Re: [Rd] X11 Problems
The message unable to open connection to X11 display '' means your own machine cannot open a xterm from the machine running R. You have to have an X server running on your own machine, and allow X display from the machine running R. Hope this helps. Dr Zong-Pei Han UNIX Systems Administrator Computational Biology Research Group University of Oxford http://www.cbrg.ox.ac.uk/ - On Thu, 1 Oct 2009, Kay Wanous wrote: Date: Thu, 01 Oct 2009 16:33:54 -0400 From: Kay Wanous kwan...@cs.earlham.edu To: r-devel@r-project.org Subject: [Rd] X11 Problems Hi all, I'm having trouble getting x11 to work with R. (This is on Debian testing.) I installed r-base and r-base-dev, and then r-cran-cairodevice. I also tried installing the Cairo package within R, which appears to work fine. This what I'm seeing: capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUEFALSEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUE TRUE TRUE x11() Error in X11(d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, : unable to start device X11cairo In addition: Warning message: In x11() : unable to open connection to X11 display '' Any help would be appreciated! Thanks, Kay __ 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] Dependency 'sma' is not available
Martin Morgan wrote: zong-pei@imm.ox.ac.uk wrote: So packages like beadarray and arrayQualityMetrics cannot be installed. The sma author no longer wishes to maintain this package. The packges beadarray and arrayQualityMetrics are Bioconductor packages that depend on sma indirectly through other packages. The other packages are being revised to no longer depend on sma, but this has not yet been completed. The workaround is to manually install sma from its archive: download http://cran.fhcrc.org/src/contrib/Archive/sma/sma_0.5.15.tar.gz and install.packages(sma_0.5.15.tar.gz, repos=NULL). beadarray and arrayQualityMetrics are Bioconductor packages, so please follow up on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html This message is mainly for Zong-pei: I don't know the circumstances or license for sma, but one of the advantages of open source is that someone else could take over maintenance of sma if it is open source and the original author is no longer interested. You should think about doing it, or recruiting someone with the necessary skills if you don't have them. Duncan Murdoch Martin __ 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
[Rd] environment( seq.int ) is NULL
... and also all objects that actually live in the .GenericArgsEnv environment. all( sapply( ls( .GenericArgsEnv ), function(.) is.null(environment(.)) ) ) [1] TRUE This has the consequence preventing argsAnywhere to get the args of seq.int. argsAnywhere( seq.int ) Error in exists(.packageName, envir = envir, inherits = FALSE) : use of NULL environment is defunct and consequently completion does not work seq.int( TABError in exists(.packageName, envir = envir, inherits = FALSE) : use of NULL environment is defunct I've tried a few things, but I don't understand the order in which things are loaded in the zzz.R of base ... Romain -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/ztCu : RGG #158:161: examples of package IDPmisc |- http://tr.im/yw8E : New R package : sos `- http://tr.im/y8y0 : search the graph gallery from R __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] environment( seq.int ) is NULL
On 10/2/2009 8:40 AM, Romain Francois wrote: ... and also all objects that actually live in the .GenericArgsEnv environment. all( sapply( ls( .GenericArgsEnv ), function(.) is.null(environment(.)) ) ) [1] TRUE This has the consequence preventing argsAnywhere to get the args of seq.int. argsAnywhere( seq.int ) Error in exists(.packageName, envir = envir, inherits = FALSE) : use of NULL environment is defunct and consequently completion does not work seq.int( TABError in exists(.packageName, envir = envir, inherits = FALSE) : use of NULL environment is defunct I've tried a few things, but I don't understand the order in which things are loaded in the zzz.R of base ... seq.int isn't a closure, so it doesn't have an environment, any more than a numeric vector does. So the problem here is with getAnywhere (which is called by argsAnywhere). I'll see if I can fix it. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] X11 Problems
Well, I feel silly - I just hadn't started the x11 server on the machine! Thanks for the help. -- Kay zong-pei@imm.ox.ac.uk wrote: The message unable to open connection to X11 display '' means your own machine cannot open a xterm from the machine running R. You have to have an X server running on your own machine, and allow X display from the machine running R. Hope this helps. Dr Zong-Pei Han UNIX Systems Administrator Computational Biology Research Group University of Oxford http://www.cbrg.ox.ac.uk/ - On Thu, 1 Oct 2009, Kay Wanous wrote: Date: Thu, 01 Oct 2009 16:33:54 -0400 From: Kay Wanous kwan...@cs.earlham.edu To: r-devel@r-project.org Subject: [Rd] X11 Problems Hi all, I'm having trouble getting x11 to work with R. (This is on Debian testing.) I installed r-base and r-base-dev, and then r-cran-cairodevice. I also tried installing the Cairo package within R, which appears to work fine. This what I'm seeing: capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUEFALSEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUE TRUE TRUE x11() Error in X11(d$display, d$width, d$height, d$pointsize, d$gamma, d$colortype, : unable to start device X11cairo In addition: Warning message: In x11() : unable to open connection to X11 display '' Any help would be appreciated! Thanks, Kay __ 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 -- - Kay Wanous Dennis 221 CS Department765 983-1784 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] X11 Problems
On 2 October 2009 at 11:01, Kay Wanous wrote: | Well, I feel silly - I just hadn't started the x11 server on the machine! That would do it. For completeness, you _can_ get cairo(), x11(), ... to work in batch mode (or from a webserver etc pp) if you use the xvfb server which (on Debian at least) has the handy front-end script xvfb-run in conjunction with graphics devices like pdf(), png(), ... Dirk -- Three out of two people have difficulties with fractions. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] suggest enhancement to segments and arrows to facilitate horizontal and vertical segments
I suggest a simple enhancement to segments() and arrows() to facilitate drawing horizontal and vertical segments -- set default values for the second x and y arguments equal to the first set. This is handy, especially when the expressions for coordinates are long. Compare: Segments: function (x0, y0, x1 = x0, y1 = y0, col = par(fg), lty = par(lty), --- function (x0, y0, x1, y1, col = par(fg), lty = par(lty), Arrows: function (x0, y0, x1 = x0, y1 = y0, length = 0.25, angle = 30, code = 2, --- function (x0, y0, x1, y1, length = 0.25, angle = 30, code = 2, Tim Hesterberg __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unable to load shared library (Symbol not found: _PQbackendPID)
Neil, I tried installing the RPostgreSQL from both within R (using install.packages(), and using R CMD INSTALL)... but did not try installing from source using the method you describe. I did install PostgreSQL from source and will give that a try... (a few days later)... I've recompiled *everything*: ftp http://www.pdfhacks.com/pdftk/pdftk-1.41.tar.gz ftp http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-3.6.3.tar.Z ftp ftp://ftp.gnu.org/gnu/glpk/glpk-4.39.tar.gz ftp http://download.osgeo.org/proj/proj-4.6.1.tar.gz ftp http://download.osgeo.org/proj/proj-datumgrid-1.4.zip ftp http://download.osgeo.org/geos/geos-3.0.3.tar.bz2 ftp http://download.osgeo.org/gdal/gdal-1.6.2.tar.gz ftp http://cran.r-project.org/src/base/R-2/R-2.9.1.tar.gz ftp http://wwwmaster.postgresql.org/redir/198/h/source/v8.3.8/postgresql-8.3.8.tar.bz2 ftp http://www.joeconway.com/plr/plr-8.3.0.8.tar.gz ftp http://postgis.refractions.net/download/postgis-1.4.0.tar.gz ftp http://grass.itc.it/grass64/source/snapshot/grass-6.4.svn_src_snapshot_2009_09_19.tar.gz ftp http://liblas.org/attachment/wiki/1.2.0/liblas-1.2.0-src.tar.bz2 ftp -o gpsbabel-1.3.6.tar.gz http://www.gpsbabel.org/plan9.php?dl=gpsbabel-1.3.6.tar.gz ftp -v ftp://ftp2.fs.fed.us/incoming/fmsc/outgoing/fvs/fvs091109.exe and the problem went away library( RPostgreSQL ) Loading required package: DBI go figure... Thanks for a great package... It's helping tremendously as I port code from seriously old R code of mine (read grad school hacks) to useful R code to server-side PostgreSQL PL/R modules. I'm working on getting PL/R running again... never a dull moment... BTW: Love your website! Mine is about 10 years old. I don't like it. I originally wanted mine to look much closer to yours, but only had about 12 hours to commit to it back then. Interested in being my website mentor after I get my monster rebuilt? The monster is an experimental intelligent software agent for forests, forestry and forestry related data that ingests data, generates forecasts, and optimal strategic, tactical, and operational plans for timberland managers. Thanks, Jeff. On Sep 30, 2009, at 5:02 AM, Neil Tiffin wrote: On Sep 29, 2009, at 8:21 PM, Dirk Eddelbuettel wrote: Jeff, On 29 September 2009 at 17:50, Jeff Hamann wrote: | I can't get the RPostgreSQL library to load on OSX and have no idea | where it's going wrong... | | library( RPostgreSQL ) | Error in dyn.load(file, DLLpath = DLLpath, ...) : |unable to load shared library '/Users/hamannj/Library/R/2.9/ library/ | RPostgreSQL/libs/i386/RPostgreSQL.so': |dlopen(/Users/hamannj/Library/R/2.9/library/RPostgreSQL/libs/ i386/ | RPostgreSQL.so, 6): Symbol not found: _PQbackendPID |Referenced from: /Users/hamannj/Library/R/2.9/library/ RPostgreSQL/ | libs/i386/RPostgreSQL.so |Expected in: flat namespace | in /Users/hamannj/Library/R/2.9/library/RPostgreSQL/libs/i386/ | RPostgreSQL.so | Error: package/namespace load failed for 'RPostgreSQL' As you know, questions / complaints about contributed packages should go to the maintainer first, i.e. me. Now, I do not have access to OS X -- but Neil (CC'ed) kindly covers that angle. Maybe the two of you can sort this out? | I've used this on OSX before and have had to recently rebuild... does | anyone know if an older archive works? The current version works for other on OS X as far as I know. RPostgreSQL is only available is source form. There are many different ways to install postgreSQL. I suspect the normal source compile from within R failed. If you were installing a bunch of packages you may have not seen the failure. Please email how you installed postgresql, what version of postgresql you have installed, and how you source compiled RPostgreSQL. I suspect this will illuminate the problem. I install postgresql with fink and use the following to install RPostgreSQL. It is working for me with R 9.2.1. Of course if you use a different source for postgresql itself, you will need to change the line below. You can try to download the source, cd into the source location and execute the command line below with any modifications for your installation. sudo R CMD INSTALL RPostgreSQL_0.1-4.tar.gz --configure-args='-- with-pgsql-libraries=/sw/lib/postgresql-8.3 --with-pgsql-includes=/ sw/include/postgresql' Sorry I did not see this as I only monitor R-Sig-Mac and R-Sig-DB. Neil Jeff Hamann, PhD PO Box 1421 Corvallis, Oregon 97339-1421 541-754-2457 jeff.hamann[at]forestinformatics[dot]com http://www.forestinformatics.com [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] lattice's mai/mar analog
Michael Ramati wrote: hello, is there a way to control figure margins using package lattice, similarly to parameters mai/mar (which presumbly works only for figures of package graphics)? thanks! Try it this way: library(lattice) trellis.device() trellis.par.set(list( layout.widths = list(left.padding = 8, right.padding = 9), layout.heights = list(top.padding = 10, bottom.padding = 11))) xyplot(Sepal.Length ~ Petal.Length | Species, data = iris) Use trellis.par.get() and check the layout.heights/widths sections. You can adjust the spacing between the labels and the axis, etc. The paddings are ordered from extreme left to extreme right. Ditto for top to bottom. See ?trellis.par.set for how to set up the options. -Peter Ehlers [[alternative HTML version deleted]] __ 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
[Rd] Multicore bootstrap
Bootstrapping can easily be sped up on multicore machines using parallel processing of the seperate bootstraps. As a proof of concept I slightly modified the boot.sem function to use multiple cores, using mclapply from the multicore package. Example code can be found on my website: http://www.jeroenooms.com/files/boot.sem.mc.R http://www.jeroenooms.com/files/semTest.R Bootstrapping using boot.sem.mc is exactly twice as fast as when using boot.sem on my machine (dual core). It might be nice to implement an option in bootstrapping functions to use multiple cores when available. - Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University Visit http://www.jeroenooms.com www.jeroenooms.com to explore some of my current projects. -- View this message in context: http://www.nabble.com/Multicore-bootstrap-tp25721774p25721774.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] Compiling with High Performance Fortran
On Oct 2, 2009, at 2:35 PM, Fabio Mathias Corrêa wrote: Dear, I looked in the list something on as to compile a code with access the High Performance FORTRAN using R CMD SHLIB, but I did not find. Would like to know if the accepted R this type of language? R supports systems with FORTRAN 77 and 90/95 compilers including any extensions such as HPF. R itself doesn't care (it accepts .f90, .f95 etc.) - it's up to you to use a compiler that suits you. Depending on the exact HPF extensions you're using it may work with a F95 compiler. The most commonly used compiler is GNU Fortran so you may test your code with that (it also supported OpenMP which effectively supersedes HPF). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Because it's Friday. was creating environments in package's C code
I hope you will forgive a serious comment on this thread, but the
new sos package makes greping through the headers shockingly easy.
It returns the 'RSiteSearch( ___ , function)' information in a
data.frame of class findFn sorted to put the package with the most
matches first. Duncan Murdoch wrote a ??? alias for this findFn
function. Union and intersection operators are defined for
findFnobjects. The findFn2xls function writes an Excel file with
three sheets giving an extended package summary, the matches (including
the URLs), and the call. An article on this is scheduled to appear in
the next issue of R Journal and is available now via vignette('sos').
This sos package is not as good as greping Ripley's frontal
lobe, but it makes it quite easy to do a literature search of all
contributed R packages.
Spencer
Jeffrey Horner wrote:
Simon Urbanek wrote on 10/01/2009 11:51 AM:
[...]
I suspect you like reinventing the wheel ;). Your NewInteger is part
of the R API and is called ScalarInteger(). When you need something,
chances are that R has it already, so it's worth greping through the
headers (and sometimes even through the main sources).
I am reminded of what Robert Gentleman said at DSC 2005 during the R/S
round-chair discussion: Brian Ripley is the only one I know who keeps
R in his frontal lobe.
I can only aspire to such greatness, Simon.
Jeff
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] plotmath documentation (PR#13978)
On 02/10/2009 7:25 AM, inp...@gmail.com wrote: Full_Name: r Version: 251 OS: linux Submission from: (NULL) (138.250.104.18) Plotmath manual does not state that an expression cannot be written with asterisk (*) at the start. See mailing list post 'plot #7506; C in graph axis label', 02-10-09 This is not a bug, because it does, in the very first sentence of the Details section: A mathematical expression must obey the normal rules of syntax for any R expression... Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
