[Rd] trivial typo in R-exts.texi
>From latest SVN release (66624).
(I think I may have reported this before?)
430-@c DESCRIPTION field Maintainer
431-The mandatory @samp{Maintainer} field should give a @emph{single} name
432:followed a @emph{valid} (RFC 2822) email address in angle brackets. It
433-should not end in a period or comma. This field is what is reported by
"followed a" should be "followed by a", I think ...
Ben Bolker
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[Rd] issue with compiling r6
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
I am painfully aware that this is most likely a problem with my
system, but I am nevertheless going to ask if anyone has any
ideas/suggestions for diagnosis and trouble-shooting.
- From a clean checkout of release 66624 on Ubuntu 12.04 (32-bit, sorry!):
gcc (Ubuntu/Linaro 4.6.4-1ubuntu1~12.04) 4.6.4
svn checkout https://svn.r-project.org/R/trunk/
tools/rsync-recommended
cd ../r-build
../r-devel/configure
R is now configured for i686-pc-linux-gnu
Source directory: ../r-devel
Installation directory:/usr/local
C compiler:gcc -std=gnu99 -g -O2
Fortran 77 compiler: gfortran -g -O2
C++ compiler: g++ -g -O2
C++ 11 compiler: g++ -std=c++0x -g -O2
Fortran 90/95 compiler:gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11, tcltk
External libraries:readline, lzma
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
Options enabled: shared BLAS, R profiling
Capabilities skipped: ICU
Options not enabled: memory profiling
make fails at:
byte-compiling 'methods'
initializing class and method definitions ...Error: .onLoad failed in
loadNamespace() for 'methods', details:
call: new("classRepresentation")
error: could not find function "isVirtualClass"
The only other oddity of my system/potential clue is that symbolic
links sometimes behave strangely because I am working on a VirtualBox
virtual machine with a virtual Linux filesystem layered over an HGFS
filesystem.
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tLvBXk7771szHDmnD3oosLaYM0c7pEUzMJIgIg3TP+CBMVsMcrPMgVJ7zvMiWwQd
/2Qji9HBLkD6ODa29JYvn1DTXZzigF/gnG7ZBx8xN8d7rQ8v/cKY2ZNk8fg+4II=
=m0Kr
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Re: [Rd] issue with compiling r6
On 17 Sep 2014, at 17:04 , Ben Bolker wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> I am painfully aware that this is most likely a problem with my
> system, but I am nevertheless going to ask if anyone has any
> ideas/suggestions for diagnosis and trouble-shooting.
>
Others have been seeing this since r66622, so I think you're just suffering the
"unsuffered consequences" (unsuffered by regular users, that is; people who run
development versions will suffer occasionally). Just hang on for a while.
> - From a clean checkout of release 66624 on Ubuntu 12.04 (32-bit, sorry!):
That's _revision_ 66624, please. It is only "released" in the sense that it
isn't kept secret.
-pd
> gcc (Ubuntu/Linaro 4.6.4-1ubuntu1~12.04) 4.6.4
>
> svn checkout https://svn.r-project.org/R/trunk/
> tools/rsync-recommended
>
> cd ../r-build
> ../r-devel/configure
>
> R is now configured for i686-pc-linux-gnu
>
> Source directory: ../r-devel
> Installation directory:/usr/local
>
> C compiler:gcc -std=gnu99 -g -O2
> Fortran 77 compiler: gfortran -g -O2
>
> C++ compiler: g++ -g -O2
> C++ 11 compiler: g++ -std=c++0x -g -O2
> Fortran 90/95 compiler:gfortran -g -O2
> Obj-C compiler:
>
> Interfaces supported: X11, tcltk
> External libraries:readline, lzma
> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
> Options enabled: shared BLAS, R profiling
>
> Capabilities skipped: ICU
> Options not enabled: memory profiling
>
> make fails at:
>
> byte-compiling 'methods'
> initializing class and method definitions ...Error: .onLoad failed in
> loadNamespace() for 'methods', details:
> call: new("classRepresentation")
> error: could not find function "isVirtualClass"
>
> The only other oddity of my system/potential clue is that symbolic
> links sometimes behave strangely because I am working on a VirtualBox
> virtual machine with a virtual Linux filesystem layered over an HGFS
> filesystem.
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.11 (GNU/Linux)
>
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> VLVfRQhM7rYDt9f9XFGwNigFAvA/47L9u0PDcYYVMJHLFUWObqMcsi4qfKA5y0LB
> K8ZVG766HZqsLLFZVx7wzP1Ict0IcO1JudtkTSCfXXIq00lj6Dhs+6vU4HWoN6vg
> rXQokhHX1cedNRKCLlXwHblN0DHZsj1EXTUSDzYJA3p1sO7KUqXmzE76+62vANKj
> tLvBXk7771szHDmnD3oosLaYM0c7pEUzMJIgIg3TP+CBMVsMcrPMgVJ7zvMiWwQd
> /2Qji9HBLkD6ODa29JYvn1DTXZzigF/gnG7ZBx8xN8d7rQ8v/cKY2ZNk8fg+4II=
> =m0Kr
> -END PGP SIGNATURE-
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
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Re: [Rd] issue with compiling r6
Thanks for the information. It's the old story -- it's only once you
finally convince yourself that the problems are always on your end and
never bugs in the other guy's (development) code that you actually
encounter bugs in the other guy's code.
Ben Bolker
On 14-09-17 11:32 AM, peter dalgaard wrote:
>
> On 17 Sep 2014, at 17:04 , Ben Bolker wrote:
>
> I am painfully aware that this is most likely a problem with my
> system, but I am nevertheless going to ask if anyone has any
> ideas/suggestions for diagnosis and trouble-shooting.
>
>
>> Others have been seeing this since r66622, so I think you're just
>> suffering the "unsuffered consequences" (unsuffered by regular
>> users, that is; people who run development versions will suffer
>> occasionally). Just hang on for a while.
>
> - From a clean checkout of release 66624 on Ubuntu 12.04 (32-bit,
> sorry!):
>
>> That's _revision_ 66624, please. It is only "released" in the sense
>> that it isn't kept secret.
>
>> -pd
>
> gcc (Ubuntu/Linaro 4.6.4-1ubuntu1~12.04) 4.6.4
>
> svn checkout https://svn.r-project.org/R/trunk/
> tools/rsync-recommended
>
> cd ../r-build ../r-devel/configure
>
> R is now configured for i686-pc-linux-gnu
>
> Source directory: ../r-devel Installation directory:
> /usr/local
>
> C compiler:gcc -std=gnu99 -g -O2 Fortran 77
> compiler: gfortran -g -O2
>
> C++ compiler: g++ -g -O2 C++ 11 compiler: g++
> -std=c++0x -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C
> compiler:
>
> Interfaces supported: X11, tcltk External libraries:
> readline, lzma Additional capabilities: PNG, JPEG, TIFF, NLS,
> cairo Options enabled: shared BLAS, R profiling
>
> Capabilities skipped: ICU Options not enabled: memory
> profiling
>
> make fails at:
>
> byte-compiling 'methods' initializing class and method definitions
> ...Error: .onLoad failed in loadNamespace() for 'methods', details:
> call: new("classRepresentation") error: could not find function
> "isVirtualClass"
>
> The only other oddity of my system/potential clue is that symbolic
> links sometimes behave strangely because I am working on a
> VirtualBox virtual machine with a virtual Linux filesystem layered
> over an HGFS filesystem.
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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[Rd] cleanup temporary directory
Hi ,
When a R session runs , it creates a temporary directory . I am using
R_CleanTempDir() to clean it up . It looks like its not working properly .
So what exactly is going on here is , my example is
main()
start__R__Interpreter
while(1)
{
execute R scripts using R_parseVector and R_tryEval . .
break;
}
R_cleanup_tempDir()
R_session_End()
So is the Rtemp directory created in every R_Tryeval call ? The R temporary
file looks like this
RtmpzgKWqU:
RtmpzieK01:
RtmpzleSGb:
RtmpzqlvWS:
Thanks,
Sandip
[[alternative HTML version deleted]]
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[Rd] Regression and inconsistency of width of apostrophes in R vignettes
My main dev machine died a well-deserved death a few weeks ago after six
and a half years of faithful service, and refused to be re-animated. A
substantial
part of setting up its replacement is re-running a lot of R vignettes (mostly
for timing to establish new performance baselines) - and also
cleaning away some such vignettes generated in the past under different
versions of R.
So I noticed a regression of behavior between R 2.x and 3.x/current. The width
of apostrophes in code output was working correctly in R 2.x and is wrong in R
3.x
generated vignettes. Specifically, it affects summary(data.frame) with some
columns
that contains NA's. Here is an edited example snipplet (you should view this
with
fixed-width font terminal):
=
\begin{Sinput}
> summary(some.data.frame)
\end{Sinput}
\begin{Soutput}
P.BB z.HWE
Min. :0.0 Min. :-3.83163
1st Qu.:0.07071 1st Qu.:-0.56856
Median :0.26263 Median : 0.18426
Mean :0.33754 Mean : 0.06581
3rd Qu.:0.56566 3rd Qu.: 0.73845
Max. :0.98990 Max. : 3.73120
NA's :2
\end{Soutput}
=
In R 2.x generated pdf's, the ":" all lined up. In R 3.x/current generated
pdf's, the "NA's"
is typesetted with a narrower apostrophe and therefore the ":" no longer line
up properly.
This is running both versions in parallel on the same system so there is no
LaTeX related
issue in the rest of the system. I see Prof Ripley is the person to have changed
R Sweave's behavior in the last few years, and all the recent changes are to do
with
quotes (which probably means apostophes also) I suspect the relevant change is
probably
r63858 (and its equivalent r63864 in the R-3.0 branch) although I'd be happy to
be
corrected. In any case, the above new behavior of summary(data.frame)
columns not lining up seems to be undesirable so I'd prefer reverting to the
older
appearance, unless there is a good reason; or at least identify what
local quirks I have which results in this, if I am the only person experiencing
this difference
of behavior between R 2.x and R 3.x.
r65917 | ripley | 2014-06-11 11:46:03 +0100 (Wed, 11 Jun 2014) | 2 lines
prefer zi4.sty, use [noupquote] only with that
r65748 | ripley | 2014-05-26 08:39:14 +0100 (Mon, 26 May 2014) | 2 lines
use [noupquote]
r63858 | ripley | 2013-09-07 07:02:08 +0100 (Sat, 07 Sep 2013) | 3 lines
add inconsolata option to Sweave
Arrange for '' and `` to render in the same way in \code, \samp as \examples.
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[Rd] Can't Find Function After requireNamespace
I have a simple function :
f <- function()
{
if(requireNamespace("ggplot2"))
qplot(Sepal.Length, Petal.Length, data = iris, color = Species)
else
message("No graphics, just text.")
}
ggplot2 is in the Suggests field of the DESCRIPTION file. When I load the
package, and run the function, I get an error :
> f()
Loading required namespace: ggplot2
Error in f() : could not find function "qplot"
I don't want all ggplot2 functions to be added to the search path, so I am not
using require(ggplot2). How can I use it correctly ?
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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Re: [Rd] Can't Find Function After requireNamespace
On Sep 17, 2014, at 10:00 PM, Dario Strbenac wrote:
> I have a simple function :
>
> f <- function()
> {
> if(requireNamespace("ggplot2"))
>qplot(Sepal.Length, Petal.Length, data = iris, color = Species)
> else
>message("No graphics, just text.")
> }
>
> ggplot2 is in the Suggests field of the DESCRIPTION file. When I load the
> package, and run the function, I get an error :
>
>> f()
> Loading required namespace: ggplot2
> Error in f() : could not find function "qplot"
>
> I don't want all ggplot2 functions to be added to the search path, so I am
> not using require(ggplot2). How can I use it correctly ?
>
ggplot2::qplot(Sepal.Length, Petal.Length, data = iris, color = Species)
Cheers,
S
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> --
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
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>
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Re: [Rd] Can't Find Function After requireNamespace
BTW: you probably also want to use requireNamespace(..., quietly=TRUE)
otherwise if sort of defeats the purpose ...
On Sep 17, 2014, at 10:46 PM, Simon Urbanek wrote:
>
> On Sep 17, 2014, at 10:00 PM, Dario Strbenac
> wrote:
>
>> I have a simple function :
>>
>> f <- function()
>> {
>> if(requireNamespace("ggplot2"))
>> qplot(Sepal.Length, Petal.Length, data = iris, color = Species)
>> else
>> message("No graphics, just text.")
>> }
>>
>> ggplot2 is in the Suggests field of the DESCRIPTION file. When I load the
>> package, and run the function, I get an error :
>>
>>> f()
>> Loading required namespace: ggplot2
>> Error in f() : could not find function "qplot"
>>
>> I don't want all ggplot2 functions to be added to the search path, so I am
>> not using require(ggplot2). How can I use it correctly ?
>>
>
> ggplot2::qplot(Sepal.Length, Petal.Length, data = iris, color = Species)
>
> Cheers,
> S
>
>
>> R version 3.1.1 (2014-07-10)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> --
>> Dario Strbenac
>> PhD Student
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
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Re: [Rd] Debug an R windows (Fortran) DLL within R with gdb?
Help, My Rgui.exe, main.f, main.o, and main.dll are all in the same directory. When I try to set a breakpoint, I get this response (gdb) b main.f:3 No source file named main.f I tried the -gdwarf-2 requirement in both the compiling and linking statements. This did not fix the problem. The cygwin site recommended the -g option. I tried this. This did not fix the problem. I did not use R CMD SHLIB ( I ran the statements manually ). Andre Mikulec andre_miku...@hotmail.com > From: r-devel-requ...@r-project.org > Subject: R-devel Digest, Vol 139, Issue 15 > To: r-devel@r-project.org > Date: Tue, 16 Sep 2014 12:00:06 +0200 > > Send R-devel mailing list submissions to > r-devel@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-devel > or, via email, send a message with subject or body 'help' to > r-devel-requ...@r-project.org > > You can reach the person managing the list at > r-devel-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-devel digest..." > > > Today's Topics: > > 1. Debug an R windows (Fortran) DLL within R with gdb? > (Andre Mikulec) > 2. Re: Debug an R windows (Fortran) DLL within R with gdb? > (Duncan Murdoch) > > > -- > > Message: 1 > Date: Mon, 15 Sep 2014 17:25:49 -0400 > From: Andre Mikulec > To: "r-devel@r-project.org" > Subject: [Rd] Debug an R windows (Fortran) DLL within R with gdb? > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Hi,? > I have a Fortran 77 subroutine (dll). > > On windows XP, how ?would I 'debug it(Fortran) within R' using gdb? > > This is how I made it. > -- > > R CMD SHLIB main.f > > gfortran -m32 ? ? -O3 ?-mtune=core2 -c main.f -o main.o > > gcc -m32 -shared -s -static-libgcc -o main.dll tmp.def main.o > -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 > -Ld:/RCompile/CRANpkg/extralibs64/local/lib -lgfortran > -LF:/ProgramFiles/R/R-3.1.1/bin/i386 -lR > > > Here is the contents of the file ?main.f > - > > ? ? ? SUBROUTINE NGCD(NA, NB, NGCDO)? > ? ? ? ? IA = NA > ? ? ? ? IB = NB > ? ? 1 ? IF (IB.NE.0) THEN > ? ? ? ? ? ITEMP = IA > ? ? ? ? ? IA = IB > ? ? ? ? ? IB = MOD(ITEMP, IB) > ? ? ? ? ? GOTO 1 > ? ? ? ? END IF > ? ? ? ? NGCDO = IA ? > ? ? ? ? RETURN > ? ? ? END > > Thank you, > Andre Mikulec > andre_miku...@hotmail.com > > > > > > -- > > Message: 2 > Date: Mon, 15 Sep 2014 18:05:36 -0400 > From: Duncan Murdoch > To: Andre Mikulec , "r-devel@r-project.org" > > Subject: Re: [Rd] Debug an R windows (Fortran) DLL within R with gdb? > Message-ID: <541762b0.1050...@gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On 15/09/2014, 5:25 PM, Andre Mikulec wrote: >> >> Hi, >> I have a Fortran 77 subroutine (dll). >> >> On windows XP, how would I 'debug it(Fortran) within R' using gdb? >> >> This is how I made it. >> -- >> >> R CMD SHLIB main.f >> >> gfortran -m32 -O3 -mtune=core2 -c main.f -o main.o >> >> gcc -m32 -shared -s -static-libgcc -o main.dll tmp.def main.o >> -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 >> -Ld:/RCompile/CRANpkg/extralibs64/local/lib -lgfortran >> -LF:/ProgramFiles/R/R-3.1.1/bin/i386 -lR >> >> >> Here is the contents of the file main.f >> - >> >> SUBROUTINE NGCD(NA, NB, NGCDO) >> IA = NA >> IB = NB >> 1 IF (IB.NE.0) THEN >> ITEMP = IA >> IA = IB >> IB = MOD(ITEMP, IB) >> GOTO 1 >> END IF >> NGCDO = IA >> RETURN >> END > > I don't think you put in any compile options to include symbolic > information. You need to do that. I think the option you want is > -gdwarf-2, but I rarely use Fortran, and never use SHLIB, so I could be > wrong. I'll assume you can figure out how to do that. > > Run R under gdb using > > gdb Rgui > > Load your DLL. > > Break to gdb using the menu entry "Misc | Break to debugger". > > Set a breakpoint, e.g. > > b main.f:3 > > to set it on line 3. Then use c to let R continue, and make a call to > your code. Then the usual gdb commands will work after it breaks. > > Duncan Murdoch > > > > -- > > ___ > R-devel@r-project.org mailing list DIGESTED > https://stat.ethz.ch/mailman/listinfo/r-devel > > > End of R-devel Digest, Vol 139, Issue 15 > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
