Re: [R] Solaris10-amd64-studio10 compilers
Prof Brian Ripley wrote: On Fri, 19 Aug 2005, Vin Everett wrote: I am trying to compile R-2.1.1 on Solaris10, with the Studio10 compilers. When I try to compile 64bit with CFLAGS=-xarch=amd64 export CFLAGS I get a configure failure on checking for rl_callback_read_char in -lreadline... no checking for history_truncate_file... no configure: error: --with-readline=yes (default) and headers/libs are not available unset CFLAGS and its fine will compile 32bit. Any ideas gratefully received. I should say I installed the readline headers etc /usr/local So, your readline is probably not 64-bit: see the R-admin manual and check in config.log. a configure with --without-readline but with CFLAGS=-xarch=amd64 goes on to checking for dummy main to link with Fortran libraries... none checking for Fortran name-mangling scheme... unknown configure: WARNING: unknown Fortran name-mangling scheme checking whether f77 appends underscores to external names... unknown configure: error: cannot use Fortran Again this is the studio10 fortran. Please note you need to set FFLAGS to match. If you consult the R-admin manual you will see that sparc users need somewhat different settings: please emulate those. Thanks Brian, I will give that a try. Cheers Vin -- [EMAIL PROTECTED] JDRF/WT Diabetes and Inflammation Laboratory (DIL) Cambridge Institute for Medical Research (CIMR) Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 2XY Tel +44 1223 763212 Fax +44 1223 762102 Mob +44 7990 966266 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] FFT, frequs, magnitudes, phases
PD == Peter Dalgaard [EMAIL PROTECTED] on 19 Aug 2005 14:16:42 +0200 writes: PD Wolfgang Waser [EMAIL PROTECTED] writes: Hi, I'm in dire need of a fast fourier transformation for me stupid biologist, i.e. I have a heartbeat signal and would like to decompose it into pure sin waves, getting three vectors, one containing the frequencies of the sin waves, one the magnitudes and one the phases (that's what I get from my data acquisition software's FFT function). I'd be very much obliged, if someone could point out which command would do the job in R. PD fft(), but notice that it gives the complex PD transform. You need to do a little homework to get at PD the magnitude/phase values. (Basically, you just have to PD take Mod() and Arg(), but there some conventions about PD the frequencies and multipliers that one can get wrong). Once you've finished the homework, others might be interested in your result... so it will be found in the future using RSiteSearch(). Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing R in Fedora Core 4
On Fri, 19 Aug 2005, Gavin Simpson wrote: On Fri, 2005-08-19 at 11:07 -0400, White, Charles E WRAIR-Wash DC wrote: -Original Message- On Fri, 8/19, Gavin Simpson wrote: Peter Dalgaard has noted, on the R-Devel list (sorry I can't provide the link to the mail - the link from the R site to the mail archives wasn't working when I tried), that there are problems with the R rpm from Fedora Extras, including a strange printing bug. I believe Peter now thinks this is a bug in R (seem to have deleted that post - doh) exposed by the compilation flags used by the maintainer of the Fedora Extras rpm. If you want and rpm to install, then Martyn Plummer provides R binaries for Red Hat / Fedora systems that are available from CRAN e.g: for FC4 http://www.stats.bris.ac.uk/R/bin/linux/redhat/fc4/ Martyn has also made these available via a yum-compatible repository, so the benefits you note of auto-notification of updates etc. apply here as well. HTH G -End Original Message- The last time I tried to use the Martyn Plummer RPMs they were compiled without enabling shared libraries and I ended up compiling R myself so that I could use JGR. Messages describing the problem with the version actually on the Extras CD were my other unstated reason for describing yum instead of downloading the CD. I haven't heard there is a problem with Fedora's new RPMs but that doesn't prove that there aren't any. I fully agree with Martyn Plummer's readme notice that describes Fedora Core as bleeding edge technology not to be trusted for production use. Fedora Core describes itself that way. Do you mean the shared library libR.so? If so, the README in the FC3 section indicates that these rpms now include the functionality you require. The absence of a README in the FC4 section means it is not clear from there if these rpms are also compiled with the shared library. They almost certainly are, for 2.1.1, since they are compiled from the same spec file. From Peter's email, it would seem that the maintainer of the R rpm for Extras continues to use the compiler flags that cause the problems previously described (I haven't confirmed that this is still the case mind you). It is confirmed not the case for R-devel, but is for 2.1.1 which is what the RPMs are for. Although FC4 is bleeding edge, I've had very few problems with in on my new laptop or my home desktop - after initial gcc v4.0.0 and gfortran teething troubles that is. Although gcc 4.0.1 has helped, there are dozens of ongoing problems which seems squarely laid at the door of gfortran, as well as an appreciable performance loss. On AMD64 there are subtle incompatibility issues between gfortran and everything else (g77, gcc3 and gcc4) that make mixing C and Fortran code tricky at best. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] diagonal matrices
Hello all, I have matrices V.i of dimension n.i x n.i, where i = 1, ..., J, and the sum of n.i equals N. (and n.i ! = n.j) goal: create one large matrix V, where V has matrices V.i on diagonal. I create each matrix V.i in a for loop (1 to J), so each time I'd like to augment V with the most recently calculated V.i, such that I'll have V after the final iteration of the for loop. question: how to initialize V and do the augmentation. any advice much appreciated. cheers, dave ps - please respond directly to [EMAIL PROTECTED], thanks! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Determining physical display dimensions
On Fri, 2005-08-19 at 13:17 -0500, Earl F. Glynn wrote: Berton Gunter [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Failing that, (how) can this be done for Windows (XP or 2000, say) ? Take a look at the Windows GetDeviceCaps API call http://msdn.microsoft.com/library/default.asp?url=/library/en-us/gdi/devcons_88s3.asp Parameters that can be queried include: HORZRES Width, in pixels, of the screen. VERTRES Height, in raster lines, of the screen. HORZSIZE Width, in millimeters, of the physical screen VERTSIZE Height, in millimeters, of the physical screen The specifics of how to use this API call will vary by language. Google will be your friend. FWIW, in case anyone should see this thread and wonder how to do this somewhat easily in R for systems running X, there is a CLI utility called 'xdpyinfo' that returns a great deal of data on the connected display(s). display.size - system(xdpyinfo | grep dimensions, intern = TRUE) display.dpi - system(xdpyinfo | grep resolution, intern = TRUE) display.size [1] dimensions:1600x1200 pixels (301x231 millimeters) display.dpi [1] resolution:135x132 dots per inch One can then parse the above using R functions as required. Such as: d.size - unlist(strsplit(display.size, split = [[:space:]|(|)|x])) d.size [1] dimensions: [5] 16001200 [9] pi els 301 [13] 231 millimeters h.pix - as.numeric(d.size[7]) v.pix - as.numeric(d.size[8]) h.mm - as.numeric(d.size[12]) v.mm - as.numeric(d.size[13]) line1 - sprintf(The current display is %d x %d pixels, h.pix, v.pix) line2 - sprintf(with a physical size of %d x %d mm, h.mm, v.mm) cat(line1, line2, sep = \n) The current display is 1600 x 1200 pixels with a physical size of 301 x 231 mm This can get more complicated with multi-monitor systems, depending upon whether you are running in xinerama (multi-monitor spanning mode) or non-xinerama mode and consideration for symmetric or asymmetric resolutions. 'man xdpyinfo' and 'man X' (noting the 'DISPLAY' environment variable) will be helpful here to determine which display/screen R is running on. For example, on my system which has two displays, each with 1600x1200, I get: Sys.getenv(DISPLAY) DISPLAY :0.0 with R running on the main laptop LCD (15 diag), versus: Sys.getenv(DISPLAY) DISPLAY :0.1 with R running on the external LCD (20.1 diag), with the DISPLAY variable indicating: :DisplayNumber.ScreenNumber Thus, on my system, the output of the system() calls are actually: display.size - system(xdpyinfo | grep dimensions, intern = TRUE) display.dpi - system(xdpyinfo | grep resolution, intern = TRUE) display.size [1] dimensions:1600x1200 pixels (301x231 millimeters) [2] dimensions:1600x1200 pixels (411x311 millimeters) display.dpi [1] resolution:135x132 dots per inch [2] resolution:99x98 dots per inch HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] diagonal matrices
On Sat, 20 Aug 2005, Afshartous, David wrote:
I have matrices V.i of dimension n.i x n.i, where i = 1, ..., J, and the
sum of n.i equals N. (and n.i ! = n.j)
goal: create one large matrix V, where V has matrices V.i on diagonal.
I create each matrix V.i in a for loop (1 to J), so each time I'd like
to augment V with the most recently calculated V.i, such that I'll have
V after the final iteration of the for loop.
question: how to initialize V and do the augmentation. any advice much
appreciated.
It is probably best to pre-create a matrix and fill in the blocks. As in
V - matrix(0, N, N)
# let n be a vector of what you called n.i
n0 - c(0, cumsum(n))
for(i in 1:J) {
ind - (n0[i]+1):n0[i+1]
V[ind, ind] - V.i
}
cheers,
dave
ps - please respond directly to [EMAIL PROTECTED], thanks!
Please set that as your reply address to ease the lot of your helpers.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] repeated - R package - Compilation Error
rab45 == rab45 rab45 on Thu, 11 Aug 2005 09:25:14 -0400 (EDT) writes: . rab45 I'm not sure what your point is. I'm getting a compilation error for a rab45 package that should compile without errors. The error message doesn't say rab45 anything about needing anything - it doesn't complain about rab45 dependencies. Now once I got repeated to compile, it did give a rab45 *warning message about needing rmutils. But rmutils won't compile and rab45 gives several error messages (in my other post). I've installed many R rab45 packages and I've never seen problems like this before. well, probably the others where CRAN or bioconductor packages ? You know, there *is* a reason why we (actually, the repository maintainers) require that a package runs R CMD check without a warning. If package authors are not willing to clean up and document their code well enough to be accepted by CRAN, you have to expect hardship when trying to install / use the package Martin Maechler __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
