > >> Disclaimer: I built the search engine above. There are obviously other > >> alternatives as well, e.g. http://rdocumentation.org, and > >> http://mran.revolutionanalytics.com/packages/ are the two I know. > >> > >> Gabor > > > > A few more thoughts: > > > > * similar topics have been discussed _many_ times over the years on > > the R mailing lists (sorry, I can't point you to any specific > > threads). So far the R core/CRAN team have not indicated any interest > > "team" should be plural here. Though there is overlap in membership, > CRAN is a separate entity from the R Core team. > > Duncan Murdoch > > > in making changes in the directions you suggest, so it's up to > > the community to implement the things it would like to see. There's > > nothing stopping you from mirroring CRAN packages in any way you'd > > like (e.g. see Revolution R's 'MRAN': > http://mran.revolutionanalytics.com/ , > > which among other things allows you to sort packages by task view). > > > > In addition to the Task Views pointed out by Gabor (you may enjoy > > this version: http://www.maths.lancs.ac.uk/~rowlings/R/TaskViews/ ), > > there have been a variety of individual/community attempts to provide > > more package information: > > > > * CRANberries http://dirk.eddelbuettel.com/cranberries/ gives a feed > > about package changes > > * CRANtastic http://crantastic.org/ attempted to set up a community > > site for package rating/voting (never got a lot of traction though). > > * download information _is_ available, unofficially, from some > > mirrors other than the RStudio mirror: see > > http://www.rpubs.com/bbolker/3750 > > > > Questions: > > > > * how would you propose to enforce package naming? (One of the > > great things about packaging code R is the relatively *low* > > barriers to entry ... but that has obvious disadvantages ...) > > * who's going to enforce and curate the metadata? > > * who's going to decide on the criteria for CRAN package removal > > (i.e. how to determine quality, or how to decide on a threshold > > for removal?) There's some filtering based on packages failing > > their automated checks and being archived as R advances ... > > > >> On Sun, Nov 9, 2014 at 11:24 AM, Steven Sagaert > >> gmail.com> wrote: > >>> Hi, > > > >>> I’ve been using R on and off for a couple of years. I think R is > >> pretty great but one thing I’d like to see improved is the way > >> packages are organised. Instead of CRAN being a long list of > >> packages having a short & usually unintelligible name I ‘d like to > >> see packages organised in a hierarchical way with that path acting > >> as a hierarchical namespace just like you have in many other > >> languages like Java, C#,Scala,… The names of the (sub)packages > >> should also be clear and unambiguous & packages should be organised > >> according to their functionality and not just for example be code > >> for a whole book thrown together and given a cryptic name. > > > >> Next to that it would be nice to have extra metadata in the > >> packages to allow for another more loose flat multi-class > >> class-action like in tagging blog systems & other metadata to allow > >> for for automatically generating something like task views. > > > >>> Due to the large number of packages it’s hard to see the forest > >> from the trees so a recommendation system for CRAN based on > >> popularity (download statistics) , ratings & other da
Re: [Rd] organisation of packages & CRAN
I"ve never looked to see if it differs among mirrors. I believe this is just an internal log file that is produced according to the default Apache (?) webserver configs on a Debian system -- I always assumed it was generated separately for different servers, but it could indeed be just a copy of the download stats for the central repository. I found about it when someone else pointed it out in some long-ago exchange on an R mailing list. As far as I know it's essentially accidental that it exists and is accessible -- if the CRAN maintainers decided to move it or cut off access they could at any time. On Sun, Nov 9, 2014 at 4:40 PM, Gábor Csárdi wrote: > On Sun, Nov 9, 2014 at 3:26 PM, Ben Bolker wrote: > [...] > > * download information _is_ available, unofficially, from some > > mirrors other than the RStudio mirror: see > > http://www.rpubs.com/bbolker/3750 > > You mean the report_cran.html file? According to my quick check it is > indeed available on some mirrors, but it also seems to be the same > file, so it is probably mirrored from cran.r-project.org. Why does it > show the (almost) last 56 days, btw.? How often is it updated? Can you > have daily values? Older data? In general, do you know any > documentation about this? > > G. > > [...] > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
Might it be appropriate to add "http://metacran.github.io/search"; and the "sos" package to the official list of R search capabilities at "www.r-project.org/search.html"? [Disclaimer: I'm the lead author of "sos".] Best Wishes, Spencer Graves On 11/9/2014 11:06 AM, Gábor Csárdi wrote: Hi, I think much of this is simply impossible to do. CRAN packages are written and maintained by thousands of people, how are you planning to convince them to reorganize their packages? Or even just rename them? This obviously won't happen. Btw. did you see 'CRAN Task Views'? That is one organizations of packages into topics. Personally, I don't think organization is the solution here. It is too costly (i.e. too much work) to maintain, impossible to enforce. I think, however, that a good search engine would definitely help. FWIW there is a simple search engine here: http://metacran.github.io/search/ This ranks packages according to the number of reverse dependencies (among other things), i.e. packages more often used by other packages will be higher up in the list. Ranking them according to downloads is also possible, but AFAIK only one CRAN mirror gives out statistics about downloads, so you don't really have the complete numbers there. Disclaimer: I built the search engine above. There are obviously other alternatives as well, e.g. http://rdocumentation.org, and http://mran.revolutionanalytics.com/packages/ are the two I know. Gabor On Sun, Nov 9, 2014 at 11:24 AM, Steven Sagaert wrote: Hi, I’ve been using R on and off for a couple of years. I think R is pretty great but one thing I’d like to see improved is the way packages are organised. Instead of CRAN being a long list of packages having a short & usually unintelligible name I ‘d like to see packages organised in a hierarchical way with that path acting as a hierarchical namespace just like you have in many other languages like Java, C#,Scala,… The names of the (sub)packages should also be clear and unambiguous & packages should be organised according to their functionality and not just for example be code for a whole book thrown together and given a cryptic name. Next to that it would be nice to have extra metadata in the packages to allow for another more loose flat multi-class class-action like in tagging blog systems & other metadata to allow for for automatically generating something like task views. Due to the large number of packages it’s hard to see the forest from the trees so a recommendation system for CRAN based on popularity (download statistics) , ratings & other data like related packages from package metadata would be most welcome. Finally the number of packages in CRAN is exponentially growing but there is also a large partial overlap in functionality between packages & so many packages make it hard to find what you are looking for. So maybe there less is more and there should be a system of removing hardly used/low quality packages on a regular basis. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
On Sun, Nov 9, 2014 at 8:24 AM, Steven Sagaert wrote: > Hi, > I’ve been using R on and off for a couple of years. I think R is pretty > great but one thing I’d like to see improved is the way packages are > organised. Instead of CRAN being a long list of packages having a short & > usually unintelligible name I ‘d like to see packages organised in a > hierarchical way with that path acting as a hierarchical namespace just > like you have in many other languages like Java, C#,Scala,… The names of > the (sub)packages should also be clear and unambiguous & packages should be > organised according to their functionality and not just for example be code > for a whole book thrown together and given a cryptic name. > > Next to that it would be nice to have extra metadata in the packages to > allow for another more loose flat multi-class class-action like in tagging > blog systems & other metadata to allow for for automatically generating > something like task views. > > Just wanted to point out that this extra metadata idea has been pursued by the Bioconductor BiocViews feature. http://www.bioconductor.org/packages/release/BiocViews.html > Due to the large number of packages it’s hard to see the forest from the > trees so a recommendation system for CRAN based on popularity (download > statistics) , ratings & other data like related packages from package > metadata would be most welcome. > > Finally the number of packages in CRAN is exponentially growing but there > is also a large partial overlap in functionality between packages & so many > packages make it hard to find what you are looking for. So maybe there less > is more and there should be a system of removing hardly used/low quality > packages on a regular basis. > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
Spencer Graves prodsyse.com> writes: > >Might it be appropriate to add "http://metacran.github.io/search"; > and the "sos" package to the official list of R search capabilities at > "www.r-project.org/search.html"? [Disclaimer: I'm the lead author of > "sos".] > >Best Wishes, >Spencer Graves > I would go farther and nominate the sos package for inclusion as a recommended package (I don't have any conflict of interest in making the suggestion). When I tell students about it many of them are puzzled that it's not part of the core R framework. I understand the arguments against migrating new functionality into core R, but this functionality is super-useful especially for beginners, and it seems worth it to lower the bar for finding help, at the cost of not a huge amount of extra code to maintain. Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
On 11/9/2014 4:50 PM, Ben Bolker wrote: Spencer Graves prodsyse.com> writes: Might it be appropriate to add "http://metacran.github.io/search"; and the "sos" package to the official list of R search capabilities at "www.r-project.org/search.html"? [Disclaimer: I'm the lead author of "sos".] Best Wishes, Spencer Graves I would go farther and nominate the sos package for inclusion as a recommended package (I don't have any conflict of interest in making the suggestion). When I tell students about it many of them are puzzled that it's not part of the core R framework. I understand the arguments against migrating new functionality into core R, but this functionality is super-useful especially for beginners, and it seems worth it to lower the bar for finding help, at the cost of not a huge amount of extra code to maintain. Thanks. For me, "sos" has provided the fastest literature search I've found for anything statistical (including using "installPackages" and "writeFindFn2xls", which could be overlooked by people using only "findFn"). Gone are the days when I'd puzzle for hours over a single line or page of mathematics. If I don't understand something, I give examples to the code, and see what I get -- possibly using debug to trace what it does line by line. If I don't find what I want with "sos", then I can look elsewhere. I only became aware of "http://metacran.github.io/search/";, "http://www.rdocumentation.org/";, and "http://www.bioconductor.org/packages/release/BiocViews.html"; through responses earlier in this thread, so I can't compare "sos" to these other capabilities. Spencer Graves Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] organisation of packages & CRAN
A little more details about the metacran search, to show how it (imo)
solves a different problem than sos, rseek, RSiteSearch, or
rdocumentation.org.
1. The most important difference is that it searches for _packages_.
The results are packages, not functions, vignettes, etc. E.g. if you
want to find all packages that interact with google apis, you can just
say (https://github.com/metacran/seer is the CLI version):
library(seer)
> see("google")
SAW "google" 25 packages in 0.013 seconds ---
# # Title # Package
1 RgoogleMaps Overlays on Google map tiles in R
2 ggmap A package for spatial visualization with Google Maps and Ope...
3 RGA A Google Analytics API client for R
4 plotKML Visualization of spatial and spatio-temporal objects in Goog...
5 googleVis Interface between R and Google Charts
6 scholar Analyse citation data from Google Scholar
7 translateR Bindings for the Google and Microsoft Translation APIs
8 plusser A Google+ Interface for R
9 gooJSON Google JSON Data Interpreter for R
10 translate Bindings for the Google Translate API v2
> more()
SAW "google" 25 packages in 0.012 seconds ---
# # Title # Package
11 ngramr Retrieve and plot Google n-gram data
12 RGoogleAnalytics R Wrapper for the Google Analytics API
13 R2G2 Converting R CRAN outputs into Google Earth.
14 plotGoogleMaps Plot spatial or spatio-temporal data over Google Maps
15 googlePublicData An R library to build Google's Public Data Explorer DSP...
16 RWeather R wrapper around the Yahoo! Weather, Google Weather and...
17 sysfonts Loading system fonts into R
18 hashFunction A collection of non-cryptographic hash functions
19 rgauges R wrapper to Gaug.es API
20 splitstackshape Stack and Reshape Datasets After Splitting Concatenated...
2. The second difference is that metacran ranks the search results
based on (among other things) the package dependency graph, so if you
search for 'graphics' lattice and ggplot2 come first.
3. Another difference is that metacran exposes a full search API of
the underlying ElasticSearch engine, so if someone wants to rank
results differently, or make more difficult complex queries, they can.
4. It does not search code and docs. I think rdocumentation.org does a
good job with docs, and http://github.com/cran is great for code, e.g.
if you want packages that call SET_SLOT in C:
https://github.com/search?l=c&q=SET_SLOT+user%3Acran&ref=searchresults&type=Code&utf8=%E2%9C%93
Gabor
On Sun, Nov 9, 2014 at 7:18 PM, Spencer Graves
wrote:
> Might it be appropriate to add "http://metacran.github.io/search"; and
> the "sos" package to the official list of R search capabilities at
> "www.r-project.org/search.html"? [Disclaimer: I'm the lead author of
> "sos".]
>
>
> Best Wishes,
> Spencer Graves
>
>
> On 11/9/2014 11:06 AM, Gábor Csárdi wrote:
>>
>> Hi,
>>
>> I think much of this is simply impossible to do. CRAN packages are
>> written and maintained by thousands of people, how are you planning to
>> convince them to reorganize their packages? Or even just rename them?
>> This obviously won't happen.
>>
>> Btw. did you see 'CRAN Task Views'? That is one organizations of
>> packages into topics.
>>
>> Personally, I don't think organization is the solution here. It is too
>> costly (i.e. too much work) to maintain, impossible to enforce. I
>> think, however, that a good search engine would definitely help.
>>
>> FWIW there is a simple search engine here:
>> http://metacran.github.io/search/
>> This ranks packages according to the number of reverse dependencies
>> (among other things), i.e. packages more often used by other packages
>> will be higher up in the list.
>>
>> Ranking them according to downloads is also possible, but AFAIK only
>> one CRAN mirror gives out statistics about downloads, so you don't
>> really have the complete numbers there.
>>
>> Disclaimer: I built the search engine above. There are obviously other
>> alternatives as well, e.g. http://rdocumentation.org, and
>> http://mran.revolutionanalytics.com/packages/ are the two I know.
>>
>> Gabor
>>
>> On Sun, Nov 9, 2014 at 11:24 AM, Steven Sagaert
>> wrote:
>>>
>>> Hi,
>>> I’ve been using R on and off for a couple of years. I think R is pretty
>>> great but one thing I’d like to see improved is the way packages are
>>> organised. Instead of CRAN being a long list of packages having a short &
>>> usually unintelligible name I ‘d like to see packages organised in a
>>> hierarchical way with that path acting as a hierarchical namespace just like
>>> you have in many other languages like Java, C#,Scala,… The names of the
>>> (sub)packages should also be clear and unambiguous & packages should be
>>> organised according to their functionality and not just for example be code
>>> for a whole book thrown together and given a cryptic nam
Re: [Rd] organisation of packages & CRAN
Hi, Gábor:
On 11/9/2014 7:58 PM, Gábor Csárdi wrote:
A little more details about the metacran search, to show how it (imo)
solves a different problem than sos, rseek, RSiteSearch, or
rdocumentation.org.
1. The most important difference is that it searches for _packages_.
The results are packages, not functions, vignettes, etc. E.g. if you
want to find all packages that interact with google apis, you can just
say (https://github.com/metacran/seer is the CLI version):
library(seer)
see("google")
SAW "google" 25 packages in 0.013 seconds ---
# # Title # Package
1 RgoogleMaps Overlays on Google map tiles in R
2 ggmap A package for spatial visualization with Google Maps and Ope...
3 RGA A Google Analytics API client for R
4 plotKML Visualization of spatial and spatio-temporal objects in Goog...
5 googleVis Interface between R and Google Charts
6 scholar Analyse citation data from Google Scholar
7 translateR Bindings for the Google and Microsoft Translation APIs
8 plusser A Google+ Interface for R
9 gooJSON Google JSON Data Interpreter for R
10 translate Bindings for the Google Translate API v2
more()
SAW "google" 25 packages in 0.012 seconds ---
# # Title # Package
11 ngramr Retrieve and plot Google n-gram data
12 RGoogleAnalytics R Wrapper for the Google Analytics API
13 R2G2 Converting R CRAN outputs into Google Earth.
14 plotGoogleMaps Plot spatial or spatio-temporal data over Google Maps
15 googlePublicData An R library to build Google's Public Data Explorer DSP...
16 RWeather R wrapper around the Yahoo! Weather, Google Weather and...
17 sysfonts Loading system fonts into R
18 hashFunction A collection of non-cryptographic hash functions
19 rgauges R wrapper to Gaug.es API
20 splitstackshape Stack and Reshape Datasets After Splitting Concatenated...
2. The second difference is that metacran ranks the search results
based on (among other things) the package dependency graph, so if you
search for 'graphics' lattice and ggplot2 come first.
3. Another difference is that metacran exposes a full search API of
the underlying ElasticSearch engine, so if someone wants to rank
results differently, or make more difficult complex queries, they can.
4. It does not search code and docs. I think rdocumentation.org does a
good job with docs, and http://github.com/cran is great for code, e.g.
if you want packages that call SET_SLOT in C:
https://github.com/search?l=c&q=SET_SLOT+user%3Acran&ref=searchresults&type=Code&utf8=%E2%9C%93
Thanks for the explanation of metacran/seer.
"sos" is also designed to identify packages, but it does it based
on the number and rank of help pages matching the search term. I often
do "a|b" to obtain the union of two different searches then use
"writeFindFn2xls" to output the result to an MS Excel file with 3
sheets: (1) a package summary, (2) the raw search results of help
pages sorted by package, and (3) info on the search terms used.
"findFn" has a "sortBy" that allows a user to change the default sort
order, but I've never used it. Part of the information from the package
summary is taken from installed packages and is missing for packages
that are not installed. "sos" includes "installPackages" to install the
highest ranking packages, but that's a poor solution to the problem.
I'd be happy to work with others who can potentially improve the
selection of information to present and get it all without installing
the packages first. Spencer
Gabor
On Sun, Nov 9, 2014 at 7:18 PM, Spencer Graves
wrote:
Might it be appropriate to add "http://metacran.github.io/search"; and
the "sos" package to the official list of R search capabilities at
"www.r-project.org/search.html"? [Disclaimer: I'm the lead author of
"sos".]
Best Wishes,
Spencer Graves
On 11/9/2014 11:06 AM, Gábor Csárdi wrote:
Hi,
I think much of this is simply impossible to do. CRAN packages are
written and maintained by thousands of people, how are you planning to
convince them to reorganize their packages? Or even just rename them?
This obviously won't happen.
Btw. did you see 'CRAN Task Views'? That is one organizations of
packages into topics.
Personally, I don't think organization is the solution here. It is too
costly (i.e. too much work) to maintain, impossible to enforce. I
think, however, that a good search engine would definitely help.
FWIW there is a simple search engine here:
http://metacran.github.io/search/
This ranks packages according to the number of reverse dependencies
(among other things), i.e. packages more often used by other packages
will be higher up in the list.
Ranking them according to downloads is also possible, but AFAIK only
one CRAN mirror gives out statistics about downloads, so you don't
really have t
