[Rd] cannot connect to an FTP server with long HELLO message
Hi, Trying to access files on the ftp server at ftp.ncbi.nih.gov will either give a time out or sometimes even a segfault on Linux. The 2 following methods give the same results: f - url(ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz;, open=r) download.file(ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz;, destfile=tempfile()) I've tried one or the other method with all release versions = 2.8 and with current R devel and they always fail to connect to this FTP server. What's particular about this FTP server is that it sends a long HELLO message before it finally sends the 220 control code. Using the Unix ftp client: - hpa...@latitude:~$ ftp ftp.ncbi.nih.gov Connected to ftp.ncbi.nih.gov. 220- Warning Notice! This is a U.S. Government computer system, which may be accessed and used only for authorized Government business by authorized personnel. Unauthorized access or use of this computer system may subject violators to criminal, civil, and/or administrative action. All information on this computer system may be intercepted, recorded, read, copied, and disclosed by and to authorized personnel for official purposes, including criminal investigations. Such information includes sensitive data encrypted to comply with confidentiality and privacy requirements. Access or use of this computer system by any person, whether authorized or unauthorized, constitutes consent to these terms. There is no right of privacy in this system. --- Welcome to the NCBI ftp server! The official anonymous access URL is ftp://ftp.ncbi.nih.gov Public data may be downloaded by logging in as anonymous using your E-mail address as a password. Please see ftp://ftp.ncbi.nih.gov/README.ftp for hints on large file transfers 220 FTP Server ready. - This seems to cause problems to the nanoftp module (src/modules/internet/nanoftp.c) used by url() and download.file() as it doesn't seem to be able to catch the 220 control code. I'm not familiar with the nanoftp module, or with socket programming in general, or with RFC 959 (FTP protocal), so I'm not really in a position to say what's going wrong exactly in the module but it seems that increasing the value of FTP_BUF_SIZE (size of the buffer for data received from the control connection) fixes the problem. Currently this is: #define FTP_BUF_SIZE1024 but, interestingly, *any* value 1024 seems to fix the problem (even though the long HELLO message above is 1091 bytes). Any idea what's going on? Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Linking to lapack
Hello all. I'm developing a package for R holding a Gibbs sampler, which tends to have better performance when written in C than in R. During each iteration in the Gibbs sampler, I need the inverse of a symmetric matrix. For this, I wish to use lapack, as is concisely suggested in Writing R extensions, since this will have better performance than I could ever write myself. After some twiddling I have got my code to compile by including R_ext/Lapack.h and using F77_CALL(dpotrf), but unfortunately, I don't get this to link properly. I get this message: testc.o:testc.c:(.text+0x255): undefined reference to `dpotrf_' which seems logical to me as far as my understanding of C reaches, but I don't know how to resolve it. I'm quite sure I need some extra parameters in my makefile, but as I come from a world where all these complexities are happily abstracted away for me by an IDE, I have no actual clue on how to surmount this. However: when I'm done with all my code, I wish to build a package for publication on CRAN, so I want to be sure that not only I can build it on my system, but it will also work well when distributed to other computers (if I understand the package process well, source files are compiled and linked during installation of the package), so I would also like to know how to do this. It should not be relevant, but either way: I'm doing all this on a Windows 7 machine, though the package will probably be used on Linux-based servers eventually. Finally: I have found no comprehensive list of the functions available to an R package developer, nor, strangely, questions about that. Does such a thing exist, or are we up to hoping we find what we are looking for in the header files? If it does not exist already, I would surely be willing to work on it. Thanks for any input. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Linking to lapack
On Fri, Oct 22, 2010 at 4:30 AM, Nick Sabbe nick.sa...@ugent.be wrote: Hello all. I'm developing a package for R holding a Gibbs sampler, which tends to have better performance when written in C than in R. During each iteration in the Gibbs sampler, I need the inverse of a symmetric matrix. You may want to check that. The first rule of numerical linear algebra is that you hardly ever need to invert a matrix. If you need to solve a linear system, you use a factorization, as below and then use one of the solvers based on that factorization. If the matrix is small calculating the inverse is not a big problem. If it is large and you do so within each iteration of your sampler then you are probably wasting time. For this, I wish to use lapack, as is concisely suggested in Writing R extensions, since this will have better performance than I could ever write myself. After some twiddling I have got my code to compile by including R_ext/Lapack.h and using F77_CALL(dpotrf), but unfortunately, I don't get this to link properly. I get this message: testc.o:testc.c:(.text+0x255): undefined reference to `dpotrf_' which seems logical to me as far as my understanding of C reaches, but I don't know how to resolve it. I'm quite sure I need some extra parameters in my makefile, but as I come from a world where all these complexities are happily abstracted away for me by an IDE, I have no actual clue on how to surmount this. Go back to section 1.2.1 of Writing R Extensions that deals with Using Makevars. However: when I'm done with all my code, I wish to build a package for publication on CRAN, so I want to be sure that not only I can build it on my system, but it will also work well when distributed to other computers (if I understand the package process well, source files are compiled and linked during installation of the package), so I would also like to know how to do this. It should not be relevant, but either way: I'm doing all this on a Windows 7 machine, though the package will probably be used on Linux-based servers eventually. Finally: I have found no comprehensive list of the functions available to an R package developer, nor, strangely, questions about that. Does such a thing exist, or are we up to hoping we find what we are looking for in the header files? If it does not exist already, I would surely be willing to work on it. Do you mean other than the section on The R API in the Writing R Extensions manual? Thanks for any input. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove __ 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] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
On Thu, Oct 21, 2010 at 9:42 AM, Rainer Hurling rhur...@gwdg.de wrote: [moved from R-help] On 21.10.2010 18:09 (UTC+1), Prof Brian Ripley wrote: If you do R CMD INSTALL --no-test-load this will skip the part that is hanging and you can try loading in stages (e.g. dyn.load on the RGtk2.so). With '--no-test-load' it installs and ends normal. Loading per dyn.load(RGtk2.so) works, just as dyn.load(RGtk2.so,F) and dyn.load(RGtk2.so,,F). Unloading works, too. Normal loading over library(RGtk2) within R does not work. R than is hanging. It seems the problem is not with the library itself? It looks like something is happening when initializing GTK+ and the event loop. This happens in the function R_gtkInit in Rgtk.c. If you could run R -d gdb and break on that function, perhaps you could step through until it hangs. Thanks, Michael I think this is rather technical for R-help, so maybe move to R-devel? I moved to R-devel. And can you check the RGtk2 version? A recent but not current version (2.12.17?) did hang initializing Gtk+ on some platforms and Michael Lawrence had to be involved. I am using RGtk2_2.12.18.tar.gz for month now. On Thu, 21 Oct 2010, Rainer Hurling wrote: Am 21.10.2010 16:12 (UTC+1) schrieb Prof Brian Ripley: On Thu, 21 Oct 2010, Rainer Hurling wrote: I am working with R-2.12.0 on FreeBSD 9.0-CURRENT for a while now. I successfully installed more than 300 packages (most as dependencies of others). There are two packages I am not able to install: RGtk2 and rggobi. For example rggobi builds fine and after that it wants to load: -- # R CMD INSTALL rggobi_2.1.16.tar.gz [..SNIP..] gcc -std=gnu99 -shared -L/usr/local/lib -o rggobi.so RSEval.o brush.o colorSchemes.o conversion.o data.o dataset.o display.o displays.o edges.o ggobi.o identify.o init.o io.o keyHandlers.o longitudinal.o modes.o plot.o plots.o plugins.o print.o session.o smooth.o ui.o utils.o -pthread -L/usr/local/lib -lggobi -lgtk-x11-2.0 -lxml2 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXext -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXfixes -lcairo -lX11 -lpango-1.0 -lm -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 installiert nach /usr/local/lib/R/library/rggobi/libs ** R ** data ** moving datasets to lazyload DB ** demo ** preparing package for lazy loading -- At this point the install process is hanging, R utilises no more CPU time. Same with package RGtk2. Is this a known error? Please let me know if I can give more information or try something different. Well, those are exactly the two packages using Gtk+. There is no known general problem, and as you could have checked from the CRAN check pages, those packages install without problems on several platforms. (Not Solaris, where ggobi does not install and RGtk2 requires gcc, and not x64 Windows where both need to be patched.) So it does look very like there is a problem with loading against the Gtk+ system libraries on your system. I think you are right. With previous versions of R (until R-2.10.x) I did not have this hanging when loading RGtk2 ... And I am pretty sure that I have no problems with gtk2 outside of R on my FreeBSD system. In the meantime I found out that the reported loading error of rggobi is a loading error of RGtk2, which fails (hangs). So there remains only a loading error with RGtk2. (Because of that I changed the subject.) After building/installing RGtk2, there are the following messages: -- [..SNIP..] gcc -std=gnu99 -shared -L/usr/local/lib -o RGtk2.so RGtkDataFrame.o Rgtk.o atkAccessors.o atkClasses.o atkConversion.o atkFuncs.o atkManuals.o atkUserFuncs.o cairo-enums.o cairoAccessors.o cairoConversion.o cairoFuncs.o cairoManuals.o cairoUserFuncs.o classes.o conversion.o eventLoop.o gdkAccessors.o gdkClasses.o gdkConversion.o gdkFuncs.o gdkManuals.o gdkUserFuncs.o glib.o gobject.o gtkAccessors.o gtkClasses.o gtkConversion.o gtkFuncs.o gtkManuals.o gtkUserFuncs.o libgladeAccessors.o libgladeFuncs.o libgladeManuals.o libgladeUserFuncs.o pangoAccessors.o pangoClasses.o pangoConversion.o pangoFuncs.o pangoManuals.o pangoUserFuncs.o utils.o zcompat.o -pthread -L/usr/local/lib -lglade-2.0 -lgtk-x11-2.0 -lxml2 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXext -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXfixes -lcairo -lX11 -lpango-1.0 -lm -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 -pthread -L/usr/local/lib -lgthread-2.0 -lglib-2.0 installiert nach /usr/local/lib/R/library/RGtk2/libs ** R ** demo ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package
Re: [Rd] Linking to lapack
On Fri, 2010-10-22 at 05:30 -0400, Nick Sabbe wrote: Hello all. I'm developing a package for R holding a Gibbs sampler, which tends to have better performance when written in C than in R. During each iteration in the Gibbs sampler, I need the inverse of a symmetric matrix. For this, I wish to use lapack, as is concisely suggested in Writing R extensions, since this will have better performance than I could ever write myself. After some twiddling I have got my code to compile by including R_ext/Lapack.h and using F77_CALL(dpotrf), but unfortunately, I don't get this to link properly. I get this message: testc.o:testc.c:(.text+0x255): undefined reference to `dpotrf_' which seems logical to me as far as my understanding of C reaches, but I don't know how to resolve it. I'm quite sure I need some extra parameters in my makefile, but as I come from a world where all these complexities are happily abstracted away for me by an IDE, I have no actual clue on how to surmount this. Yes. You need to ensure that your program is linked with a Lapack library where the symbol dpotrf_ is defined. In an R package, using a 'Makevars' file in your 'src' directory is used to specify additional linking. See Writing R Extensions section 1.2.1 Using ‘Makevars’. If you are compiling your code with a custom Makefile, then you will need to add an argument to the linker/compiler specifying a Lapack library to be linked. For example, here is a command that dynamically links the R Lapack and Blas libraries to a pre-compiled 'test.o' on my system: gcc -std=gnu99 -shared -L/usr/local/lib -o test.so test.o -L/usr/local/lib/R/lib -lRlapack -L/usr/local/lib/R/lib -lRblas -lgfortran -lm However: when I'm done with all my code, I wish to build a package for publication on CRAN, so I want to be sure that not only I can build it on my system, but it will also work well when distributed to other computers (if I understand the package process well, source files are compiled and linked during installation of the package), so I would also like to know how to do this. It might be a good idea to build your package simultaneously with your code, and use a Makevars file. It should not be relevant, but either way: I'm doing all this on a Windows 7 machine, though the package will probably be used on Linux-based servers eventually. Finally: I have found no comprehensive list of the functions available to an R package developer, nor, strangely, questions about that. Does such a thing exist, or are we up to hoping we find what we are looking for in the header files? If it does not exist already, I would surely be willing to work on it. Three of the R manuals (R-exts, R-ints, R-admin; http://cran.r-project.org/doc/manuals/) partially describe some aspect of the R API, where Writing R Extensions is the most comprehensive. Function descriptions are generally not biolerplate. For good or bad, a look into the C headers is often necessary to use an R API function. -Matt Thanks for any input. Nick Sabbe -- ping: nick.sa...@ugent.be link: http://biomath.ugent.be wink: A1.056, Coupure Links 653, 9000 Gent ring: 09/264.59.36 -- Do Not Disapprove __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
On 22.10.2010 14:57 (UTC+1), Michael Lawrence wrote: On Thu, Oct 21, 2010 at 9:42 AM, Rainer Hurling rhur...@gwdg.de mailto:rhur...@gwdg.de wrote: [moved from R-help] On 21.10.2010 18:09 (UTC+1), Prof Brian Ripley wrote: If you do R CMD INSTALL --no-test-load this will skip the part that is hanging and you can try loading in stages (e.g. dyn.load on the RGtk2.so). With '--no-test-load' it installs and ends normal. Loading per dyn.load(RGtk2.so) works, just as dyn.load(RGtk2.so,F) and dyn.load(RGtk2.so,,F). Unloading works, too. Normal loading over library(RGtk2) within R does not work. R than is hanging. It seems the problem is not with the library itself? It looks like something is happening when initializing GTK+ and the event loop. This happens in the function R_gtkInit in Rgtk.c. If you could run R -d gdb and break on that function, perhaps you could step through until it hangs. Michael, thank you for answering. As I wrote earlier (on R-help@), unfortunately I have no experience with debugging (I am not a programmer). So I would need some more assistence. Is there a difference between 'library(RGtk2)' and 'dyn.load(RGtk2)' in initializing GTK+? I am able to dyn.load, but library does not work. After starting with 'R -d gdb' is the following right? (gdb) break R_gtkInit Function R_gtkInit not defined. Make breakpoint pending on future shared library load? (y or [n]) y Breakpoint 1 (R_gtkInit) pending. When I try to proceed, it gives me the following message (gdb) run Starting program: /usr/local/lib/R/bin/exec/R /libexec/ld-elf.so.1: Shared object libRblas.so not found, required by R Program exited with code 01. Obviously there is some wrong with my try? Thanks again, Rainer Thanks, Michael I think this is rather technical for R-help, so maybe move to R-devel? I moved to R-devel. And can you check the RGtk2 version? A recent but not current version (2.12.17?) did hang initializing Gtk+ on some platforms and Michael Lawrence had to be involved. I am using RGtk2_2.12.18.tar.gz for month now. On Thu, 21 Oct 2010, Rainer Hurling wrote: Am 21.10.2010 16:12 (UTC+1) schrieb Prof Brian Ripley: On Thu, 21 Oct 2010, Rainer Hurling wrote: I am working with R-2.12.0 on FreeBSD 9.0-CURRENT for a while now. I successfully installed more than 300 packages (most as dependencies of others). There are two packages I am not able to install: RGtk2 and rggobi. For example rggobi builds fine and after that it wants to load: -- # R CMD INSTALL rggobi_2.1.16.tar.gz [..SNIP..] gcc -std=gnu99 -shared -L/usr/local/lib -o rggobi.so RSEval.o brush.o colorSchemes.o conversion.o data.o dataset.o display.o displays.o edges.o ggobi.o identify.o init.o io.o keyHandlers.o longitudinal.o modes.o plot.o plots.o plugins.o print.o session.o smooth.o ui.o utils.o -pthread -L/usr/local/lib -lggobi -lgtk-x11-2.0 -lxml2 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXext -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXfixes -lcairo -lX11 -lpango-1.0 -lm -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 installiert nach /usr/local/lib/R/library/rggobi/libs ** R ** data ** moving datasets to lazyload DB ** demo ** preparing package for lazy loading -- At this point the install process is hanging, R utilises no more CPU time. Same with package RGtk2. Is this a known error? Please let me know if I can give more information or try something different. Well, those are exactly the two packages using Gtk+. There is no known general problem, and as you could have checked from the CRAN check pages, those packages install without problems on several platforms. (Not Solaris, where ggobi does
[Rd] Reference classes
Dear all,
First, many thanks to John Chambers, and anyone else who was involved,
for the new support for reference classes in R 2.12.0. It's nice to
see this kind of functionality appear in a relatively R-like form, and
with the blessing of the core team. In some contexts it is undoubtedly
appealing to associate a set of methods with a class directly, rather
than defining a load of generics which are only ever likely to be
implemented for a single class, or some other such arrangement. (I was
actually in the process of writing a package which did something
similar to the reference class idea, although it is less fully
realised.)
My initial experiences with this functionality have been very
positive. I've stumbled over one minor issue so far: default values of
method parameters are not displayed by the help() method, viz.
library(methods)
Regex - setRefClass(Regex, fields=string, methods=list(
+ isMatch = function (text, ignoreCase = FALSE)
+ {
+ 'Returns a logical vector of the same length as text,
indicating whether or not each element is a match to the regular
expression.'
+ grepl(string, text, ignore.case=ignoreCase, perl=TRUE)
+ }
+ ))
Regex$help(isMatch)
Call: $isMatch(text, ignoreCase = )
Returns a logical vector of the same length as text, indicating
whether or not each element is a match to the regular expression.
It seems unlikely that this is intentional, but correct me if I'm
wrong. It still seems to happen with the latest R-patched (Mac OS X
10.5.8).
As a suggestion, it would be nice if the accessors() method could be
used to create just getters or just setters for particular fields,
although I realise this can be worked around by removing the unwanted
methods afterwards.
More generally, I was wondering how firm the commitment is to
providing this kind of programming mechanism. I know it's likely to
change in some ways in future releases, but can I use it in packages,
trusting that only a few tweaks will be needed for compatibility with
future versions of R, or is it possible that the whole infrastructure
will be removed in future?
All the best,
Jon
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[Rd] CRAN: Windows builds/pages outdated?
FYI, in case you are not aware of it, both http://cran.r-project.org/bin/windows/base/rpatched.html http://cran.r-project.org/bin/windows/base/rdevel.html link to old builds (2010-10-14 r53300). /Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] new.env does not recognize parents from subclassesof environment
Yet another inconsistency. environment- does not work with S4:
setClass(myenv, contains = environment)
[1] myenv
env - new(myenv)
tf - function(x){x}
environment(tf) - env
Error in environment(tf) - env :
replacement object is not an environment
Vitally.
John Chambers j...@stanford.edu writes:
This is a problem related to the introduction of exact= into the [[ and [[-
functions. As Bill says, the current
method misuses eval.parent() when that argument is added.
However, a simpler and more efficient solution is to migrate the checks for
subclasses of environment used in
other base code into the code for [[- (and for $-), at which point the
methods for these functions are no longer
needed.
A solution on these lines is being tested now and will find its way into
r-devel and 2.12 patched.
One other point about the original posting:
Please don't use constructions like e...@.xdata. This depends on the current
implementation and is not part of the
user-level definition. Use as(env, environment) or equivalent. (In this
case, the assignment of the object's own
environment was irrelevant to the error.)
John Chambers
On 10/21/10 9:21 AM, William Dunlap wrote:
The traceback looks very similar to a problem
in R 2.11.1 reported earlier this month by Troy Robertson.
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Troy Robertson
Sent: Wednesday, October 06, 2010 6:13 PM
To: 'r-devel@R-project.org'
Subject: Re: [Rd] Recursion error after upgrade to
R_2.11.1[Sec=Unclassified]
It was due to a miscount of how many frames to go
up before evaluating an expression in
getMethod([[-,.environment) because setMethod()
introduced a local function in the new method.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Vitally S.
Sent: Thursday, October 21, 2010 9:00 AM
To: John Chambers
Cc: r-devel@r-project.org
Subject: Re: [Rd] new.env does not recognize parents from
subclassesof environment
Here is an infinite recursion error which occurs only with S4
subclasses assignment.
setClass(myenv, contains = environment)
#[1] myenv
env- new(myenv)
env[[.me]]- ∑
#Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?
With basic types it works as expected:
env1- new.env()
env1[[.me]]- env1
May be this is related to active bindings that you mentioned,
but I am still
reporting it here.
Vitally.
Thanks for the report. Should now be fixed in r-devel and
2.12 patched (rev 53383).
Please do report any cases where a subclass of environment
doesn't work. There are some known cases in locking and
active binding, that will be fixed in due course.
The workaround for any such problem is usually as.environment().
On 10/20/10 3:17 AM, Vitaly S. wrote:
Dear Developers,
A lot has been changed in the R12.0 with respect to
behavior of environment
subclasses. Many thanks for that.
One small irregularity, though; new.env does not allow the
parent to be from S4
subclass.
setClass(myenv, contains=environment)
[1] myenv
new.env(parent=new(myenv))
Error in new.env(parent = new(myenv)) : 'enclos' must be
an environment
I wonder if this is a planed behavior.
The use of .xData slot obviously works:
new.env(parent=new(myenv)@.xData)
environment: 063bb9e8
Thanks,
Vitaly.
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Re: [Rd] Reference classes
Last question first:
More generally, I was wondering how firm the commitment is to
providing this kind of programming mechanism. I know it's likely to
change in some ways in future releases, but can I use it in packages,
trusting that only a few tweaks will be needed for compatibility with
future versions of R, or is it possible that the whole infrastructure
will be removed in future?
Speaking just for myself, I'd say it's pretty solid. Reasons:
- it's essentially an add-on and essentially all R code, so as long as
there is some interest, it's not hurting other code--it builds directly
on some valuable existing tools for environments, such as active bindings;
- this is something I've wanted to do for a while. The essential step
was being able to subclass environments, and that has been in place for
some time now;
- initial experience has been largely positive. The Rcpp package in
its newest version depends on reference classes.
Now as to what tweaks will be needed, that remains to be seen. But my
guess is that most will be issues of implementation. The user interface
is sufficiently standardized among languages that it has a reasonable
chance to stay compatible.
Other comments below.
John
On 10/22/10 7:21 AM, Jon Clayden wrote:
Dear all,
First, many thanks to John Chambers, and anyone else who was involved,
for the new support for reference classes in R 2.12.0. It's nice to
see this kind of functionality appear in a relatively R-like form, and
with the blessing of the core team. In some contexts it is undoubtedly
appealing to associate a set of methods with a class directly, rather
than defining a load of generics which are only ever likely to be
implemented for a single class, or some other such arrangement. (I was
actually in the process of writing a package which did something
similar to the reference class idea, although it is less fully
realised.)
My initial experiences with this functionality have been very
positive. I've stumbled over one minor issue so far: default values of
method parameters are not displayed by the help() method, viz.
library(methods)
Regex- setRefClass(Regex, fields=string, methods=list(
+ isMatch = function (text, ignoreCase = FALSE)
+ {
+ 'Returns a logical vector of the same length as text,
indicating whether or not each element is a match to the regular
expression.'
+ grepl(string, text, ignore.case=ignoreCase, perl=TRUE)
+ }
+ ))
Regex$help(isMatch)
Call: $isMatch(text, ignoreCase = )
Returns a logical vector of the same length as text, indicating
whether or not each element is a match to the regular expression.
It seems unlikely that this is intentional, but correct me if I'm
wrong. It still seems to happen with the latest R-patched (Mac OS X
10.5.8).
It's a bug.
As a suggestion, it would be nice if the accessors() method could be
used to create just getters or just setters for particular fields,
although I realise this can be worked around by removing the unwanted
methods afterwards.
In other words, read-only fields. There is a facility for that
implemented already, but it didn't yet make it into the documentation,
and it could use some more testing. The generator object has a $lock()
method that inserts a write-once type of method for one or more fields.
Example:
fg - setRefClass(foo, list(bar = numeric, flag = character),
+ methods = list(
+ addToBar = function(incr) {
+ b = bar + incr
+ bar - b
+ b
+ }
+ ))
fg$lock(bar)
ff = new(foo, bar = 1.5)
ff$bar - 2
Error in function (value) : Field bar is read-only
A revision will document this soon.
(And no, the workaround is not to remove methods. To customize access
to a field, the technique is to write an accessor function for the field
that, in this case, throws an error if it gets an argument. See the
documentation for the fields argument. The convention here and the
underlying mechanism are taken from active bindings for environments.)
More generally, I was wondering how firm the commitment is to
providing this kind of programming mechanism. I know it's likely to
change in some ways in future releases, but can I use it in packages,
trusting that only a few tweaks will be needed for compatibility with
future versions of R, or is it possible that the whole infrastructure
will be removed in future?
All the best,
Jon
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Re: [Rd] Reference classes
One correction:
On 10/22/10 10:55 AM, John Chambers wrote:
.
As a suggestion, it would be nice if the accessors() method could be
used to create just getters or just setters for particular fields,
although I realise this can be worked around by removing the unwanted
methods afterwards.
In other words, read-only fields. There is a facility for that
implemented already, but it didn't yet make it into the documentation,
and it could use some more testing. The generator object has a $lock()
method that inserts a write-once type of method for one or more fields.
Example:
fg - setRefClass(foo, list(bar = numeric, flag = character),
+ methods = list(
+ addToBar = function(incr) {
+ b = bar + incr
+ bar - b
+ b
+ }
+ ))
fg$lock(bar)
ff = new(foo, bar = 1.5)
ff$bar - 2
Error in function (value) : Field bar is read-only
Actually it is documented in the section on generator objects. But
since I also didn't see it, maybe it needs an example. ;-)
John
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Re: [Rd] new.env does not recognize parents from subclassesof environment
John Chambers j...@stanford.edu writes:
You need to update your version of R (r-devel or 2.12 patched) to rev
53385 or later, and read NEWS, particularly the line:
- Assignment of an environment to functions or as an attribute to other
objects now works for subclasses of environment.
I am following the news in daily snapshots from here
ftp://ftp.stat.math.ethz.ch/Software/R
and the above line is still not in the NEWS of today's version.
Thanks for the patch. Looking forward to the stable release.
Vitally.
On 10/22/10 10:20 AM, Vitally S. wrote:
Yet another inconsistency. environment- does not work with S4:
setClass(myenv, contains = environment)
[1] myenv
env - new(myenv)
tf - function(x){x}
environment(tf) - env
Error in environment(tf) - env :
replacement object is not an environment
Vitally.
John Chambers j...@stanford.edu writes:
This is a problem related to the introduction of exact= into the [[ and
[[- functions. As Bill says, the
current
method misuses eval.parent() when that argument is added.
However, a simpler and more efficient solution is to migrate the checks for
subclasses of environment used in
other base code into the code for [[- (and for $-), at which point the
methods for these functions are no
longer
needed.
A solution on these lines is being tested now and will find its way into
r-devel and 2.12 patched.
One other point about the original posting:
Please don't use constructions like e...@.xdata. This depends on the
current implementation and is not part of
the
user-level definition. Use as(env, environment) or equivalent. (In this
case, the assignment of the object's
own
environment was irrelevant to the error.)
John Chambers
On 10/21/10 9:21 AM, William Dunlap wrote:
The traceback looks very similar to a problem
in R 2.11.1 reported earlier this month by Troy Robertson.
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Troy Robertson
Sent: Wednesday, October 06, 2010 6:13 PM
To: 'r-devel@R-project.org'
Subject: Re: [Rd] Recursion error after upgrade to
R_2.11.1[Sec=Unclassified]
It was due to a miscount of how many frames to go
up before evaluating an expression in
getMethod([[-,.environment) because setMethod()
introduced a local function in the new method.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Vitally S.
Sent: Thursday, October 21, 2010 9:00 AM
To: John Chambers
Cc: r-devel@r-project.org
Subject: Re: [Rd] new.env does not recognize parents from
subclassesof environment
Here is an infinite recursion error which occurs only with S4
subclasses assignment.
setClass(myenv, contains = environment)
#[1] myenv
env- new(myenv)
env[[.me]]- ∑
#Error: evaluation nested too deeply: infinite recursion /
options(expressions=)?
With basic types it works as expected:
env1- new.env()
env1[[.me]]- env1
May be this is related to active bindings that you mentioned,
but I am still
reporting it here.
Vitally.
Thanks for the report. Should now be fixed in r-devel and
2.12 patched (rev 53383).
Please do report any cases where a subclass of environment
doesn't work. There are some known cases in locking and
active binding, that will be fixed in due course.
The workaround for any such problem is usually as.environment().
On 10/20/10 3:17 AM, Vitaly S. wrote:
Dear Developers,
A lot has been changed in the R12.0 with respect to
behavior of environment
subclasses. Many thanks for that.
One small irregularity, though; new.env does not allow the
parent to be from S4
subclass.
setClass(myenv, contains=environment)
[1] myenv
new.env(parent=new(myenv))
Error in new.env(parent = new(myenv)) : 'enclos' must be
an environment
I wonder if this is a planed behavior.
The use of .xData slot obviously works:
new.env(parent=new(myenv)@.xData)
environment: 063bb9e8
Thanks,
Vitaly.
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Re: [Rd] [R] R-2.12.0 hangs while loading RGtk2 on FreeBSD
On 22.10.2010 16:18 (UTC+2), Rainer Hurling wrote: On 22.10.2010 14:57 (UTC+1), Michael Lawrence wrote: On Thu, Oct 21, 2010 at 9:42 AM, Rainer Hurling rhur...@gwdg.de mailto:rhur...@gwdg.de wrote: [moved from R-help] On 21.10.2010 18:09 (UTC+1), Prof Brian Ripley wrote: If you do R CMD INSTALL --no-test-load this will skip the part that is hanging and you can try loading in stages (e.g. dyn.load on the RGtk2.so). With '--no-test-load' it installs and ends normal. Loading per dyn.load(RGtk2.so) works, just as dyn.load(RGtk2.so,F) and dyn.load(RGtk2.so,,F). Unloading works, too. Normal loading over library(RGtk2) within R does not work. R than is hanging. It seems the problem is not with the library itself? It looks like something is happening when initializing GTK+ and the event loop. This happens in the function R_gtkInit in Rgtk.c. If you could run R -d gdb and break on that function, perhaps you could step through until it hangs. Michael, thank you for answering. As I wrote earlier (on R-help@), unfortunately I have no experience with debugging (I am not a programmer). So I would need some more assistence. Is there a difference between 'library(RGtk2)' and 'dyn.load(RGtk2)' in initializing GTK+? I am able to dyn.load, but library does not work. After starting with 'R -d gdb' is the following right? (gdb) break R_gtkInit Function R_gtkInit not defined. Make breakpoint pending on future shared library load? (y or [n]) y Breakpoint 1 (R_gtkInit) pending. When I try to proceed, it gives me the following message (gdb) run Starting program: /usr/local/lib/R/bin/exec/R /libexec/ld-elf.so.1: Shared object libRblas.so not found, required by R Program exited with code 01. Ok, I am one step further now: (gdb) run Starting program: /usr/local/lib/R/bin/exec/R [..SNIP..] library(RGtk2) [New LWP 100174] Breakpoint 2 at 0x318bd490: file Rgtk.c, line 104. Pending breakpoint R_gtkInit resolved [New Thread 2f408b00 (LWP 100174)] [Switching to Thread 2f408b00 (LWP 100174)] Breakpoint 2, R_gtkInit (rargc=0x30b11d10, rargv=0x30a98458, success=0x30afbad0) at Rgtk.c:104 104 Rgtk.c: No such file or directory. in Rgtk.c (gdb) What do you suggest I should do next? Thanks again, Rainer Thanks, Michael I think this is rather technical for R-help, so maybe move to R-devel? I moved to R-devel. And can you check the RGtk2 version? A recent but not current version (2.12.17?) did hang initializing Gtk+ on some platforms and Michael Lawrence had to be involved. I am using RGtk2_2.12.18.tar.gz for month now. On Thu, 21 Oct 2010, Rainer Hurling wrote: Am 21.10.2010 16:12 (UTC+1) schrieb Prof Brian Ripley: On Thu, 21 Oct 2010, Rainer Hurling wrote: I am working with R-2.12.0 on FreeBSD 9.0-CURRENT for a while now. I successfully installed more than 300 packages (most as dependencies of others). There are two packages I am not able to install: RGtk2 and rggobi. For example rggobi builds fine and after that it wants to load: -- # R CMD INSTALL rggobi_2.1.16.tar.gz [..SNIP..] gcc -std=gnu99 -shared -L/usr/local/lib -o rggobi.so RSEval.o brush.o colorSchemes.o conversion.o data.o dataset.o display.o displays.o edges.o ggobi.o identify.o init.o io.o keyHandlers.o longitudinal.o modes.o plot.o plots.o plugins.o print.o session.o smooth.o ui.o utils.o -pthread -L/usr/local/lib -lggobi -lgtk-x11-2.0 -lxml2 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lXext -lXrender -lXinerama -lXi -lXrandr -lXcursor -lXcomposite -lXdamage -lpangoft2-1.0 -lgio-2.0 -lXfixes -lcairo -lX11 -lpango-1.0 -lm -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lgthread-2.0 -lglib-2.0 installiert nach /usr/local/lib/R/library/rggobi/libs ** R ** data ** moving datasets to lazyload DB ** demo ** preparing package for lazy loading -- At this point the install process is hanging, R utilises no more CPU time. Same with package RGtk2. Is this a known error? Please let me know if I can give more information or try something different. Well, those are exactly the two packages using Gtk+. There is no known general problem, and as you could have checked from the CRAN check pages, those packages install without problems on several platforms. (Not Solaris, where ggobi does not install and RGtk2 requires gcc, and not x64 Windows where both need to be patched.) So it does look very like there is a problem with loading against the Gtk+ system libraries on your system. I think you are right. With previous versions of R (until R-2.10.x) I did not have this hanging when loading RGtk2 ... And I am pretty sure that I have no problems with gtk2 outside of R on my FreeBSD system. In the meantime I found out that the reported loading error of rggobi is a loading error of RGtk2, which fails (hangs). So there remains only a loading error with RGtk2. (Because of that I changed the subject.) After
Re: [Rd] Reference classes
On 22 October 2010 18:55, John Chambers j...@r-project.org wrote:
As a suggestion, it would be nice if the accessors() method could be
used to create just getters or just setters for particular fields,
although I realise this can be worked around by removing the unwanted
methods afterwards.
In other words, read-only fields. There is a facility for that implemented
already, but it didn't yet make it into the documentation, and it could use
some more testing. The generator object has a $lock() method that inserts a
write-once type of method for one or more fields. Example:
fg - setRefClass(foo, list(bar = numeric, flag = character),
+ methods = list(
+ addToBar = function(incr) {
+ b = bar + incr
+ bar - b
+ b
+ }
+ ))
fg$lock(bar)
ff = new(foo, bar = 1.5)
ff$bar - 2
Error in function (value) : Field bar is read-only
A revision will document this soon.
(And no, the workaround is not to remove methods. To customize access to a
field, the technique is to write an accessor function for the field that, in
this case, throws an error if it gets an argument. See the documentation
for the fields argument. The convention here and the underlying mechanism
are taken from active bindings for environments.)
OK, yes - I see. This is clearly much less superficial than removing
the setter method for a field which can be directly set anyway. I'll
have to try out field accessor functions and get a feel for the
semantics.
Many thanks for the rapid and very helpful response.
Regards,
Jon
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[Rd] possible error checking bug and documentation bug in ts
The documentation for ts says Only one of ‘frequency’ or ‘deltat’ should be provided but why doesn't it enforce this with stopifnot(missing(frequency) || missing(deltat)) Wouldn't that work? Also the documentation does not say what valid time series parameters are. To find that out one must know to RTFS in src/main/attrib.c and find that end - start = (n - 1) / frequency or end - start = (n - 1) * deltat is required to avoid an error, where n is either length(data) or nrow(data). Why can the help page for ts say that? I suppose this is picky, but a newbie just wasted a couple of days with the mysterious error thrown in badtsp in src/main/attrib.c when he ran afoul of R's argument matching rules and unintentionally supplied both frequency and deltat (thinking he was supplying deltat and ts.eps). It took me more time that it should have to figure it out too. -- Charles Geyer Professor, School of Statistics University of Minnesota char...@stat.umn.edu __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
