[Rd] Rtools questions
Hello:
1. How can I tell when the development version of Rtools has
changed? For the past few years, I've installed the development version
of R tools with each new release of R. I encountered problems with this
a few days ago, so I rolled back to Rtools212.exe. Unfortunately, I
seem to have more problems with that version. My latest install was
under Windows 7 Home Edition. My previous problems were on Vista, but I
also have access to Fedora 13 Linux.
2. "R CMD check" ends with the following:
* checking examples ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, :
unable to run 'pdflatex' on 'Rd2.tex'
Error in running tools::texi2dvi
You may want to clean up by 'rm -rf
C:/Users/sgraves/AppData/Local/Temp/Rtmpr6z3
r6/Rd2pdf55b96c9a'
This is using Rtools213, downloaded April 4 from
"www.murdoch-sutherland.com/Rtools" with R installed as follows:
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Thanks,
Spencer
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Re: [Rd] Rtools questions
On 4/5/2011 5:01 PM, Gabor Grothendieck wrote: On Tue, Apr 5, 2011 at 7:51 PM, Henrik Bengtsson wrote: On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch wrote: On 11-04-05 6:22 PM, Spencer Graves wrote: Hello: 1. How can I tell when the development version of Rtools has changed? I don't make announcements of the changes, you just need to check the web site. There are online tools that can do this for you automatically, but I don't know which one to recommend. Google suggests lots of them. I also asked myself this before and I must admit it took me a while to interpret the contents of the webpage. There are multiple sections, e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes since R 2.11.0', and so on. Then within each section there are some dates mentioned. Given my current R version (say R 2.13.0 beta) and Rtools (Rtools213.exe), it not fully clear to me which section to look at, e.g. 'Changes since R 2.12.2'? It might be more clear if there instead the sections would be 'Changes in Rtools213', 'Changes in Rtools212' and so on, and within each maybe list updates by dates/version. More like a NEWS file. Then it would be easier to see if there is an updated available or not. Even a NEWS file only available as part of the installation will help decide whether the version you have installed differ from the one available online. Something like the following: == Changes in Rtools213 == [...] == Changes in Rtools212 == 2011-03-25: - Rtools 2.12 has been frozen. - We have updated all of the tools to current Cygwin versions as of March 25, 2011. We added the "du" utility from Cygwin. We have dropped Vanilla Perl. The libjpeg version has been updated to 8c, and libpng has been updated to 1.5.1. 2010-10-18: [v2.12.0.1892]<== Is this an Rtools version?!? - Prior to October 18, 2010, builds of Rtools212.exe did not correctly install the "extras" required to build R. Version 2.12.0.1892 or later should fix this. - We have now updated all of the tools to current Cygwin versions, and have updated the compilers, and included the 64 bit compilers into Rtools. See Prof. Ripley's page for the details. - Perl is rarely needed in R since R 2.12.0, so it is by default not installed. 2010-??-??: - The 32 bit version of R-devel (to become R 2.12.0 in fall, 2010) will be built with gcc 4.5.x, so Rtools212 contains a completely new MinGW toolchain based on gcc 4.5.0. == Changes in Rtools211 == [...] Just a suggestion ...and thanks for providing Rtools! /Henrik If a NEWS file were included in the Rtools distribution itself (and not just on the web site) it would be helpful since its not always clear which version you have on your system in the first place. However, adding a NEWS file increases the labor, and I'd be happy letting Duncan and others continue doing what they do without asking them to take the time to tell the rest of us what they did. Something simpler would suffice for my needs, e.g., a revision number in the name of the download file, like Rtools213.5107.exe for SVN revision number 5107. Windows 7 gives me the date my copy was downloaded, not the date of the last patch. On March 31, I downloaded and installed basic-miktex-2.9.3972.exe from "http://miktex.org/2.9/setup";. Today, I downloaded basic-miktex-2.9.4106.exe and basic-miktex-2.9.4106-x64.exe. From comparing names, I inferred (a) the first was a newer version of what I had previously installed, and (b) that was 32 bit and the other is 64 bit. I installed the latter, and the problem with pdflatex disappeared. Spencer __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On 11-04-05 7:51 PM, Henrik Bengtsson wrote: > On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch wrote: >> On 11-04-05 6:22 PM, Spencer Graves wrote: >>> >>> Hello: >>> >>> >>> 1. How can I tell when the development version of Rtools has >>> changed? >> >> I don't make announcements of the changes, you just need to check the web >> site. There are online tools that can do this for you automatically, but I >> don't know which one to recommend. Google suggests lots of them. > > I also asked myself this before and I must admit it took me a while to > interpret the contents of the webpage. There are multiple sections, > e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes > since R 2.11.0', and so on. Then within each section there are some > dates mentioned. Given my current R version (say R 2.13.0 beta) and > Rtools (Rtools213.exe), it not fully clear to me which section to look > at, e.g. 'Changes since R 2.12.2'? Well, that depends on when you downloaded it. I use the R version releases as bookmarks. If you last downloaded Rtools after the release of R 2.12.2, then you only need to look at the last section. The problem with collecting changes into those that apply to each Rtools version is just that the change lists would be longer: Rtools212 will get changes through several R releases. When there are compiler changes, RtoolsXYZ generally comes out during the previous R version, because the compiler may only work with the R-devel version. For instance, Rtools212 was introduced between R 2.11.0 and 2.11.1 and was updated a number of times up to quite recently. (It is now frozen, so if you download it now and are working with the R versions it supports you never need to worry about updates to it.) However, if you want to reformat the page, go ahead, and send me the new version. It's a hand edited HTML page so I'd be happy to incorporate changes that make it more readable, as long as it's still easy to edit by hand. Gabor asked how to know which version was downloaded. If you have the installer file you can tell: right click on it, choose Properties, look at the Version tab. If you didn't keep the installer, I don't know a way to find out, but it might be recorded in the unins000.dat file that the uninstaller uses. Of course, without downloading the new one you can't find out its version: so back to my original suggestion to monitor changes to the web page. I'll see if there's a way to automatically include the revision number in the filename. Duncan Murdoch It might be more clear if there > instead the sections would be 'Changes in Rtools213', 'Changes in > Rtools212' and so on, and within each maybe list updates by > dates/version. More like a NEWS file. Then it would be easier to see > if there is an updated available or not. Even a NEWS file only > available as part of the installation will help decide whether the > version you have installed differ from the one available online. > Something like the following: > > == Changes in Rtools213 == > > [...] > > > == Changes in Rtools212 == > > 2011-03-25: > - Rtools 2.12 has been frozen. > - We have updated all of the tools to current Cygwin versions as of > March 25, 2011. We added the "du" utility from Cygwin. We have dropped > Vanilla Perl. The libjpeg version has been updated to 8c, and libpng > has been updated to 1.5.1. > > 2010-10-18: [v2.12.0.1892]<== Is this an Rtools version?!? > - Prior to October 18, 2010, builds of Rtools212.exe did not correctly > install the "extras" required to build R. Version 2.12.0.1892 or later > should fix this. > - We have now updated all of the tools to current Cygwin versions, and > have updated the compilers, and included the 64 bit compilers into > Rtools. See Prof. Ripley's page for the details. > - Perl is rarely needed in R since R 2.12.0, so it is by default not installed. > > 2010-??-??: > - The 32 bit version of R-devel (to become R 2.12.0 in fall, 2010) > will be built with gcc 4.5.x, so Rtools212 contains a completely new > MinGW toolchain based on gcc 4.5.0. > > == Changes in Rtools211 == > > [...] > > > Just a suggestion ...and thanks for providing Rtools! > > /Henrik > >> >> >> For the past few years, I've installed the development version >>> >>> of R tools with each new release of R. I encountered problems with this >>> a few days ago, so I rolled back to Rtools212.exe. Unfortunately, I >>> seem to have more problems with that version. My latest install was >>> under Windows 7 Home Edition. My previous problems were on Vista, but I >>> also have access to Fedora 13 Linux. >> >> I know that Windows 7 64 bit has problems with Rtools. Brian Ripley has had >> some luck using the tools (the bin directory) and Cygwin DLLs from last >> summer, along with the current compilers. I'm reluctant to back out the new >> versions, because I use Cygwin for other things (including OpenSSH) and >> don't want to get locked out
Re: [Rd] Rtools questions
On Wed, Apr 6, 2011 at 7:54 AM, Duncan Murdoch wrote: > On 11-04-05 7:51 PM, Henrik Bengtsson wrote: >> On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch >> wrote: >>> On 11-04-05 6:22 PM, Spencer Graves wrote: Hello: 1. How can I tell when the development version of Rtools has changed? >>> >>> I don't make announcements of the changes, you just need to check the web >>> site. There are online tools that can do this for you automatically, but >>> I >>> don't know which one to recommend. Google suggests lots of them. >> >> I also asked myself this before and I must admit it took me a while to >> interpret the contents of the webpage. There are multiple sections, >> e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes >> since R 2.11.0', and so on. Then within each section there are some >> dates mentioned. Given my current R version (say R 2.13.0 beta) and >> Rtools (Rtools213.exe), it not fully clear to me which section to look >> at, e.g. 'Changes since R 2.12.2'? > > Well, that depends on when you downloaded it. I use the R version releases > as bookmarks. If you last downloaded Rtools after the release of R 2.12.2, > then you only need to look at the last section. > > The problem with collecting changes into those that apply to each Rtools > version is just that the change lists would be longer: Rtools212 will get > changes through several R releases. When there are compiler changes, > RtoolsXYZ generally comes out during the previous R version, because the > compiler may only work with the R-devel version. For instance, Rtools212 > was introduced between R 2.11.0 and 2.11.1 and was updated a number of times > up to quite recently. (It is now frozen, so if you download it now and are > working with the R versions it supports you never need to worry about > updates to it.) > > However, if you want to reformat the page, go ahead, and send me the new > version. It's a hand edited HTML page so I'd be happy to incorporate > changes that make it more readable, as long as it's still easy to edit by > hand. > > Gabor asked how to know which version was downloaded. If you have the > installer file you can tell: right click on it, choose Properties, look at > the Version tab. If you didn't keep the installer, I don't know a way to > find out, but it might be recorded in the unins000.dat file that the > uninstaller uses. Of course, without downloading the new one you can't find > out its version: so back to my original suggestion to monitor changes to > the web page. I'll see if there's a way to automatically include the > revision number in the filename. The situation is that you have several versions of Rtools installers and have experimented with several of them to see which one seems to work and now can't remember which one you installed. If you keep multiple versions of R as many people do this is particularly problematic. Using strings on unins000.dat did not reveal anything although there was so much text it would be easy to miss. -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] S4 generic functions/methods vs enclosures
Apologies for asking something that is probably very obvious, i just started with S4 classes and i guess i am not finding documentation that lays out the grammar rules and gives enough examples. I understand that main method of writing a member function is to write a generic function and setMethod for this particular class. This, however, presumes that there is "virtuality" for this function, i.e. it could be used with other inherited classes . Truth is, many, if not most of my functions don't have virtuality in mind. I want to write them inside classes to achieve incapsulaton only -- use class member data without passing it as parameters or making global to a bunch of functions and have some specific class member functions that don't pollute a global namespace and can be called only for a particular class. This is what enclosured do in R. Is there some obvious way of setting this environment local to a class and without writing generic functions that i am missing? Would appreciate any pointers -- View this message in context: http://r.789695.n4.nabble.com/S4-generic-functions-methods-vs-enclosures-tp3430950p3430950.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rtools questions
On 06/04/2011 8:16 AM, Gabor Grothendieck wrote: On Wed, Apr 6, 2011 at 7:54 AM, Duncan Murdoch wrote: > On 11-04-05 7:51 PM, Henrik Bengtsson wrote: >> On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch >>wrote: >>> On 11-04-05 6:22 PM, Spencer Graves wrote: Hello: 1. How can I tell when the development version of Rtools has changed? >>> >>> I don't make announcements of the changes, you just need to check the web >>> site. There are online tools that can do this for you automatically, but >>> I >>> don't know which one to recommend. Google suggests lots of them. >> >> I also asked myself this before and I must admit it took me a while to >> interpret the contents of the webpage. There are multiple sections, >> e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes >> since R 2.11.0', and so on. Then within each section there are some >> dates mentioned. Given my current R version (say R 2.13.0 beta) and >> Rtools (Rtools213.exe), it not fully clear to me which section to look >> at, e.g. 'Changes since R 2.12.2'? > > Well, that depends on when you downloaded it. I use the R version releases > as bookmarks. If you last downloaded Rtools after the release of R 2.12.2, > then you only need to look at the last section. > > The problem with collecting changes into those that apply to each Rtools > version is just that the change lists would be longer: Rtools212 will get > changes through several R releases. When there are compiler changes, > RtoolsXYZ generally comes out during the previous R version, because the > compiler may only work with the R-devel version. For instance, Rtools212 > was introduced between R 2.11.0 and 2.11.1 and was updated a number of times > up to quite recently. (It is now frozen, so if you download it now and are > working with the R versions it supports you never need to worry about > updates to it.) > > However, if you want to reformat the page, go ahead, and send me the new > version. It's a hand edited HTML page so I'd be happy to incorporate > changes that make it more readable, as long as it's still easy to edit by > hand. > > Gabor asked how to know which version was downloaded. If you have the > installer file you can tell: right click on it, choose Properties, look at > the Version tab. If you didn't keep the installer, I don't know a way to > find out, but it might be recorded in the unins000.dat file that the > uninstaller uses. Of course, without downloading the new one you can't find > out its version: so back to my original suggestion to monitor changes to > the web page. I'll see if there's a way to automatically include the > revision number in the filename. The situation is that you have several versions of Rtools installers and have experimented with several of them to see which one seems to work and now can't remember which one you installed. If you keep multiple versions of R as many people do this is particularly problematic. Sure, I understand the problem. I've taken a look at the installer, and it looks as though I can put the revision number in the filename and not the installer version number or vice versa (as current), but not both, without typing it twice, or adding an extra layer of scripting to insert it twice, or some other ugly solution. I've left a query on the Inno Setup newsgroup to see if I missed something, but it looks to me as though I'm likely to leave it as is. If you are installing multiple versions of Rtools, you should remember to name them so you don't forget which is which. Duncan Murdoch Using strings on unins000.dat did not reveal anything although there was so much text it would be easy to miss. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 generic functions/methods vs enclosures
Look at ?ReferenceClasses for this OOP paradigm in R, which is quite different from the functional paradigm of S4 methods. On 4/6/11 7:54 AM, A Zege wrote: Apologies for asking something that is probably very obvious, i just started with S4 classes and i guess i am not finding documentation that lays out the grammar rules and gives enough examples. I understand that main method of writing a member function is to write a generic function and setMethod for this particular class. This, however, presumes that there is "virtuality" for this function, i.e. it could be used with other inherited classes . Truth is, many, if not most of my functions don't have virtuality in mind. I want to write them inside classes to achieve incapsulaton only -- use class member data without passing it as parameters or making global to a bunch of functions and have some specific class member functions that don't pollute a global namespace and can be called only for a particular class. This is what enclosured do in R. Is there some obvious way of setting this environment local to a class and without writing generic functions that i am missing? Would appreciate any pointers -- View this message in context: http://r.789695.n4.nabble.com/S4-generic-functions-methods-vs-enclosures-tp3430950p3430950.html Sent from the R devel mailing list archive at Nabble.com. __ 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] Rtools questions
On Wed, Apr 6, 2011 at 4:54 AM, Duncan Murdoch wrote: > On 11-04-05 7:51 PM, Henrik Bengtsson wrote: >> On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch >> wrote: >>> On 11-04-05 6:22 PM, Spencer Graves wrote: Hello: 1. How can I tell when the development version of Rtools has changed? >>> >>> I don't make announcements of the changes, you just need to check the web >>> site. There are online tools that can do this for you automatically, but >>> I >>> don't know which one to recommend. Google suggests lots of them. >> >> I also asked myself this before and I must admit it took me a while to >> interpret the contents of the webpage. There are multiple sections, >> e.g. 'Changes since R 2.12.2', 'Changes since R 2.11.1', 'Changes >> since R 2.11.0', and so on. Then within each section there are some >> dates mentioned. Given my current R version (say R 2.13.0 beta) and >> Rtools (Rtools213.exe), it not fully clear to me which section to look >> at, e.g. 'Changes since R 2.12.2'? > > Well, that depends on when you downloaded it. I use the R version releases > as bookmarks. If you last downloaded Rtools after the release of R 2.12.2, > then you only need to look at the last section. > > The problem with collecting changes into those that apply to each Rtools > version is just that the change lists would be longer: Rtools212 will get > changes through several R releases. When there are compiler changes, > RtoolsXYZ generally comes out during the previous R version, because the > compiler may only work with the R-devel version. For instance, Rtools212 > was introduced between R 2.11.0 and 2.11.1 and was updated a number of times > up to quite recently. (It is now frozen, so if you download it now and are > working with the R versions it supports you never need to worry about > updates to it.) I understand, and I suspected this was the reason too. > > However, if you want to reformat the page, go ahead, and send me the new > version. It's a hand edited HTML page so I'd be happy to incorporate > changes that make it more readable, as long as it's still easy to edit by > hand. > > Gabor asked how to know which version was downloaded. If you have the > installer file you can tell: right click on it, choose Properties, look at > the Version tab. If you didn't keep the installer, I don't know a way to > find out, but it might be recorded in the unins000.dat file that the > uninstaller uses. Of course, without downloading the new one you can't find > out its version: so back to my original suggestion to monitor changes to > the web page. I'll see if there's a way to automatically include the > revision number in the filename. This is useful - I didn't know about this version number of InnoSetup. I've browsed the online InnoSetup help, but I couldn't locate what the version parameter is called. With it, would it be possible to use a [Code] block having InnoSetup write the version number to a VERSION file in the Rtools installation directory? That would make it possible to compare what's online and what's installed. Another alternative for figuring out if Rtools have changed would be to compare the timestamp of the installed Rtools directory (because you typically install immediately after download) and the Rtools213.exe timestamp on the web server. This could be achieved by moving the files to, say, http://www.murdoch-sutherland.com/Rtools/download/ and enable indexing of files in that directory. Either way, know about the version number is certainly good enough for me. After installing Rtools, I can simply put the installer file in the Rtools directory to allow me to compare to it later. (I kind of did this before by comparing file sizes.) Thanks Henrik > > Duncan Murdoch > > > > > > It might be more clear if there >> instead the sections would be 'Changes in Rtools213', 'Changes in >> Rtools212' and so on, and within each maybe list updates by >> dates/version. More like a NEWS file. Then it would be easier to see >> if there is an updated available or not. Even a NEWS file only >> available as part of the installation will help decide whether the >> version you have installed differ from the one available online. >> Something like the following: >> >> == Changes in Rtools213 == >> >> [...] >> >> >> == Changes in Rtools212 == >> >> 2011-03-25: >> - Rtools 2.12 has been frozen. >> - We have updated all of the tools to current Cygwin versions as of >> March 25, 2011. We added the "du" utility from Cygwin. We have dropped >> Vanilla Perl. The libjpeg version has been updated to 8c, and libpng >> has been updated to 1.5.1. >> >> 2010-10-18: [v2.12.0.1892]<== Is this an Rtools version?!? >> - Prior to October 18, 2010, builds of Rtools212.exe did not correctly >> install the "extras" required to build R. Version 2.12.0.1892 or later >> should fix this. >> - We have now updated all of the tools to current Cygwin versions, and >> have updated the compi
Re: [Rd] S4 generic functions/methods vs enclosures
This looks awesome -- it is precisely what i wanted. I have started hacking with passing around environments to simulate behavior of classes i was after, but this is so much neater. Reference classes seem to do precisely what i wanted. Thank you very much. -- View this message in context: http://r.789695.n4.nabble.com/S4-generic-functions-methods-vs-enclosures-tp3430950p3431755.html Sent from the R devel mailing list archive at Nabble.com. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Activating a Regular Binding
Greeting R-devel,
I find myself wanting to attach an active binding to an existing
object in the global environment (R 2.12.2), but there doesn't seem to
be an easy way to do this:
> x = 5
> makeActiveBinding("x", function(d) "hi", .GlobalEnv)
Error in makeActiveBinding("x", function(d) "hi", .GlobalEnv) :
symbol already has a regular binding
Now I can get around this with some fancy assignment, but this seems
ugly and underhanded:
> x = 5
> y = x
> rm(x)
> makeActiveBinding("x", function(d) print("hi"), .GlobalEnv)
> x = y
[1] "hi"
So my question is: is there a legitimate way to do this?
Thanks,
Gabe
P.S. sessionInfo:
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.12.2
--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis
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Re: [Rd] R CMD check for 2.13 rc
Original message >Date: Tue, 5 Apr 2011 17:21:55 -0700 >From: henrik.bengts...@gmail.com (on behalf of Henrik Bengtsson >) >Subject: Re: [Rd] R CMD check for 2.13 rc >To: d.strbe...@garvan.org.au >Cc: r-devel@r-project.org Yes, I think the warning about normalizePath will be fine when packages ours depends on get updated. Has anyone got a comment yet, about why setOldClass() classes must now be documented ? - Dario. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
