Re: [ESS] Feature idea: insert expression before <- at point
+1, good idea. In some ways this is the edit-time equivalent of the pipe operator and its back reference ".", which can place cognitive burden on the reader. You give examples of replacement. Repetition also arises in extraction, e.g., with [(). data[,"columnA"][_POINT_ > 10] One concern is that this might discourage semantic labeling of expressions through assignment (a problem shared with the pipe). On Tue, Apr 30, 2019 at 11:25 AM Sven Hartenstein via ESS-help < ess-help@r-project.org> wrote: > Dear ESS users and developers, > > when writing R code to manipulate an object or data frame column, I > often find myself retyping the expression on the left side of "<-" as > some argument for a function call or assignment on the right side of > "<-". > > Here are two examples. Imagine your point is at _POINT_ and you want to > insert 'data[,"columnA"]' in the first example and in the second example > 'data[ data[,"columnB"] < 123 ,"columnA"]' at point. > > data[,"columnA"] <- tolower(_POINT_) > > data[ data[,"columnB"] > 123 ,"columnA"] <- gsub("xxx", > "yyy", > _POINT_, > fixed=TRUE) > > Wouldn't it be handy to have a lisp function which copies the expression > on the left side of "<-" and inserts it at point? > > Or is something like this already available in ESS? > > Or is my coding process unusual and you are not in the situation to use > such a function? > > What do you think? > > (I am not very familiar with lisp and thus do not try to write such a > function. I might use a macro.) > > Thanks, > > Sven > > __ > ESS-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/ess-help > [[alternative HTML version deleted]] __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [R] dplyr - add/expand rows
Or with the Bioconductor IRanges package: df <- with(input, DataFrame(station, year=IRanges(from, to), record)) expand(df, "year") DataFrame with 24 rows and 3 columns station year record 1 07EA001 1960 QMS 2 07EA001 1961 QMC 3 07EA001 1962 QMC 4 07EA001 1963 QMC 5 07EA001 1964 QMC ... ... ... ... 20 07EA001 1979 QRC 21 07EA001 1980 QRC 22 07EA001 1981 QRC 23 07EA001 1982 QRC 24 07EA001 1983 QRC If you tell the computer more about your data, it can do more things for you. Michael On Tue, Nov 28, 2017 at 7:34 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 11/26/2017 08:42 PM, jim holtman wrote: > >> try this: >> >> ## >> >> library(dplyr) >> >> input <- tribble( >>~station, ~from, ~to, ~record, >> "07EA001" ,1960 , 1960 , "QMS", >> "07EA001" , 1961 , 1970 , "QMC", >> "07EA001" ,1971 , 1971 , "QMM", >> "07EA001" ,1972 , 1976 , "QMC", >> "07EA001" ,1977 , 1983 , "QRC" >> ) >> >> result <- input %>% >>rowwise() %>% >>do(tibble(station = .$station, >> year = seq(.$from, .$to), >> record = .$record) >>) >> >> ### >> > > In a bit more 'base R' mode I did > > input$year <- with(input, Map(seq, from, to)) > res0 <- with(input, Map(data.frame, station=station, year=year, > record=record)) >as_tibble(do.call(rbind, unname(res0)))# A tibble: 24 x 3 > > resulting in > > > as_tibble(do.call(rbind, unname(res0)))# A tibble: 24 x 3 >station year record > > 1 07EA001 1960QMS > 2 07EA001 1961QMC > 3 07EA001 1962QMC > 4 07EA001 1963QMC > 5 07EA001 1964QMC > 6 07EA001 1965QMC > 7 07EA001 1966QMC > 8 07EA001 1967QMC > 9 07EA001 1968QMC > 10 07EA001 1969QMC > # ... with 14 more rows > > I though I should have been able to use `tibble` in the second step, but > that leads to a (cryptic) error > > > res0 <- with(input, Map(tibble, station=station, year=year, > record=record))Error in captureDots(strict = `__quosured`) : > the argument has already been evaluated > > The 'station' and 'record' columns are factors, so different from the > original input, but this seems the appropriate data type for theses columns. > > It's interesting to compare the 'specialized' knowledge needed for each > approach -- rowwise(), do(), .$ for tidyverse, with(), do.call(), maybe > rbind() and Map() for base R. > > Martin > > > >> >> >> Jim Holtman >> Data Munger Guru >> >> What is the problem that you are trying to solve? >> Tell me what you want to do, not how you want to do it. >> >> On Sun, Nov 26, 2017 at 2:10 PM, Bert Gunter>> wrote: >> >> To David W.'s point about lack of a suitable reprex ("reproducible >>> example"), Bill's solution seems to be for only one station. >>> >>> Here is a reprex and modification that I think does what was requested >>> for >>> multiple stations, again using base R and data frames, not dplyr and >>> tibbles. >>> >>> First the reprex with **two** stations: >>> >>> d <- data.frame( station = rep(c("one","two"),c(5,4)), >>> from = c(60,61,71,72,76,60,65,82,83), >>> to = c(60,70,71,76,83,64, 81, 82,83), >>> record = c("A","B","C","B","D","B","B","D","E")) >>> >>> d >>>station from to record >>> 1 one 60 60 A >>> 2 one 61 70 B >>> 3 one 71 71 C >>> 4 one 72 76 B >>> 5 one 76 83 D >>> 6 two 60 64 B >>> 7 two 65 81 B >>> 8 two 82 82 D >>> 9 two 83 83 E >>> >>> ## Now the conversion code using base R, especially by(): >>> >>> out <- by(d, d$station, function(x) with(x, { >>> +i <- to - from +1 >>> +data.frame(YEAR =sequence(i) -1 +rep(from,i), RECORD =rep(record,i)) >>> + })) >>> >>> >>> out <- data.frame(station = >>> rep(names(out),sapply(out,nrow)),do.call(rbind,out), row.names = NULL) >>> >>> >>> out >>> station YEAR RECORD >>> 1 one 60 A >>> 2 one 61 B >>> 3 one 62 B >>> 4 one 63 B >>> 5 one 64 B >>> 6 one 65 B >>> 7 one 66 B >>> 8 one 67 B >>> 9 one 68 B >>> 10 one 69 B >>> 11 one 70 B >>> 12 one 71 C >>> 13 one 72 B >>> 14 one 73 B >>> 15 one 74 B >>> 16 one 75 B >>> 17 one 76 B >>> 18 one 76 D >>> 19 one 77 D >>> 20 one 78 D >>> 21 one 79 D >>> 22 one 80 D >>> 23 one 81 D >>> 24 one 82 D >>> 25 one 83 D >>> 26 two 60 B >>> 27
[R] The R Journal, Volume 8, Issue 1
Dear all, The latest issue of The R Journal is now available at http://journal.r-project.org/archive/2016-1/ Many thanks to all contributors. Michael Lawrence ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is that an efficient way to find the overlapped , upstream and downstream ranges for a bunch of ranges
For the sake of prosterity, this question was asked and answered here: https://support.bioconductor.org/p/80448 On Tue, Apr 5, 2016 at 10:27 AM, 何尧wrote: > I do have a bunch of genes ( nearly ~5) from the whole genome, which > read in genomic ranges > > A range(gene) can be seem as an observation has three columns chromosome, > start and end, like that > >seqnames start end width strand > > gene1 chr1 1 5 5 + > > gene2 chr110 15 6 + > > gene3 chr112 17 6 + > > gene4 chr120 25 6 + > > gene5 chr130 4011 + > > I just wondering is there an efficient way to find overlapped, upstream and > downstream genes for each gene in the granges > > For example, assuming all_genes_gr is a ~5 genes genomic range, the > result I want like belows: > > gene_nameupstream_genedownstream_geneoverlapped_gene > gene1NAgene2NA > gene2gene1gene4gene3 > gene3gene1gene4gene2 > gene4gene3gene5NA > > Currently , the strategy I use is like that, > library(GenomicRanges) > find_overlapped_gene <- function(idx, all_genes_gr) { > #cat(idx, "\n") > curr_gene <- all_genes_gr[idx] > other_genes <- all_genes_gr[-idx] > n <- countOverlaps(curr_gene, other_genes) > gene <- subsetByOverlaps(curr_gene, other_genes) > return(list(n, gene)) > } > > system.time(lapply(1:100, function(idx) find_overlapped_gene(idx, > all_genes_gr))) > However, for 100 genes, it use nearly ~8s by system.time().That means if I > had 5 genes, nearly one hour for just find overlapped gene. > > I am just wondering any algorithm or strategy to do that efficiently, perhaps > 5 genes in ~10min or even less > > > > > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to filter data using sets generated by flattening with dcast, when I can't store those sets in a data frame
The data structures you mention are complex, and too much of their complexity leaks into client code. Instead, aim to use higher level code constructs on simpler data structures. In R, the most convenient operations are those that are statistical in nature. For example, one might solve your problem by saying: restrict to the subset of the important days (1, 4, 7), and count the occurrences of each patient in that subset to find those patients with the sufficient number of important measurements. criticalDays - c(1, 4, 8) criticalDf - subset(df, Day %in% criticalDays) keepPatients - table(criticalDf$ID) == length(criticalDays) df[keepPatients[df$ID],] Note that the code above assumes that the ID variable is a factor, which it should be. Michael On Thu, Mar 12, 2015 at 12:55 AM, Jocelyn Ireson-Paine p...@j-paine.org wrote: This is a fairly long question. It's about a problem that's easy to specify in terms of sets, but that I found hard to solve in R by using them, because of the strange design of R data structures. In explaining it, I'm going to touch on the reshape2 library, dcast, sets, and the non-orthogonality of R. My problem stems from some drug-trial data that I've been analysing for the Oxford Pain Research Unit. Here's an example. Imagine a data frame representing patients in a trial of pain-relief drugs. The trial lasts for ten days. Each patient's pain is measured once a day, and the values are recorded in a data frame, one row per patient per day. Like this: ID Day Pain 11 10 12 9 14 7 17 2 22 8 23 7 31 10 33 6 34 6 38 2 Unfortunately, many patients have measurements missing. Thus, in the example above, patient 1 was only observed on days 1, 2, 4, and 7, rather than on the full ten days. But a patient's measurements are only useful to us if that patient has a certain minimum set of days, so I need to check for patients who lack those days. Let's assume that these days are numbers 1, 4, and 9. Such a question is trivial to state in terms of sets. Let D(i) denote the set of days on which patient i was measured: then I want to find out which patients p, or how many patients p, have a D(p) that contains the set {1,4,9}. The obvious way to solve this is to write a function that tells me whether one set is a superset of another. Then flatten my data frame so that it looks like this: ID Days 1 {1,2,4,7} 2 {2,3} 3 {1,3,4,8} And finally, filter it by some R translation of flattened[ includes( flattened$Days, {1,4,9} ), ] I started with the built-in functions that operate on sets represented as vectors. These are described in https://stat.ethz.ch/R-manual/R-devel/library/base/html/sets.html , Set Operations. For example: union( c(1,2,3), c(2,4,6) ) [1] 1 2 3 4 6 intersect( c(1,2,3), c(2,4,6) ) [1] 2 So I first wrote a set-inclusion function: # True if vector a is a superset of vector b. # includes - function( a, b ) { return( setequal( union( a, b ), a ) ) } Here are some sample calls: includes( c(1), c() ) [1] TRUE includes( c(1), c(1) ) [1] TRUE includes( c(1), c(1,2) ) [1] FALSE includes( c(2,1), c(1,2) ) [1] TRUE includes( c(2,1,3), c(1,2) ) [1] TRUE includes( c(2,1,3), c(4,1,2) ) [1] FALSE I then made myself a variable holding my sample data frame: df - data.frame( ID = c( 1, 1, 1, 1, 2, 2, 3, 3, 3, 3 ) , Day = c( 1, 2, 4, 7, 2, 3, 1, 3, 4, 8 ) ) And I tried flattening it, using dcast and an aggregator function as described in (amongst many other places) http://seananderson.ca/2013/ 10/19/reshape.html , An Introduction to reshape2 by Sean C. Anderson. The idea behind this is that (for my data) dcast will call the aggregator function once per patient ID, passing it all the Day values for the patient. The aggregator must combine them in some way, and dcast puts its results into a new column. For example, here's an aggregator that merely sums its arguments: aggregator_making_sum - function( ... ) { return( sum( ... ) ) } If I call it, I get this: dcast( df, ID~. , fun.aggregate=aggregator_making_sum ) Using Day as value column: use value.var to override. ID . 1 1 14 2 2 5 3 3 16 And here's an aggregator that converts the argument list to a string: aggregator_making_string - function( ... ) { return( toString( ... ) ) } Calling it gives this: dcast( df, ID~. , fun.aggregate=aggregator_making_string ) Using Day as value column: use value.var to override. ID . 1 1 1, 2, 4, 7 2 2 2, 3 3 3 1, 3, 4, 8 In both of these, the three dots denote all arguments to the aggregator, as explained in Burns Statistics's http://www.burns-stat.com/the- three-dots-construct-in-r/ . My first aggregator sums them; my
Re: [R] Installing gWidgetsRGtk2: R session is headless
Perhaps this is a permissions (Xauthority) issue: is the same user running both the X11 display and the R session? On Thu, Oct 23, 2014 at 2:40 AM, R rainer.schuerm...@gmx.net wrote: I have written some gWidgets scripts before in the past but have a different box now (Debian KWheezy) and cannot get gWidgets working. It may be an obvious mistake but auntie Google (who has helped me a lot to get as far as I am now) leaves me in the dark now. Here is where I am stuck: - - - - - library( gWidgets ) library( gWidgetsRGtk2 ) Loading required package: RGtk2 No protocol specified R session is headless; GTK+ not initialized. obj - gbutton(Hello world, container = gwindow()) (R:15675): GLib-GObject-WARNING **: invalid (NULL) pointer instance (R:15675): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed (R:15675): Gtk-WARNING **: Screen for GtkWindow not set; you must always set a screen for a GtkWindow before using the window (R:15675): Gdk-CRITICAL **: IA__gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed (R:15675): Gdk-CRITICAL **: IA__gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed (R:15675): Gdk-CRITICAL **: IA__gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed (R:15675): Gdk-CRITICAL **: IA__gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed (R:15675): Gdk-CRITICAL **: IA__gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed (R:15675): Gdk-CRITICAL **: IA__gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed *** caught segfault *** address 0x18, cause 'memory not mapped' Traceback: 1: .Call(name, ..., PACKAGE = PACKAGE) 2: .RGtkCall(S_gtk_widget_show, object, PACKAGE = RGtk2) 3: method(obj, ...) 4: window$Show() 5: .gwindow(toolkit, title, visible, width, height, parent, handler, action, ...) 6: .gwindow(toolkit, title, visible, width, height, parent, handler, action, ...) 7: gwindow() 8: .gbutton(toolkit, text, border, handler, action, container, ...) 9: .gbutton(toolkit, text, border, handler, action, container, ...) 10: gbutton(Hello world, container = gwindow()) - - - - - sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.1.1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2 drawing area as cairo device - no points
Just wanted to acknowledge this. It's a known issue, and one that has been tricky to solve, because it's platform-specific, so it's probably some sort of bug in the abstraction (GDK). On Wed, Sep 17, 2014 at 12:26 AM, François Rebaudo francois.reba...@legs.cnrs-gif.fr wrote: Hi, The following code adapted from Michael post (https://stat.ethz.ch/ pipermail/r-help/2012-March/306069.html) works just fine on Linux Debian, but not on Windows 7 (no points on plots 2 and 3). More surprisingly, if the first plot is a boxplot, it works on both OS... and if I do a pdf (using pdf()), I get my points... Thanks in advance for your help. library(RGtk2) library(cairoDevice) win = gtkWindow(show = FALSE) win$setDefaultSize(500, 500) da = gtkDrawingArea() asCairoDevice(da) win$add(da) win$showAll() layout(matrix(c(1,1,2,3),2,2,byrow=TRUE)) par(mar=c(0,0,0,0)) plot(1:10) #boxplot(1:10) plot(1:10) plot(1:10) sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.1.0 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/ posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] interactive labeling/highlighting on multiple xy scatter plots
You should check out the animint package. https://github.com/tdhock/animint On Mon, Jul 28, 2014 at 5:48 PM, Shi, Tao shida...@yahoo.com wrote: hi list, I'm comparing the changes of ~100 analytes in multiple treatment conditions. I plotted them in several different xy scattter plots. It would be nice if I mouse over one point on one scatter plot, the label of the analyte on that scatter plot AS WELL AS on all other scatter plots will be automatically shown. I know brushing in rggobi does this, but its interface is not good and it needs R or ggobi to run (I want send the results to the collaborators and let them to play with it without the need of installing R or ggobi on their machine). rCharts is nice but so far it can only create one scatter plot at a time. Any good suggestions? Many thanks! Tao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unable to compile install rggobi
GGobi needs a 64 bit binary before we can get rggobi available on Windows again. On Fri, Apr 27, 2012 at 6:27 PM, Indrajit Sengupta indra_cali...@yahoo.comwrote: I came across this web site: http://cran.r-project.org/bin/windows/contrib/2.15/check/ Where I checked the file: rggobi-check.log The contents of this file is giving the same kind of error that I am facing. Does that mean, this package does not work with R 2.15 yet? Is it a bug? Regards, Indrajit From: Prof Brian Ripley rip...@stats.ox.ac.uk Cc: R Help r-help@r-project.org Sent: Friday, April 27, 2012 2:21 PM Subject: Re: [R] Unable to compile install rggobi On 27/04/2012 08:56, Indrajit Sengupta wrote: I am currently using R 2.15.0 with R Tools 2.15 (in Windows XP). I downloaded the source for RGgobi and extracted it to a folder. Then I tried compiling and installing with the following command and got an error message: -- D:\Work\tmpR CMD INSTALL --build D:\\DPF\\Rggobi\\rggobi * installing to library 'C:/Program Files/R/R-2.15.0/library' * installing *source* package 'rggobi' ... ** libs cygwin warning: MS-DOS style path detected: C:/PROGRA~1/R/R-215~1.0/etc/i386/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-215~1.0/etc/i386/Makeconf CYGWIN environment variable option nodosfilewarning turns off this warning. Consult the user's guide for more details about POSIX paths: http://cygwin.com/cygwin-ug-net/using.html#using-pathnames gcc -IC:/PROGRA~1/R/R-215~1.0/include -DNDEBUG -D_R_=1 -DUSE_R=1 -mms-bitfields -I/include/gtk-2.0 -I/include/gdk-pixbuf-2.0 -I/../lib/gtk-2.0/include - I/include/atk-1.0 -I/include/cairo -I/include/pango-1.0 -I/include/glib-2.0 -I/../lib/glib-2.0/include -I/include/libxml2 -I/include -I/include/ggobi -IC:/ PROGRA~1/R/R-215~1.0/include -I/include/libxml-O3 -Wall -std=gnu99 -mtune=core2 -c RSEval.c -o RSEval.o In file included from RSEval.c:6:0: RSGGobi.h:5:22: fatal error: GGobiAPI.h: No such file or directory compilation terminated. make: *** [RSEval.o] Error 1 ERROR: compilation failed for package 'rggobi' * removing 'C:/Program Files/R/R-2.15.0/library/rggobi' -- Can anybody help in figuring out what is the problem? I have installed GGobi RGtk2 previously. You need to set some environment variables: study the rggobi sources for what. E.g. I bet GGobi is not installed in the root, so -I/include/ggobi will not work. Regards, Indrajit [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Please do as you were asked: no HTML, programming questions to R-devel, questions about packages to the maintainer -- Brian D. Ripley, rip...@stats.ox.ac.uk 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] figure margins too large in RGtk2 drawing area as cairo device - why?
Hi Mark, This comes down to the way that GTK+ allocates size to its widgets. The allocation of a widget is initialized to have a width and height of 1. When a child is added to a visible parent, the parent will execute its lay out algorithm and allocate a certain amount of space to the widget. The widget is notified of this change via an event that arrives after an iteration of the event loop. An event loop iteration may be forced in a number of ways; you've discovered the Sys.sleep() method. However, it is generally not good practice to show a container before adding its children, unless widgets are being added in the middle of a session, which is rare. If you were to instead do something like this: win = gtkWindow(show = FALSE) win$setDefaultSize(500, 500) da = gtkDrawingArea() asCairoDevice(da) win$add(da) win$showAll() plot(1:10) Then GTK+ will correctly initialize the allocation of the widget, I think even before a configure event is received. The above approach is my recommended solution to your problem. Thanks, Michael On Fri, Mar 9, 2012 at 1:39 AM, Mark Heckmann mark.heckm...@gmx.de wrote: Thanks, Peter. I did the following: restart R and run the same code with and without a minimal system pause (Sys.sleep) after the line that adds the device to the GTK window. Adding a pause will make it work, though I do not understand what is happening here. Note the different settings of par(din). This is probably not the expected behavior, I guess. Any ideas why this is the case? It seems as if din is not adjusted on time? Might that be? library(RGtk2) library(cairoDevice) win = gtkWindow() da = gtkDrawingArea() asCairoDevice(da) [1] TRUE win$add(da) plot(1:10) Fehler in plot.new() : Grafikränder zu groß par(c(din, mai)) $din [1] 0.0139 0.0139 $mai [1] 0.7791667 0.6263889 0.6263889 0.3208333 win = gtkWindow() da = gtkDrawingArea() asCairoDevice(da) [1] TRUE win$add(da) Sys.sleep(.1) plot(1:10) par(c(din, mai)) $din [1] 2.78 2.78 $mai [1] 0.7791667 0.6263889 0.6263889 0.3208333 Thanks in advance --- Mark Am 09.03.2012 um 00:01 schrieb peter dalgaard: On Mar 8, 2012, at 23:25 , Mark Heckmann wrote: Peter, thanks for the answer! Indeed, it does work if I set par(mar=c(0,0,0,0)) but not when it is set to the default values mar=c(5.1, 4.1, 4.1, 2.1). The par settings returned in the example are the defaults, so no extraordinary big mar settings or char size (see below). Also, it does not matter what size the drawing area is set to (e.g. 1000x 1000). The error always occurs. Any idea? The other parameters... What about din and mai? The margin problem usually means that the sum of the relevant margins is bigger than the device size. E.g. quartz() par(mai=rep(4,4)) plot(0) Error in plot.new() : figure margins too large examples: win = gtkWindow() da = gtkDrawingArea() win$add(da) asCairoDevice(da) [1] TRUE par(c(mar, cra, oma)) $mar [1] 5.1 4.1 4.1 2.1 $cra [1] 7 11 $oma [1] 0 0 0 0 plot(1:10) Fehler in plot.new() : Grafikränder zu groß ###ERROR### Thanks Mark Am 08.03.2012 um 22:48 schrieb peter dalgaard: On Mar 8, 2012, at 20:27 , Mark Heckmann wrote: When using a gtkDrawingArea as a Cairo device I very often encounter the error: figure margins too large Even for the below getting started example from http://www.ggobi.org/rgtk2/ this is the case. win = gtkWindow() da = gtkDrawingArea() win$add(da) asCairoDevice(da) [1] TRUE plot(1:10) Fehler in plot.new() : Grafikränder zu groß Also enlarging the drawing area does not help. win = gtkWindow() da = gtkDrawingArea() win$add(da) asCairoDevice(da) [1] TRUE da$setSizeRequest(700, 700) plot(1:10) Fehler in plot.new() : Grafikränder zu groß Any ideas? I'd check the par() settings for the device. Especially mar/mai and cra/cin to see whether margins are set unusually large and/or character sizes are unusually big, but check help(par) yourself. -- 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 Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com -- 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 Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help
Re: [R] changing the drawing context using Cairo and RGtk2
On Wed, Mar 7, 2012 at 1:47 PM, Mark Heckmann mark.heckm...@gmx.de wrote: Michael, thanks for your answer! The attribute solution has its problems though. First, how it will work: foo - function(){ w - gtkWindow() da - gtkDrawingArea() w$add(da) asCairoDevice(da) print(dev.cur()) gObjectSetData(da, dev.number, data = dev.cur()) dev.set(gObjectGetData(da, dev.number)) par(mar=c(0,0,0,0)) plot(1:10) } The problem arises when I try to convert a drawing area to Cairo WITHIN another function. Than dev.cur() does not work as I expected. The device returned is the Null device instead. foo_2 - function(){ da - gtkDrawingArea() asCairoDevice(da) print(dev.cur())# NULL DEVICE! gObjectSetData(da, dev.number, data = dev.cur()) da } foo - function(){ w - gtkWindow() e - environment() da - foo_2() w$add(da) dev.cur() dev.set(gObjectGetData(da, dev.number)) par(mar=c(0,0,0,0)) plot(1:10) } As in most cases the code for creating and converting a drawing area is not located in the main function but rather inside a handler etc. the attribute solution will often work. Or am I missing something here? The R graphics device is not actually created until the widget is realized (in GTK terms), because it cannot plot anything until then. The difference in the code above is that in the first case you are adding the drawing area to the visible window (and thus realizing it) prior to calling dev.cur(). The order is reversed in the second case. Michael I think this problem is very general when working with RGtk2, Cairo and multiple drawing areas (e.g. on notebook tabs). So I wonder if there is another way to go about it. Do you have an idea? Thanks in advance --Mark Am 06.03.2012 um 13:52 schrieb Michael Lawrence: Currently, the GtkDrawingArea object has no real knowledge that it is being used as a graphics device. You could do something like: stick the device ID on da1/da2 as an attribute, and then have a function that does dev.set with that attribute. Michael On Mon, Mar 5, 2012 at 1:14 PM, Mark Heckmann mark.heckm...@gmx.dewrote: I am not too familiar with Cairo and RGtk2 and have the following problem: I have a container with two GTK drawing areas converted into Cairo devices. I know that I can set the current drawing context e.g. using dev.set(). But this is tedious. How can I set the context using the objects da1 or da2? w - gtkWindow() w$setSizeRequest(400, 400) vbox - gtkVBox() da1 - gtkDrawingArea() da2 - gtkDrawingArea() vbox$add(da1) vbox$add(da2) dummy - asCairoDevice(da1) dummy - asCairoDevice(da2) w$add(vbox) par(oma=c(0,0,0,0), mar=c(0,0,0,0)) plot(1:10) THX --Mark Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] changing the drawing context using Cairo and RGtk2
Currently, the GtkDrawingArea object has no real knowledge that it is being used as a graphics device. You could do something like: stick the device ID on da1/da2 as an attribute, and then have a function that does dev.set with that attribute. Michael On Mon, Mar 5, 2012 at 1:14 PM, Mark Heckmann mark.heckm...@gmx.de wrote: I am not too familiar with Cairo and RGtk2 and have the following problem: I have a container with two GTK drawing areas converted into Cairo devices. I know that I can set the current drawing context e.g. using dev.set(). But this is tedious. How can I set the context using the objects da1 or da2? w - gtkWindow() w$setSizeRequest(400, 400) vbox - gtkVBox() da1 - gtkDrawingArea() da2 - gtkDrawingArea() vbox$add(da1) vbox$add(da2) dummy - asCairoDevice(da1) dummy - asCairoDevice(da2) w$add(vbox) par(oma=c(0,0,0,0), mar=c(0,0,0,0)) plot(1:10) THX --Mark Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2: How to overlay a gtkDrawingArea with a button or any other widget?
Sorry for the late reply to this one. You'll need to make sure that the drawing area is realized prior to plotting, i.e., it should be in a visible container. Also, since you are using GtkFixed, you will need to set an explicit size request on the drawing area (otherwise it has zero area). Michael On Wed, Dec 21, 2011 at 4:31 PM, Mark Heckmann mark.heckm...@gmx.de wrote: I try to overlay a plot inside a gtkDrawingArea with a button (or any other widget). I tried to put both into a gtkFixed container. But this does not work, no printing occurs. Does someone know a solution? What I tried: w - gtkWindow() w$setSizeRequest(400,400) fx - gtkFixed() da - gtkDrawingArea() fx$put(da, 100, 100) asCairoDevice(da) par(mar=c(0,0,0,0)) plot(1:10) btn.1 - gtkButton(button) fx$put(btn.1, 200, 200) w$add(fx) Thanks Mark Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2 problems
The gain from updating will be that RGtk2 now looks in a specific (internal) place for the libraries, so you should no longer need to worry about library conflicts and PATH settings. In theory. Michael On Tue, Oct 25, 2011 at 5:46 PM, Aref arefnamm...@gmail.com wrote: Thank you for the response and I am sorry about the html--will remember next time. The version of RGtk2 installed is 2.20.8 I installed it through R from CRAN repository. I believe that the problem is that during the installation the environment variable GTK_BASEPATH was set to some other location than where GTK+ was installed--overwritten by the R installation process. I found this after I fixed the issue by copying the libraries into R \bin. This is probably not the best solution but it works. I will be updating R soon to 2.14 when it comes out and hopefully things will work better now that I have the environment variable pointing to the right place for the GTK+ libraries. On Oct 24, 12:12 am, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: Please update your R (and probably your RGtk2: you did not tell us its version), as the posting guide asked you to do before posting. On Sun, 23 Oct 2011, Aref Nammari wrote: Hello, I hope this is the right place to ask for help with a problem I am having with RGtk2 installation with R on Windows XP. I am running R 2.11.1 and have installed the package RGtk2 from CRAN. As a binary package, I guess, but please tell us (it matters). I also have GTK 2.10.11 installed as well as GTK2-runtime 2.22.0. I have added the environment variable GTK_PATH and set its value to the root location where GTK is installed. But you need the Gtk+ bin directory in your PATH. Environment variable GTK_PATH is only needed when RGtk2 is installed from the sources. Which Gtk+ you need in your path depends on the version of RGtk2 you have and how you installed it. For current binary versions, see http://cran.r-project.org/bin/windows/contrib/2.13/@ReadMe When I try to run RGtk2 in R by typing library(RGtk2) a popup dialog appears with the following error message: The procedure entry point gdk_app_launch_context_get_type could not be located in the dynamic link library libgdk-win32-2.0-0.dll In the R window I get : Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-211~1.1/library/RGtk2/ libs/RGtk2.dll': LoadLibrary failure: The specified procedure could not be found. Failed to load RGtk2 dynamic library, attempting to install it. Error : .onLoad failed in loadNamespace() for 'RGtk2', details: call: install_all() error: This platform is not yet supported by the automatic installer. Please install GTK+ manually, if necessary. See: http://www.gtk.org http://www.google.com/url?sa=Dq=http://www.gtk.orgusg=AFQjCNFJhHsdo... Error: package/namespace load failed for 'RGtk2' Any help in figuring out what could be the problem is greatly appreciated. Cheers, [[alternative HTML version deleted]] Please do as the posting guide asked of you and not send HTML. __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp:// www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk 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-h...@r-project.org mailing listhttps:// stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp:// www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cairo device and locator on windows
I will look into this. Michael On Sun, Apr 17, 2011 at 8:34 PM, Richard M. Heiberger r...@temple.eduwrote: In several tries, I am finding the locator and identify functions on the cairo device on Windows, with R-2.13.0, do not seem to work correctly. Here is my experience with locator where I click the four corners of the device window. First, with the windows() device, the results are consistent with what I see on screen windows() plot(1,1) locator() $x [1] 0.6075000 1.3981252 1.3653126 0.6090625 $y [1] 0.6117440 0.6239533 1.3931395 1.3983721 Second, with the Cairo device, the results are not consistent with what I see on screen. library(cairoDevice) Cairo() plot(1,1) locator() $x [1] 0.6715602 1.7007429 1.7071620 0.6672808 $y [1] 0.2775717 0.2945700 1.3144688 1.3290388 Any guidance on making Cairo work would be appreciated. Rich [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2: How to populate an GtkListStore data model?
On Sun, Apr 3, 2011 at 8:29 PM, Cleber N. Borges kle...@yahoo.com.brwrote: hello all I am trying to learn how to use the RGtk2 package... so, my first problem is: I don't get the right way for populate my gtkListStore object! any help is welcome... because I am trying several day to mount the code... Thanks in advanced Cleber N. Borges --- # my testing code library(RGtk2) win - gtkWindowNew() datamodel - gtkListStoreNew('gchararray') treeview - gtkTreeViewNew() renderer - gtkCellRendererText() col_0 - gtkTreeViewColumnNewWithAttributes(title=TitleXXX, cell=renderer, text=Bar) nc_next - gtkTreeViewInsertColumn(object=treeview, column=col_0, position=0) gtkTreeViewSetModel( treeview, datamodel ) win$add( treeview ) # is there an alternative function for this? # iter - gtkTreeModelGetIterFirst( datamodel )[[2]] # this function don't give VALID iter # gtkListStoreIterIsValid( datamodel, iter ) result in FALSE iter - gtkListStoreInsert( datamodel, position=0 )[[2]] gtkListStoreIterIsValid( datamodel, iter ) # the help of this function say to terminated in -1 value # but -1 crash the R-pckage (or the gtk)... Sorry about this. The help is autogenerated from the GTK+ C documentation. gtkListStoreSet(object=datamodel, iter=iter, 0, textFoo) # don't make any difference in the window... :-( It would be much easier to use rGtkDataFrame for populating this list. See the help for that function. R version 2.13.0 alpha (2011-03-27 r55091) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Portuguese_Brazil.1252 [2] LC_CTYPE=Portuguese_Brazil.1252 [3] LC_MONETARY=Portuguese_Brazil.1252 [4] LC_NUMERIC=C [5] LC_TIME=Portuguese_Brazil.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] RGtk2_2.20.8 loaded via a namespace (and not attached): [1] tools_2.13.0 my gtk version == 2.16.2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk in a windows 64 bits machine
Have you installed the 64 bit binaries of GTK+? http://ftp.gnome.org/pub/gnome/binaries/win64/gtk+/2.22/gtk+-bundle_2.22.1-20101229_win64.zip Michael On Mon, Mar 14, 2011 at 4:56 AM, Joaquim Tinoco jabtin...@civil.uminho.ptwrote: Dear all, I am relatively new to R! I migrated from a windows 32-bits machine to windows 64-bits machine and now when I try loading and use RGtk2 library the following error message is presented: library(RGtk2) Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'C:/Users/JOAQUIM/Documents/R/win-library/2.12/RGtk2/libs/x64/RGtk2.dll': LoadLibrary failure: %1 não é uma aplicação de Win32 válida. Failed to load RGtk2 dynamic library, attempting to install it. Error : .onLoad failed in loadNamespace() for 'RGtk2', details: call: install_all() error: This platform is not yet supported by the automatic installer. Please install GTK+ manually, if necessary. See: http://www.gtk.org Error: package/namespace load failed for 'RGtk2' Someone know why this error appears?? I am running Windows 7, with R 2.12.2 Thanks you. Best regards, Joaquim Tinoco [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problems with playwith
Do you get an error message in a dialog box? My guess is that you just need to update your GTK+. On Tue, Mar 1, 2011 at 8:58 AM, R Heberto Ghezzo, Dr heberto.ghe...@mcgill.ca wrote: hello, i tried to run playwith but : library(playwith) Loading required package: lattice Loading required package: cairoDevice Loading required package: gWidgetsRGtk2 Loading required package: gWidgets Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'H:/R/cran/RGtk2/libs/i386/RGtk2.dll': LoadLibrary failure: The specified procedure could not be found. Failed to load RGtk2 dynamic library, attempting to install it. Learn more about GTK+ at http://www.gtk.org If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error : .onAttach failed in attachNamespace() for 'gWidgetsRGtk2', details: call: .Call(name, ..., PACKAGE = PACKAGE) error: C symbol name S_gtk_icon_factory_new not in DLL for package RGtk2 Error: package 'gWidgetsRGtk2' could not be loaded Sys.getenv(PATH) PATH H:\\R/GTK/bin;H:\\R/GTK/lib;H:\\R/ImageMagick;C:\\windows\\system32;C:\\windows;C:\\windows\\System32\\Wbem;C:\\windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files\\Common Files\\Ulead Systems\\MPEG;C:\\Program Files\\QuickTime\\QTSystem\\;H:\\R\\GTK\\GTK2-Runtime\\bin;H:\\PortableUSB/PortableApps/MikeTex/miktex/bin packages(lattice, cairoDevice, gWidgetsRGtk2, gWidgets, RGtk2, playwith) were reinstalled program GTK was reinstalled. using R-2-12-2 on Windows 7 Can anybody suggest a solution? thanks R.Heberto Ghezzo Ph.D. Montreal - Canada __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Failing to install {rggobi} on win-7 R 2.12.0
Hi Tal, Thanks for working through this. GGobi needs to be rebuilt for the new version of GTK+. I'm probably the person to do that, but my time is short these days. I'll try to get to it soon. The new binary will just include the necessary DLLs, so that this GTK+ installation step is unnecessary. Michael On Sat, Feb 5, 2011 at 2:57 AM, Tal Galili tal.gal...@gmail.com wrote: Dear Prof Brian Ripley and others, After (finally) checking again, I found that ggobi doesn't work with the newer GTK (probably needed for R 2.12.0). Here is the results of my experimentations: *What works:* Installing ggobi and the GTK (version 2.12.9) provided on: http://www.ggobi.org/downloads/ Will *work* with R 2.11.1 + rggobi (version 2.1.14) (notice that the newest version 2.1.16, is not available for windows users. And the newer version 2.1.16-3 is not available on CRAN: http://cran.r-project.org/web/packages/rggobi/index.html) *What doesn't work:* Trying this with R 2.12.0 with rggobi (version 2.1.16-3), will *crash* with the error: the procedure entry point g_malloc_n could not be located in the dynamic link library libglic-2.0-0.dll When then trying to install gtk+ from the dialog box offered, then it downloads GTK (version 2.22.0 instead of 2.12.9) from here: http://downloads.sourceforge.net/gtk-win/gtk2-runtime-2.22.0-2010-10-21-ash.exe?download ' After doing this, ggobi (not rggobi) itself, won't run. It will crash with the error: the procedure entry point g_assertion_message_error could not be located in the dynamic link library libglib-2.0-0.dll Trying then to insert the dll's from the packages Prof Brian Ripley suggested (libxml2.dll and iconv.dll) won't fix the problem. Also using the libglib-2.0-0.dll from the old GTK package won't help. Also, reinstalling ggobi won't work. Any suggestions on how to make ggobi work with the newer version of GTK ? Thanks, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Wed, Jan 26, 2011 at 4:50 PM, Tal Galili tal.gal...@gmail.com wrote: I checked it using: Sys.getenv(PATH) And the output includes the PATH to the GTK2 installation (it's the last item in the following list): C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\Common Files\\Ulead Systems\\MPEG;C:\\Program Files\\TortoiseGit\\bin;C:\\Program Files (x86)\\QuickTime\\QTSystem\\;C:\\Program Files (x86)\\ggobi;C:\\Program Files (x86)\\GTK2-Runtime\\bin What else might I try? (Thanks) Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Wed, Jan 26, 2011 at 4:23 PM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: Your GTK+ installation is not being found: check your PATH. On Wed, 26 Jan 2011, Tal Galili wrote: Hello Prof Brian Ripley, Yihui and Tom, Thank you for your suggestions. It seemed to have made some differences in the error massages - but rggobi still fails to load. Steps taken: 1) I removed the old GTK (through the uninstall interface) 2) I ran library(RGtk2) which downloaded the new GTK-runtime version 2.22.0-2010-10-21 (instead of the one I got from ggobi, which was 2.12.9-2). 3) I downloaded both ftp://ftp.zlatkovic.com/libxml/libxml2-2.7.7.win32.zip and ftp://ftp.zlatkovic.com/libxml/iconv-1.9.2.win32.zip Unzipped them, and moved their dll's (from their bin directory), into - C:\Program Files (x86)\GTK2-Runtime\bin 4) I then tried starting rggobi: library(rggobi) and got the following error massages: Error 1: the program can't start because libgdk-win32-2.0-0.dll is missing from your computer. Try reinstalling the program to fix this problem. It then tried to reinstall GTK, and after I refused to, it sent the second Error massage: the program can't start because libfreetype-6.dll is missing from your computer. Try reinstalling the program to fix this problem. Any suggestions what else I should try? Many thanks for helping, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English)
Re: [R] RGtk2 compilation problem
On Thu, Jan 6, 2011 at 8:53 AM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: You need RGtk2 2.20.7 which is now on CRAN. Others have seen this, but it has taken a while to track down the exact cause. The diagnosis was that ML used a recent GNU tar which created a tarball with hard links that R's untar was not prepared to deal with. We consider that is a bug in GNU tar, but untar() has been updated in R-patched to cope. After a lot of back and forth with the GNU tar guys, it turns out they do not consider this to be a bug. I had to refresh my knowledge of hard linking to understand. A hard link is from a file name to the actual inode in the file system. Typically every file has a single hard link (the name of the file). The -h option used to resolve a symbolic link differently, based on whether the hard link count of the target was 1 or =2. This was practically useful in my mind, because symlinks to any files without any explicitly added hard links would become a regular file in the archive. They have now dropped this distinction, calling it an inconsistency (apparently other implementations of tar have never made such a distinction). So symlinks now become hard links in the archive (as long as the target is in the archive). We may need to keep the fix in untar() to handle this. Either way, RGtk2 2.20.7 should work now. Thanks, Michael If you have such a tarball, try setting the environment variable R_INSTALL_TAR to 'tar' (or whatever GNU tar is called on your system) when installing the tarball. For those packaging source packages: in the unusual event that your package sources contains symbolic (or even hard) links, don't use GNU tar 1.24 or 1.25. On Thu, 6 Jan 2011, Shige Song wrote: Look forward to it. Thanks. Shige On Sat, Jan 1, 2011 at 8:45 AM, Michael Lawrence lawrence.mich...@gene.com wrote: Please watch for 2.20.5 and let me know if it helps. Not really sure what is going on here, but someone else has reported the same issue. Thanks, Michael On Wed, Dec 29, 2010 at 6:44 AM, Shige Song shiges...@gmail.com wrote: Dear All, I am trying to compileinstall the package RGtk2 on my Ubuntu 10.04 box. I did not have problem with earlier versions, but with the new version, I got the following error message : ... -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2 compilation problem
Please watch for 2.20.5 and let me know if it helps. Not really sure what is going on here, but someone else has reported the same issue. Thanks, Michael On Wed, Dec 29, 2010 at 6:44 AM, Shige Song shiges...@gmail.com wrote: Dear All, I am trying to compileinstall the package RGtk2 on my Ubuntu 10.04 box. I did not have problem with earlier versions, but with the new version, I got the following error message : - * installing *source* package RGtk2 ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for INTROSPECTION... no checking for GTK... yes checking for GTHREAD... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for uintptr_t... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/local/lib/R/include -g -D_R_=1 -pthread -D_REENTRANT -I/usr/include/gtk-2.0 -I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/directfb -I/usr/include/libpng12 -I. -DHAVE_UINTPTR_T -I/usr/local/include -fpic -g -O2 -c RGtkDataFrame.c -o RGtkDataFrame.o In file included from RGtk2/gtk.h:19, from RGtkDataFrame.h:1, from RGtkDataFrame.c:1: ./RGtk2/gdkClasses.h:4:23: error: RGtk2/gdk.h: No such file or directory make: *** [RGtkDataFrame.o] Error 1 ERROR: compilation failed for package RGtk2 * removing /usr/local/lib/R/library/RGtk2 * restoring previous /usr/local/lib/R/library/RGtk2 The downloaded packages are in /tmp/RtmprSWbka/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(RGtk2, dep = T) : installation of package 'RGtk2' had non-zero exit status I noticed the requirement for the package (http://cran.r-project.org/web/packages/RGtk2/index.html) saying ...GTK+ (= 2.8.0)... The latest GTK+ is 2.20, could this be the problem? Many thanks. Best, Shige __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Playwith-problem with loading
On Tue, Nov 16, 2010 at 10:59 AM, Fencl, Martin martin.fe...@eawag.chwrote: Helllo, I am having trouble with running the library Playwith in the R-2.12.0. running under 32bit Windows XP. After calling the library the error message The procedure entry point gdk_cairo_reset_clip could not be located in the dynamic library libgdk-win32-2.0-0.dll. occurs and the R asks for instaling the GTK+ package. However the instalation of GTK+ thorugh the R fails. I have installed GTK+ by installing GIMP 2.0 version 2.6.10 and set the path of environment variables. But it still does not work. It seems to be that the problem is in gtk2 (which I also installed). Thank you for any hints! The GIMP binary of GTK+ has been known not to work well with R, and probably simply is not new enough in this case. What do you mean the GTK+ installer fails? Some details on that would be helpful. Thanks, Michael library(playwith) Loading required package: lattice Loading required package: cairoDevice Loading required package: gWidgetsRGtk2 Loading required package: gWidgets Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared object 'C:/PROGRA~1/R/R-212~1.0/library/RGtk2/libs/i386/RGtk2.dll': LoadLibrary failure: The specified procedure could not be found. Failed to load RGtk2 dynamic library, attempting to install it. trying URL ' http://downloads.sourceforge.net/gtk-win/gtk2-runtime-2.22.0-2010-10-21-ash.exe?download ' Content type 'application/x-msdos-program' length 7820679 bytes (7.5 Mb) opened URL downloaded 7.5 Mb Learn more about GTK+ at http://www.gtk.org If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error : .onAttach failed in attachNamespace() for 'gWidgetsRGtk2', details: call: .Call(name, ..., PACKAGE = PACKAGE) error: C symbol name S_gtk_icon_factory_new not in DLL for package RGtk2 Error: package 'gWidgetsRGtk2' could not be loaded __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem in installing and starting Rattle
On Mon, Nov 15, 2010 at 10:57 AM, Graham Williams graham.willi...@anu.edu.au wrote: On 16 November 2010 02:40, Feng Mai maif...@gmail.com wrote: I also have the problem trying to start rattle Windows 7 32-bit R 2.12.0 When I try library(rattle) I get an error message The procedure entry point deflateSetHeader could not be located in the dynamic link library zilb1.dll I hit OK and it prompts me to install GTK+ again. I tried to uninstall GTK+ first and delete all related files as Dieter suggested but still wont work :( Yes, this is another issue that arose with R 2.12.0 and discussed on the rattle-users mailing list (http://groups.google.com/group/rattle-users). Be sure to use the newest version of Rattle (currently 2.5.47) where this has been fixed. I've not worked out why, but if the XML package is loaded before the RGtk2 package we see this error, but not if RGtk2 is loaded first. Rattle now loads RGtk2 first. The reason is that the zlib1.dll provided with XML is older than the one expected by the automatically installed GTK+ binaries. I'm working on a way to make installing RGtk2 easier for others. Regards, Graham -- View this message in context: http://r.789695.n4.nabble.com/Problem-in-installing-and-starting-Rattle-tp3042502p3043262.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] RGtk2 2.20.x
This is to announce the release of the RGtk2 2.20.x series. RGtk2 is an interface between R and the GTK+ GUI toolkit and friends. The new release updates the bindings to support up to GTK+ 2.20 (and remains backwards compatible to 2.8). Previously, the interface supported only up to GTK+ 2.12, which is several years old. New features in GTK 2.20 (relative to 2.12) include: * GtkInfoBar widget: Displays transient popup notifications, generally at the bottom of the window (near the status bar). * Off-screen rendering of widgets, e.g., automatically save a widget or visualization to disk. * GtkSpinner: Animated widget for indicating activity * GtkToolPalette: Essentially a multi-row toolbar with drag and drop of toolbar items between the palette and other tool item containers. The bindings to Pango and Cairo were also updated to the latest stable versions. RGtk2 also adds a new library to its interface: GIO (2.22), a low-level library supporting asynchronous streaming I/O, mounting of volumes, networking, etc. Might be useful. There is also a new mode of error handling available, that is disabled by default. By setting the option RGtk2::newErrorHandling to TRUE, errors in the libraries will result in errors in R (instead of warnings), and the error object is no longer returned, which often simplifies return values by no longer requiring a list to hold both the error and the original return value. This is probably a more sensible strategy. Windows users: The new binaries for Windows are being built against 2.20, so you'll need to get GTK+ 2.20 (or higher, 2.22 is released but does not really add any new features) for Windows at: http://gtk-win.sourceforge.net/home/index.php/en/Downloads. Thanks, Michael [[alternative HTML version deleted]] ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGTK2 - Entry Point not found
2010/10/28 W Eryk Wolski wewol...@gmail.com Failed to load RGtk2 dynamic library, attempting to install it. trying URL ' http://downloads.sourceforge.net/gladewin32/gtk-2.12.9-win32-2.exe' Content type 'application/x-msdownload' length 7378984 bytes (7.0 Mb) I run the complete setup of GTK . Hence, I assume Version 2.12.9 is installed on my box. My path variable starts with: %GTK_BASEPATH%\bin; Any other ideas? It may be that you have some other cairo DLL in your PATH that is somehow conflicting with the one installed with GTK+... 2010/10/28 £ukasz Rêc³awowicz lukasz.reclawow...@gmail.com: The stable version of RGtk2 requires GTK version 2.8.0 or higher (and its dependencies). -- Mi³ego dnia -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Zoom in in a plot
You might want to check out the Qt stuff we've been working on. The qtutils package has a graphics device that supports zooming and other fun stuff. Also, qtpaint provides a flexible low-level engine for interactive graphics. See: http://github.com/ggobi/qtpaint and http://github.com/ggobi/qtutils. They require qtbase from: http://github.com/ggobi/qtbase. They require the installation of Qt: http://qt.nokia.com. Still working on Windows support. Michael On Tue, Oct 26, 2010 at 11:19 PM, Alaios ala...@yahoo.com wrote: Actually I want to see how close are some point to a line segment so I want to use some zoom lenses and zoom in and out into different parts of the plot and see how some places look like. Best Regards From: Greg Snow greg.s...@imail.org Sent: Tue, October 26, 2010 6:47:32 PM Subject: RE: [R] Zoom in in a plot For a quick exploration of the plot you can use the zoomplot function in the TeachingDemos package. But for production graphs it is better to explicitly set the xlim and ylim parameters in creating the plot up front. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Alaios Sent: Tuesday, October 26, 2010 9:31 AM To: Rhelp Subject: [R] Zoom in in a plot in a simple plot. When i do plot is it possible to zoom in or out or this is not possible at all? Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem loading RGtk2 (iconv.dll)
This sounds like a DLL conflict to me. For example, do you have Matlab installed? Sometimes if Matlab is on the PATH, the DLLs can conflict. Michael On Thu, May 27, 2010 at 11:06 PM, Tal Galili tal.gal...@gmail.com wrote: Hello dear R-help list and Michael Lawrence. I wish to use GTK with R. I installed the newest RGtk2 and GTK from: http://sourceforge.net/projects/gladewin32/files/gtk%2B-win32-devel/2.12.9/gtk-dev-2.12.9-win32-2.exe/download on the path: C:\Program Files\Common Files\GTK\2.0\ And followed the instructions on the installation manual for RGtk2, and added the line: GTK_PATH=C:/Program Files/Common Files/GTK/2.0 To the etc/Renviron.site file. Yet when I come to load the package via require(RGtk2), I get the following *error massage*: the procedure entry point libiconv_set_relocation_prefix could not be located in the dynamic linke library iconv.dll And then (in the R console) I get: Loading required package: RGtk2 Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/Program Files/R/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: The specified procedure could not be found. The interesting thing is that after I install GTK (through the auto-install), then RGtk2 loads without error in R. But if I try to run something, for example: demo(alphaSlider) I will get the error massage: Error in .Call(name, ..., PACKAGE = PACKAGE) : C symbol name S_gtk_window_new not in DLL for package RGtk2 Upon restarting R, again, I wouldn't be able to use require(RGtk2) Here is my sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 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 other attached packages: [1] RGtk2_2.12.18 loaded via a namespace (and not attached): [1] tools_2.11.0 (I am running win XP) I tried searching for this error on the mailing list and on google, but couldn't find a solution. Thanks, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Follow up on installing formatR...
On Mon, Apr 19, 2010 at 5:28 AM, Brian Lunergan ff...@ncf.ca wrote: Good morning folks: Made a second go at installing this and succeeded, but with some strange behaviours along the way. First the system back story. My only guess is that installing RGtk2 from source is only possible if you have the gtk-devel package installed, i.e., the one with the headers. Otherwise, you'll need the r-cran-rgtk2 binary. Michael Using up to date edition Ubuntu 8.04 Using up to date edition of R 2.10.1 Using the Toronto, Ontario repository to draw from. After the first attempt ended up with two of the four dependencies installed so only the Rgtk related items would be needed this time. Went into synaptic and found r-cran-rgtk2. Okay. Sounded likely so I installed it successfully. Using a root terminal session I went back into R and ran install.packages(formatR). Pulled in two dependencies plus the main choice. Rejected one and kept two when it came time to install but still installed successfully, or so it seemed when I ran library(formatR). Go figure. A copy of the message run follows. Any comments or suggestions will be of interest. install.packages(formatR) Warning in install.packages(formatR) : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done also installing the dependencies RGtk2, gWidgetsRGtk2 trying URL 'http://probability.ca/cran/src/contrib/RGtk2_2.12.18.tar.gz' Content type 'application/x-gzip' length 2206504 bytes (2.1 Mb) opened URL == downloaded 2.1 Mb trying URL ' http://probability.ca/cran/src/contrib/gWidgetsRGtk2_0.0-64.tar.gz' Content type 'application/x-gzip' length 138192 bytes (134 Kb) opened URL == downloaded 134 Kb trying URL 'http://probability.ca/cran/src/contrib/formatR_0.1-3.tar.gz' Content type 'application/x-gzip' length 2672 bytes opened URL == downloaded 2672 bytes * installing *source* package RGtk2 ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for LIBGLADE... no configure: WARNING: libglade not found checking for INTROSPECTION... no checking for GTK... no configure: error: GTK version 2.8.0 required ERROR: configuration failed for package RGtk2 * removing /usr/local/lib/R/site-library/RGtk2 * installing *source* package gWidgetsRGtk2 ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... * DONE (gWidgetsRGtk2) * installing *source* package formatR ... ** R ** preparing package for lazy loading Loading required package: gWidgets Loading required package: MASS ** help *** installing help indices ** building package indices ... * DONE (formatR) The downloaded packages are in /tmp/RtmpNL20Be/downloaded_packages Warning message: In install.packages(formatR) : installation of package 'RGtk2' had non-zero exit status -- Brian Lunergan Nepean, Ontario Canada __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2:::gdkColorToString throws an error
Actually, the problem is more likely that RGtk2 is not built against GTK+ 2.12 on Windows. I assume you're using an up-to-date version of R. I'll ask Uwe about getting a newer version of GTK+. On Mon, Mar 8, 2010 at 7:29 PM, Wincent ronggui.hu...@gmail.com wrote: Dear Michael, thanks. I have installed gtk+ 2-12.9 revision 2 from http://gladewin32.sourceforge.net/, it still doesn't work. I tried gtk2-runtime-2.16.6-2010-02-24-ash.exe from http://gtk-win.sourceforge.net/home/index.php/en/Downloads, it did not solve the issue neither. Could you please give me more hints? My OS is windows vista. Regards Ronggui On 26 October 2009 23:27, Michael Lawrence mflaw...@fhcrc.org wrote: Hi and sorry for the late reply. The Gdk library is part of the GTK+ bundle (GTK+, Gdk and GdkPixbuf are distributed together and have synchronized versions). So you'll just need GTK+ 2.12 or higher. Michael On Tue, Oct 20, 2009 at 8:16 AM, Ronggui Huang ronggui.hu...@gmail.com wrote: Dear all, I try to use RGtk2:::gdkColorToString, but it throws an error: Error in .RGtkCall(S_gdk_color_to_string, object, PACKAGE = RGtk2) : gdk_color_to_string exists only in Gdk = 2.12.0 I know what it means, but don't know to solve this problem because I don't know where I can download the referred gdk library. Any information? Thank you. -- HUANG Ronggui, Wincent Doctoral Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html -- Wincent Ronggui HUANG Doctoral Candidate Dept of Public and Social Administration City University of Hong Kong http://asrr.r-forge.r-project.org/rghuang.html [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to put ggobi display into a GUI window setup by gWidgets
On Mon, Nov 30, 2009 at 7:49 AM, j verzani jverz...@gmail.com wrote: jerry83 chaohan1983 at yahoo.com writes: Jerry, see below: Hi John, Thanks A LOT for your reply and the code. What I want to do is to include the ggobi display window to the widget window setup by me. I tried add before but it said can not do it for GGobiScatterplotDisplay. Do you have any idea about add displays? Thanks again for your help.  From: jverzaniNWBKZ [via R] ml-node+930927-1354988502 at n4.nabble.com Sent: Sun, November 29, 2009 5:19:43 PM Subject: Re: [R] how to put ggobi display into a GUI window setup by gWidgets jerry83 chaohan1983 at yahoo.com writes: Hi, I want to put a ggobi display into a GUI window setup by gWidgets, but error occur said it is not a S4 object. Does anyone have any idea about how to put it in or maybe it can not be put into a widget at all? Thanks A LOT! To embed a GTK widget into gWidgets isn't too hard, just call the add method. I'm not sure how  to get the GTK object you want from the ggobi interface. Below is an example that you might be able to modify: ## library(RGtk2) library(rggobi) library(gWidgets) options(guiToolkit=RGtk2) ## ggoobi object x - ggobi(mtcars) ## grab child from main window. Modify (how?) to get ## other widgets toplevel - ggobi_gtk_main_window(x) child - toplevel[[1]]  # toplevel has only one child toplevel$remove(child)  # remove child if keeping toplevel toplevel$destroy()    # or destroy if not ## add to a gWidget instance using gWidgetsRGtk2: w - gwindow(A gwidget's window) g - ggroup(cont = w, expand=TRUE) add(g, child, expand=TRUE) --John Here is some code to grab the display for a new display. I don't know how to get the initial display or even how to suppress it, but I'm not a ggobi user at this point. library(RGtk2) library(rggobi) library(gWidgets) options(guiToolkit=RGtk2) x - ggobi(mtcars) ## not sure how to get the initial display, ## here we create a new display and move that disp - display(x[1]) ## see display.GGobiData Try plotWidget - display(x[1], embed=TRUE) That will give you a display widget without hacking up the GGobi GUI. ## find table in the display heirarchy table - disp[[2]] ## plot is third child (rulers are first two) plotWidget - table[[3]]$getWidget() table$remove(plotWidget) ## hide window that held display. Destroy() causes errors disp$getParent()$hide() ## now we need to declass things so that gWidgets will ## recognize. The S3 classes from RGtk2 that gWidgets ## knows about are declared in package (should be ## dynamic, but aren't) class(plotWidget) - class(plotWidget)[-(1:3)] w - gwindow(A gwidget's window) g - ggroup(cont = w, expand=TRUE) add(g, plotWidget, expand=TRUE) __ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. View message @ http://n4.nabble.com/how-to-put-ggobi-display-into-a-GUI-window-setup-by-gWidgets-tp930529p930927.html To unsubscribe from how to put ggobi display into a GUI window setup by gWidgets, click here. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2:::gdkColorToString throws an error
Hi and sorry for the late reply. The Gdk library is part of the GTK+ bundle (GTK+, Gdk and GdkPixbuf are distributed together and have synchronized versions). So you'll just need GTK+ 2.12 or higher. Michael On Tue, Oct 20, 2009 at 8:16 AM, Ronggui Huang ronggui.hu...@gmail.comwrote: Dear all, I try to use RGtk2:::gdkColorToString, but it throws an error: Error in .RGtkCall(S_gdk_color_to_string, object, PACKAGE = RGtk2) : gdk_color_to_string exists only in Gdk = 2.12.0 I know what it means, but don't know to solve this problem because I don't know where I can download the referred gdk library. Any information? Thank you. -- HUANG Ronggui, Wincent Doctoral Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Redblack tree data structure
Not sure of a RB tree available directly in R, but there's a nice public domain C implementation from the UCSC genome browser library. It's used by the IRanges Bioconductor package for implementing an interval tree. On Fri, Sep 4, 2009 at 9:14 AM, Rune Schjellerup Philosof rphilo...@health.sdu.dk wrote: I need to use a red-black tree, which package provides that data structure? -- Best regards Rune Schjellerup Philosof Ph.d-stipendiat, Forskningsenheden for Biostatistik Telefon: 6550 3607 E-mail: rphilo...@health.sdu.dk Adresse: J.B. Winsløwsvej 9, 5000 Odense C SYDDANSK UNIVERSITET ___ * Campusvej 55 * 5230 * Odense M * 6550 1000 * www.sdu.dk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I define the method for gcheckboxgroup in gWidgets?
On Thu, Jun 25, 2009 at 8:29 AM, Bryan Hanson han...@depauw.edu wrote: Hi All... I¹m trying to build a small demo using gWidgets which permits interactive scaling and selection among different things to plot. I can get the widgets for scaling to work just fine. I am using gcheckboxgroup to make the (possibly multiple) selections. However, I can¹t seem to figure out how to properly define the gcheckboxgroup; I can draw the widget properly, I think my handler would use the svalue right if it actually received it. Part of the problem is using the index of the possible values rather than the values themselves, but I'm pretty sure this is not all of the problem. I've been unable to find an example like this in any of the various resources I've come across. BTW, report.which is really only there for troubleshooting. It works to return the values, I can't get it to return the indices, which are probably what I need in this case. A demo script is at the bottom and the error is just below. tmp - gcheckboxgroup(stuff, handler = report.which, index = TRUE, + checked = c(TRUE, FALSE, FALSE, FALSE, FALSE), container = leftPanel) The above code should define the gcheckboxgroup. add(tmp, value = 1, expand = TRUE) I'm not sure what you are trying to add here. Error in function (classes, fdef, mtable) : unable to find an inherited method for function .add, for signature gCheckboxgroupRGtk, guiWidgetsToolkitRGtk2, numeric This error suggests that I don't have a method - I agree, but I don't know what goes into the method for gcheckboxgroup. For the sliders, it's clear to me how the actions and drawing of the widgets differ, but not so for gcheckboxgroup. A big TIA, Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA Full Script: x - 1:10 y1 - x y2 - x^2 y3 - x^0.5 y4 - y^3 df - as.data.frame(cbind(x, y1, y2, y3, y4)) stuff - c(y = x, y = x^2, y = x^0.5, y = x^3) which.y - 2 # inital value, to be changed later by the widget # Define a function for the widget handlers update.Plot - function(h,...) { plot(df[,1], df[,svalue(which.y)], type = l, ylim = c(0, svalue(yrange)), main = Interactive Selection Scaling, xlab = x values, ylab = y values) } report.which - function(h, ...) { print(svalue(h$obj), index = TRUE) } In the above handler, do you mean to pass the 'index' parameter to the svalue() function? # Define the actions type of widget, along with returned values. # Must be done before packing widgets. yrange - gslider(from = 0, to = max(y), by = 1.0, value = max(y), handler = update.Plot) which.y - gcheckboxgroup(stuff, handler = report.which, index = TRUE, checked = c(TRUE, FALSE, FALSE, FALSE, FALSE)) # Assemble the graphics window groups of containers mainWin - gwindow(Interactive Plotting) bigGroup - ggroup(cont = mainWin) leftPanel - ggroup(horizontal = FALSE, container = bigGroup) # Format and pack the widgets, link to their actions/type tmp - gframe(y range, container = leftPanel) add(tmp, yrange, expand = TRUE) tmp - gcheckboxgroup(stuff, handler = report.which, index = TRUE, checked = c(TRUE, FALSE, FALSE, FALSE, FALSE), container = leftPanel) add(tmp, value = 1, expand = TRUE) # Put it all together add(mainWin, ggraphics()) # puts the active graphic window w/i mainWin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programmatically copying a graphic to the clipboard
Possible using RGtk2. Just need to get it into a GdkPixbuf. See gtkClipboardSetImage(). To get a graphic as a pixbuf, you can use cairoDevice (drawing to a GdkPixmap and copying over), or output the graphic to a temporary file and read it back in. Michael On Fri, Jun 12, 2009 at 5:42 AM, Hadley Wickham had...@rice.edu wrote: Hi all, Is there a cross-platform way to do this? On the mac, I cando this by saving an eps file, and then using pbcopy. Is it possible on other platforms? Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Gtk objects disappears
I would recommend just running gtkMain(), so that GTK+ blocks R. Then you need your GUI to call gtkMainQuit() when it's time to kill R. On Fri, Jun 12, 2009 at 6:59 AM, Olivier Nuñez onu...@iberstat.es wrote: Dear John, I have a question. When I run a RGtk code in my terminal (without using the R GUI) R --vanilla EOF source(myRGtkcode.R) EOF the GTK objects do not remain on the screen. Until now, I bypass this problem using the following commands: require(tcltk) tkmessageBox(Press to exit) But it is not really satisfactory and the tcltk Box cannot be minimized (at least in Mac OSX). Any idea? Best regards. Olivier -- Olivier G. Nuñez Email: onu...@iberstat.es Tel : +34 663 03 69 09 Web: http://www.iberstat.es [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGtk2 help: Show list of column names from dataset and categorize as factor or numeric
On Thu, Jun 4, 2009 at 7:53 AM, Harsh singhal...@gmail.com wrote: Hi UseRs, I recently started working with the RGtk2 library. The documentation is comprehensive and I've tried learning from the examples in most Gtk tutorials (which have C code). This is a little problematic, but has helped quite a bit in getting me started. I would like to create a GUI for file selection, which then displays the column names from the selected file, and provides the user with checkboxes with each column name for the user to select. Two columns of check boxes (Factor Type, Numeric Type) and one column of names is what I would like to display. This would use what is known as a GtkTreeView widget. There is RGtkDataFrame object that will tie an R data frame directly to a GtkTreeView as its GtkTreeModel. See help(RGtkDataFrame). Using a GtkTreeView is pretty complicated, but powerful. Basically, you create your RGtkDataFrame from an R data.frame and pass it as the model to the gtkTreeView constructor. You then need to add columns to the tree view to map the data to the view. Your best bet is to check out the demos included with RGtk2, like editableCells and treeStore. Moreover, I am planning to create a GUI tool that would have tabs in a notebook layout, each tab providing a certain functionality, beginning from basic charting of data, and going on to applying regression models and such on the data. help(GtkNotebook) This requires extensive knowledge in components that RGtk2 provides which could be implemented for the task outlined above. I have looked at the omegahat.org examples, but would like to see examples for such simple tasks as to how one could create a drop down list of column names to choose for x axis and another drop down allowing the choice of y axis, etc. See help(GtkComboBox) and gtkComboBoxNewText(). Having made the choice to use RGtk2, I would appreciate if users could share their RGtk experience with me. I wrote a paper on RGtk2, but for some reason it has never been published. Probably time to write a book. Regards Harsh Singhal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GTK Tooltips under Linux
On Thu, May 28, 2009 at 7:35 PM, Ronggui Huang ronggui.hu...@gmail.comwrote: Dear all, I want to set tool-tips for a gtkButton. I use the following code which works under Windows. However, it doesn't work under Linux. Any hints? Thanks. Unfortunately, on platforms besides Windows, the event loop runs via an input handler connected to X11. If you're waiting for a tooltip to show up, there's obviously no input, so the event loop is not iterated. I think I could fix this by creating a separate thread that writes to a file descriptor connected to an input handler. I'll try to do that. Michael library(RGtk2) b-gtkButtonNewWithLabel(OK) gtkTooltips()$setTip(b,Memo for a Button.) gw - gtkWindow(show=F) gw$Add(b) gw$Show() sessionInfo() R version 2.8.0 Patched (2008-12-10 r47137) i686-pc-linux-gnu locale: LC_CTYPE=zh_CN.UTF-8;LC_NUMERIC=C;LC_TIME=zh_CN.UTF-8;LC_COLLATE=zh_CN.UTF-8;LC_MONETARY=C;LC_MESSAGES=C;LC_PAPER=zh_CN.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RGtk2_2.12.11RQDA_0.1-8 igraph_0.5.2-2 [4] gWidgetsRGtk2_0.0-51 gWidgets_0.0-35 RSQLite_0.7-1 [7] DBI_0.2-4 loaded via a namespace (and not attached): [1] tools_2.8.0 -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Interface R -- Processing
On Fri, May 29, 2009 at 3:47 AM, simon_mail...@quantentunnel.de wrote: Dear Group members I was wondering whether there is any interface to use processing ( www.processing.org) to visualize R analyses? Nothing direct, to my knowledge. As far as I know, Processing is a high-level language on top of drawing and user interface libraries. R is already a nice language for data analysis, so there have been many efforts to connect R to existing libraries for doing Processing-like things. Examples include iPlots, rggobi, RGtk2, and there are several systems currently under development. If so could somebody point me to relevant ressources? If not, are there any attempts to build such an interface / package? Best Regards, Simon -- Nur bis 31.05.: GMX FreeDSL Komplettanschluss mit DSL 6.000 Flatrate und Telefonanschluss nur 17,95 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Draw a rectangle on top of an image using RGtk2?
On Sat, May 23, 2009 at 8:27 AM, Ronggui Huang ronggui.hu...@gmail.comwrote: Thanks, Michael. Just one more follow-up question. Is there other way to get the GdkDrawable (here da2) without using - or other assignment operation from within expose_fn? I thought da$GetRootWindow() would work, but it does not. You need to be drawing the rectangle within expose_fn, otherwise it won't show up. There should be no need to access the GdkWindow (da2) of the drawing area outside of expose_fn. Michael da - gtkDrawingArea() da2 - NULL expose_fn - function(widget,event,...){ img - gdkPixbufNewFromFile(/media/wind/Pictures/kaehatu.jpg)$retval da2 -widget[[window]] gdkDrawPixbuf(da2, gc = NULL, pixbuf=img, event[[area]][[x]], event[[area]][[y]], event[[area]][[x]], event[[area]][[y]], event[[area]][[width]], event[[area]][[height]]) return(FALSE) } gSignalConnect(da,expose-event,expose_fn) w-gtkWindow(show=F) w$SetSizeRequest(400,300) w$Add(da) w$Show() dgc - gdkGCNew(da2) gdkGCSetLineAttributes(dgc, line.width=2, line.style=solid,round,round) gdkDrawRectangle(da2,dgc,FALSE,10,10,100,100) Ronggui 2009/5/23 Michael Lawrence mflaw...@fhcrc.org: On Fri, May 22, 2009 at 11:27 PM, Ronggui Huang ronggui.hu...@gmail.com wrote: Dear all, I use gtkImageFromFile to display an image. Then I want to do some gsignal to handle mouse event. I click the mouse and move a another position and release. I can get the position of the firs click and the release position, then I would to draw a rectangle to display the region I have selected. I need some hints on what functions should I look for. I tried to google but don't know how. The GtkImage widget is just for showing images. If you want to start doing interactive graphics, I'd suggest moving to the more general GtkDrawingArea widget and connecting to the expose-event signal. You can then use GdkPixbuf for loading and drawing the image onto the drawing area. And then draw a rectangle on top with gdkDrawRectangle(). See demos drawingArea and images. Michael Thanks. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Draw a rectangle on top of an image using RGtk2?
On Fri, May 22, 2009 at 11:27 PM, Ronggui Huang ronggui.hu...@gmail.comwrote: Dear all, I use gtkImageFromFile to display an image. Then I want to do some gsignal to handle mouse event. I click the mouse and move a another position and release. I can get the position of the firs click and the release position, then I would to draw a rectangle to display the region I have selected. I need some hints on what functions should I look for. I tried to google but don't know how. The GtkImage widget is just for showing images. If you want to start doing interactive graphics, I'd suggest moving to the more general GtkDrawingArea widget and connecting to the expose-event signal. You can then use GdkPixbuf for loading and drawing the image onto the drawing area. And then draw a rectangle on top with gdkDrawRectangle(). See demos drawingArea and images. Michael Thanks. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building GUI for custom R application
On Tue, Apr 14, 2009 at 1:23 AM, Harsh singhal...@gmail.com wrote: HI R users, I would appreciate information/examples/suggestions on building GUIs for R applications. I am currently working on a project that would require the following functionalities : 1) Display a window to the user. Provide a function to scan local drive and choose dataset file. 2) Display the column names for the user to choose the dependent variable and the independent variables. 3) Fit regression and display statistics. While researching the possibility of creating a GUI which would allow for the above mentioned computations, I came across: 1) rpanel: Simple Interactive Controls for R Functions Using the tcltk Package Found In: Journal of Statistical Software, January 2007, Volume 17, Issue 9. 2) Putting RGtk to Work, James Robison-Cox Found In:Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003),March 2022, Vienna, Austria ISSN 1609-395X http://www.ci.tuwien.ac.at/Conferences/DSC-2003/ Item 2 provides an example of creating a regression application with slider controls for a parameter in loess function used in the example application in that paper. For documentation on RGtk the author recommends reading the Gtk tutorial and documentation. I seem to have difficulty in making sense of the Gtk documentation since most of it is in C and documentation is available for use of Gtk with Perl and Python. I am not a C/Perl/Python programmer. RGtk2 is completely documented within the R help system, with all code examples converted to R code. There are also a couple dozen demos. For a simple GUI like the one above, try gWidgets. The pmg package implements a gWidgets GUI that includes functionality much like what you describe. Moreover, I am creating a Windows Application and is using RGtk2 the only way to create a GUI for an R application? Or should I use the the VB approach and create the GUI separately and call R scripts where required to do the back-end computation? Another approach (to make the visualization more rich and dynamic) is to use Adobe FLEX front end and communicate with R using the RSOAP library. There is very sparse documentation relevant to using RSOAP. I have not been able to find examples or tutorials using RSOAP. Any information in this regard will be highly appreciated. The Biocep project provides 'R for cloud computing' but unfortunately I have not been able to extract relevant 'juice' from their webpage. What i did get is their R workbench, but that has not answered my above mentioned queries. Regards, Harsh Singhal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mature SOAP Interface for R
On Sat, Mar 28, 2009 at 6:08 PM, zubin binab...@bellsouth.net wrote: Hello, we are writing rich internet user interfaces and like to call R for some of the computational needs on the data, as well as some creation of image files. Our objects communicate via the SOAP interface. We have been researching the various packages to expose R as a SOAP service. No current CRAN SOAP packages however. Found 3 to date: RSOAP (http://sourceforge.net/projects/rsoap/) SSOAP http://www.omegahat.org/SSOAP/ looks like a commercial version? http://random-technologies-llc.com/products/rsoap Does anyone have experience with these 3 and can recommend the most 'mature' R - SOAP interface package? Well, SSOAP is (the last time I checked) just a SOAP client. rsoap (if we're talking about the same package) is actually a python SOAP server that communicates to R via rpy. You might want to check out the RWebServices package in Bioconductor. I think it uses Java for its SOAP handling. Michael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Chromatogram deconvolution and peak matching
Just to be sure you're aware, there are packages for chromatograpy and mass spec data in Bioconductor. Like xcms. Don't think any will directly address your problem, but they might be useful. Michael On Tue, Feb 17, 2009 at 5:44 AM, bartjoosen bartjoo...@hotmail.com wrote: Hi, I'm trying to match peaks between chromatographic runs. I'm able to match peaks when they are chromatographed with the same method, but not when there are different methods are used and spectra comes in to play. While searching I found the ALS package which should be usefull for my application, but I couldn't figure it out. I made some dummy chroms with R, which mimic my actual datasets, to play with, but after looking at the manuals of ALS, I'm affraid I can't get the job done. Can someone put me on the right way? Here is my code to generate the dummy chroms, which also plots the 2 chroms and the spectra of the 3 peaks: #2D chromatogram generation par(mfrow=c(3,1)) time - seq(0,20,by=0.05) f - function(x,rt) dnorm((x-rt),mean=0,sd=rt/35) c1 - f(time,6.1) c2 - f(time,5.6) c3 - f(time,15) plot(c1+c2+c3~time,type=l,main=chrom1) #spectrum generation spectra - function(x,a,b,c,d,e) a + b*(x-e) + c*((x-e)^2) + d*((x-e)^3) x - 220:300 s1 - spectra(x,(-194.2),2.386,(-0.009617),(1.275e-05),0) s2 - spectra(x,(-1.054e02),1.3,(-5.239e-03),(6.927e-06),-20) s3 - spectra(x,(-194.2),2.386,(-0.009617),(1.275e-05),20) chrom1.tot - data.frame(time,outer(c1,s1,*)+outer(c2,s2,*)+outer(c2,s2,*)) names(chrom.tot)[-1] - x #generation of chromatogram 2 c1 - f(time,2.1) c2 - f(time,4) c3 - f(time,8) plot(c1+c2+c3~time,type=l,main=chrom2) chrom2.tot - data.frame(time,outer(c1,s1,*)+outer(c2,s2,*)+outer(c2,s2,*)) names(chrom.tot)[-1] - x plot(s1~x,type=l,main=spectra) lines(s2~x,col=2) lines(s3~x,col=3) Thanks for your time Kind Regards Bart -- View this message in context: http://www.nabble.com/Chromatogram-deconvolution-and-peak-matching-tp22057592p22057592.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggobi install
On Thu, Feb 12, 2009 at 3:41 PM, Michael Bibo michael_b...@health.qld.gov.au wrote: Mark Ungrin mark.ungrin at utoronto.ca writes: * Installing *source* package 'RGtk2' ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for LIBGLADE... no configure: WARNING: libglade not found checking for INTROSPECTION... no checking for GTK... no configure: error: GTK version 2.8.0 required ERROR: configuration failed for package 'RGtk2' ** Removing '/home/mark/R/i486-pc-linux-gnu-library/2.6/RGtk2' * Installing *source* package 'rggobi' ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GGOBI... configure: error: Package requirements (ggobi = 2.1.6) were not met: Package gtk+-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing `gtk+-2.0.pc' to the PKG_CONFIG_PATH environment variable Package 'gtk+-2.0', required by 'libggobi', not found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. Alternatively, you may set the environment variables GGOBI_CFLAGS and GGOBI_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details. Mark, The first thing I would look at is whether there are any *-dev packages in synaptic for the libraries etc that are 'missing'. These -dev packages contain the header files and are not necessary for running the application, but are necessary for installing other apps from source that interact with them. This is a surprisingly little-advertised issue with Linux packaging that I found out about from the R installation manual. Just to be a bit more specific, for building RGtk2 and rggobi you'll need gtk-dev(el?) and libxml2-devel which should install all the other devel dependencies. It's kind of strange that the GGobi package installs its header files (it is implicitly a devel package), but it does not bring in the devel packages of its dependencies. But aren't there binary Ubuntu/Debian packages on the repository for RGtk2 and rggobi? Michael Bibo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] example of gladeXML - RGtk2
A good example of using glade with RGtk2 is the rattle package. See: http://rattle.togaware.com/ On Mon, Dec 8, 2008 at 8:15 AM, Cleber Nogueira Borges [EMAIL PROTECTED]wrote: hello all, where I find a example or tutorial of RGtk2 package? I would like to know about the gladeXML functions in R. thanks in advance Cleber Borges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] gWidgets install
On Tue, Oct 14, 2008 at 7:15 PM, john verzani [EMAIL PROTECTED] wrote: Tim Smith tim_smith_666 at yahoo.com writes: Thanks Charlie - I just tried it, but still get the same error: --- install.packages(gWidgets,dependencies=TRUE) ... library(gWidgets) Error in fun(...) : *** gWidgets requires a toolkit implementation to be installed, for instance gWidgetsRGtk2, gWidgetstcltk, or gWidgetsrJava*** Try installing gWidgetstcltk. That will allow you to use gWidgets with the tcltk package. Although the RGtk2 package works better with gWidgets, the tcltk one will require no extra software to install under windows. Perhaps the gWidgets package should prompt the user to install one of these? --John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating GUIs for R
On Sun, Oct 12, 2008 at 4:50 PM, Dirk Eddelbuettel [EMAIL PROTECTED] wrote: On 12 October 2008 at 12:53, cls59 wrote: | On a related note... does anyone know good resources for binding a C++ | program to the R library? RCpp, at http://rcpp.r-forge.r-project.org, formerly known as RCppTemplate, is pretty mature and testing having been around since 2004 or 2005. Introductory documentation could be better, feedback welcome. | Basically, I would like to start with just a plain vanilla R session running | inside a Qt widget. Any suggestions? Isn't RKWard a Qt-based GUI for R? They probably have some reusable console code in there. Deepayan once did just that in a test application. I am not sure if that was ever made public. Cheers, Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Creating GUIs for R
On Tue, Oct 7, 2008 at 10:32 AM, Wade Wall [EMAIL PROTECTED] wrote: Sorry that my post wasn't very clear. What I am wanting to do is learn to build some simple GUIs for a limited number of functions. Basically, I am envisioning a screen with check boxes, a drop down menu etc. that users could select to run analyses on imported data. My guess is you'll get the best usability if you design a GUI specific for your task, rather than constraining yourself to the model of 1-1 mapping between R functions and dialogs. In that case, I highly recommend using gWidgets as your first shot at a GUI in R. I have worked with VB before, but it has been several years and I am not sure how it interfaces with R. On Tue, Oct 7, 2008 at 1:20 PM, Bert Gunter [EMAIL PROTECTED] wrote: Seek and ye shall find ... Check the RGUI's link on the other web page on CRAN. If you are on Windows, there is some simple built-in GUI functionality. ?winMenuAdd, ?select.list and the links therein will get you started there. Cheers, Bert Gunter -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Wade Wall Sent: Tuesday, October 07, 2008 9:56 AM To: [EMAIL PROTECTED] Subject: [R] Creating GUIs for R Hi all, I have looked around for help on creating GUIs for R, but haven't found anything. I would be interested in any advice or webpages that have information on the best language, tutorials etc. for creating simple GUIs. Mainly I want to do this as a heuristic exercise. Thanks for any help. Wade Wall [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] crashes while using Rattle (GTK+)
Just saw this one. This should be fixed in RGtk2 2.12.7 on CRAN. Thanks, Michael On Tue, Sep 30, 2008 at 12:03 AM, Tomislav Puða [EMAIL PROTECTED] wrote: Hi, I'm using R 2.7.2 for Windows.I have also installed gtk-dev-2.12.9 and rattle 2.3.65. When I work in rattle, I occasionally get these messages : GLib-WARNING (recurser) **: g_main_context_prepare() called recursively from within a source's check() or prepare() member. aborting or GLib-WARNING (recurser) **: g_main_context_prepare() called recursively from within a source's check() or prepare() member. aborting (Rgui.exe : 3580): GLib-WARNING **: g_main_context_prepare() called recursively from within a source's check() or prepare() member. and then R crashes. I tried to reinstall R, reinstall all packages (i have all dependent packages installed), I was looking on GTK+ pages and Google but I only found similar post without an answer. I think that problem lies in GTK. But I don't have any idea how to get the things working. Please help ! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] programming
Am I missing something or does that list not include Emacs/ESS? It's also missing TextMate (for the Mac people). There's probably a bunch more stuff for Eclipse than it mentions. Michael On Mon, Sep 1, 2008 at 6:17 PM, Gabor Grothendieck [EMAIL PROTECTED]wrote: Check out: http://www.sciviews.org/_rgui/projects/Editors.html On Mon, Sep 1, 2008 at 8:52 PM, Yuan Jian [EMAIL PROTECTED] wrote: Hi, I am looking for R editor. does anyone know good editor? which tells you syntax error and it has function to beautify format (insert TAB etc.). Yu [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Opening a web browser from R?
browseURL() On Fri, Aug 15, 2008 at 3:55 AM, [EMAIL PROTECTED] wrote: Hi, I was wondering if there's a way in R to open a web browser (such as Internet Explorer, or Firefox or whatever). I'm doing some analyses that have associated urls, and it would be nice to have the ability to directly open the relevant page from within R. I was looking at the help for 'url' and I can see I can probably access the information I need and display it in my own way, but can I somehow just open the given url with my web browser of choice? many thanks for any help, Jose -- Dr. Jose I. de las Heras Email: [EMAIL PROTECTED] The Wellcome Trust Centre for Cell BiologyPhone: +44 (0)131 6513374 Institute for Cell Molecular BiologyFax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Link to newest R GUI
On Mon, Aug 11, 2008 at 9:27 AM, [EMAIL PROTECTED] wrote: I have used Rattle ( R Analytical tool to learn easily )and R Commander and found them to be quite good. I don't use the command line interface because I find it too time consuming from other languages like SAS,SPSS. I am not sure on Vista compatibility though. Rattle should have no problems on Vista, especially with the latest GTK+ binaries from gladewin32.sf.net. A general comment though: learning the command line of R is probably worth the time investment, unless you have a very specific task in mind and there is an existing GUI that supports that task. The Rattle log file auto generates the code, so it can be of some initial help. For advanced stuff, it is best to learn command line. Also heres a link to SPSS to R guide at http://RforSASandSPSSusers.com Regards, Ajay www.decisionstats.com On 8/11/08, stephen sefick [EMAIL PROTECTED] wrote: you've a couple of options- maybe they will fit your needs maybe they won't. Look at the GUI page on CRAN http://www.sciviews.org/_rgui/ you could google this and find out on your own what may or may not suit your needs. Most everybody on this list uses the command line interface stephen sefick On Mon, Aug 11, 2008 at 11:47 AM, Charles R. Partridge [EMAIL PROTECTED] wrote: Greetings, Please forward Web links for the most recent R GUI and a list of add-ons that will run in the graphic interface. I need either the R GUI for (MS) Windows Vista, or a Web-based GUI that will run longitudinal models with covariates (e.g., multilevel modeling, latent growth curves, and ARIMA interrupted time-series). I believe that R's functions will meet nearly every program evaluator's needs. However, most consultants in my geographic region have no programming background, and instead have used (and have been trained to use) statistical programs with GUIs such as SPSS. Thanks in advance. Regards, Charles R. Partridge, Ph.D. C.H.I.P. Evaluation Consulting Columbus, Ohio USA [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] playwith package crashes on Mac
For some reason, cairoDevice has been crashing the Mac for a while. It has something to do with the rotation of text through Pango. That's all I've been able to determine. Kind of tough without access to a Mac... but it DID work once upon a time.. 2008/7/15 Felix Andrews [EMAIL PROTECTED]: Dear Professor Kubovy I do not have a Mac to test it on, but please try this: library(cairoDevice) Cairo() grid::grid.newpage() I expect that you will see a similar crash; if so, it would seem to be a problem with your GTK+ libraries. I have heard that you need to have Apple X11 installed (from MacOS system CDs?) for RGtk2 to work. But I am not sure whether that advice is still current. Hope that helps. Felix On Tue, Jul 15, 2008 at 10:40 PM, Michael Kubovy [EMAIL PROTECTED] wrote: Dear R-helpers, I tried the playwith packages for the first time, and it crashed R: require(playwith) Loading required package: playwith Loading required package: lattice Loading required package: grid Loading required package: gWidgets Loading required package: gWidgetsRGtk2 Loading required package: RGtk2 Loading required package: cairoDevice sessionInfo() R version 2.7.1 (2008-06-23) i386-apple-darwin8.10.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] playwith_0.9-3 cairoDevice_2.8 gWidgetsRGtk2_0.0-35 RGtk2_2.12.5-3 gWidgets_0.0-28 [6] lattice_0.17-10 loaded via a namespace (and not attached): [1] gridBase_0.4-3 tools_2.7.1 Making links in per-session dir ... done rownames(USArrests) - state.name playwith(plot(Assault ~ UrbanPop, data=USArrests, + xlab=Percent urban population, 1973, + ylab=Assault arrests (per 100,000), 1973)) *** caught bus error *** address 0xa8, cause 'non-existent physical address' Traceback: 1: .Call(L_newpage) 2: grid.newpage() 3: playNewPlot(playState) 4: playwith(plot(Assault ~ UrbanPop, data = USArrests, xlab = Percent urban population, 1973, ylab = Assault arrests (per 100,000), 1973)) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Selection: 3 *** caught segfault *** address 0x611912ca, cause 'memory not mapped' Traceback: 1: .Call(L_newpage) 2: grid.newpage() 3: playNewPlot(playState) 4: playwith(plot(Assault ~ UrbanPop, data = USArrests, xlab = Percent urban population, 1973, ylab = Assault arrests (per 100,000), 1973)) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 2 Mac OS details: System Version: Mac OS X 10.5.4 (9E17) Kernel Version: Darwin 9.4.0 _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/http://www.people.virginia.edu/%7Emk9y/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Felix Andrews / $B0BJ!N)(B PhD candidate Integrated Catchment Assessment and Management Centre The Fenner School of Environment and Society The Australian National University (Building 48A), ACT 0200 Beijing Bag, Locked Bag 40, Kingston ACT 2604 http://www.neurofractal.org/felix/ 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Alternative of Cairo
On Fri, Jun 27, 2008 at 12:05 AM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Hi All, I am a new member to R programming. Am generating some visuals by using Cairo library. But Cairo is not compatible with all compilers May I ask which compiler you are using? There are other vector graphics libraries, but they're mostly C++ rather than C... (Box plot,histogram and RNA degradation plots-I would prefer to use some libraries rather than R native functions).Can anyone suggest an alternative for this library. Thanks in Advance Gireesh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] longest common substring
See: http://www.omegahat.org/Rlibstree/ Binds R to libstree for suffix tree operations. Libstree is included with the package, so don't worry about building it separately. Michael On Tue, Jun 17, 2008 at 10:28 PM, Daren Tan [EMAIL PROTECTED] wrote: i need to compute the longest common substring of two strings, can R do that ? _ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Differential Equations
On Tue, Jun 17, 2008 at 6:25 PM, David Arnold [EMAIL PROTECTED] wrote: All, I've found odesolve and lsoda. Any other packages for differential equations? There's Rsundials, which gives you an algebraic ode solver. Any good tutorials on using R and solving differential and partial differential equations? D. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unexpected behaviour in reading genomic coordinate files of R-2.7.0
This is not really addressing your problem, but I thought you might want to know that the rtracklayer package in Bioconductor already supports parsing BED files, as well as GFF and WIG. It's main purpose is to load the tracks into genome browsers, like UCSC. Michael On Wed, May 28, 2008 at 1:11 AM, Margherita [EMAIL PROTECTED] wrote: Great R people, I have noticed a strange behaviour in read.delim() and friends in the R 2.7.0 version. I will describe you the problem and also the solution I already found, just to be sure it is an expected behaviour and also to tell people, who may experience the same difficulty, a way to overcome it. And also to see if it is a proper behaviour or maybe a correction is needed. Here is the problem: I have some genomic coordinates files (bed files, a standard format, for example) containing a column (Strand) in which there is either a + or a -. In R-2.6.2patched (and every past version I have used) I never had problems in reading them in, as for example: a - read.table(coords.bed, skip=1) disp(a) class data.frame dimensions are 38650 6 first rows: V1V2V3V4 V5 V6 1 chr1 100088396 100088446 seq1 0 + 2 chr1 100088764 100088814 seq2 0 - If I do exactly the same command on the same file in R-2.7.0 the result I obtain is: a - read.table(coords.bed, skip=1) disp(a) class data.frame dimensions are 38650 6 first rows: V1V2V3V4 V5 V6 1 chr1 100088396 100088446 seq1 0 0 2 chr1 100088764 100088814 seq2 0 0 and I completely loose the strand information, they are all zeros! I have also tried to put quotes around + and - in the file before reading it, to set in read.table() call stringsAsFactors=FALSE, to set encoding to a few different alternatives, but the result was always the same: they are all transformed in 0. Then I tried scan() and I saw it was reading the character + properly: scan(coords.bed, skip=1, nlines=1, what=ch) Read 6 items [1] chr1 100088396100088446.00 seq1 0 [6] + ...my conclusion is that the lone + or - are not taken as characters in the data frame creation step, they are taken as numeric but, being without numbers are all converted to 0. Is it correct if this behaviour happens also if they are surrounded by quotes? Anyway, my temporary solution (which works without the need of changing the files) is: a - read.table(coords.bed, skip=1, colClasses=c(character, numeric, numeric, character, numeric, character)) a[1:2,] V1V2V3V4 V5 V6 1 chr1 100088396 100088446 seq1 0 + 2 chr1 100088764 100088814 seq2 0 - Another way to avoid loosing strand information was to manually substitute an R to - and an F to + in the file before reading it in R. But it is much more cumbersome since the use of + and - is, for example, a standard format in bed files accepted and generated by the Genome Browser and other genome sites. Please let me know what do you think. Ps. I saw this first in the Fedora version (rpm automatically updated), but it is reproduced also in the Windows version. Thank you all people for your work and for making R the wonderful tool it is! Cheers, Margherita -- -- --- Margherita Mutarelli, PhD Seconda Universita' di Napoli Dipartimento di Patologia Generale via L. De Crecchio, 7 80138 Napoli - Italy Tel/Fax. +39.081.5665802 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] IDE
emacs + ess On Fri, May 23, 2008 at 8:54 AM, Alexandra Almeida [EMAIL PROTECTED] wrote: People, I'm a ubunto user and I used to write my scipts in Java Gui for R, but it is a very slow tool to run my scripts... Do you know some efficient IDE for R? Thank!!! Alexandra Almeida -- Alexandra R M de Almeida [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Alternatives to rJava and JRI
There's SJava, http://www.omegahat.org/RSJava. On Thu, May 22, 2008 at 12:50 PM, Munir, Danish [EMAIL PROTECTED] wrote: Has anyone come across any alternatives to rJava and JRI? Are they any good? Better perhaps? Please give your reasons. Thanks, Danish - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This message is intended only for the personal and confidential use of the designated recipient(s) named above. If you are not the intended recipient of this message you are hereby notified that any review, dissemination, distribution or copying of this message is strictly prohibited. This communication is for information purposes only and should not be regarded as an offer to sell or as a solicitation of an offer to buy any financial product, an official confirmation of any transaction, or as an official statement of Lehman Brothers. Email transmission cannot be guaranteed to be secure or error-free. Therefore, we do not represent that this information is complete or accurate and it should not be relied upon as such. All information is subject to change without notice. IRS Circular 230 Disclosure: Please be advised that any discussion of U.S. tax matters contained within this communication (including any attachments) is not intended or written to be used and cannot be used for the purpose of (i) avoiding U.S. tax related penalties or (ii) promoting, marketing or recommending to another party any transaction or matter addressed herein. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rggobi is crashing R-2.7.0
On Tue, May 6, 2008 at 11:11 PM, Mark Kimpel [EMAIL PROTECTED] wrote: Hard as it is for me to imagine, the ggobi windows stay open and functional while R (in emacs) has crashed in the background after throwing the error messages. As a perhaps naive Linux user, I thought that if a parent process crashed any processes it spawned would crash too. I guess not in this case. Well running it within Emacs may explain it. We actually aren't spawning a new GGobi process - just dynamically linking the GGobi library and starting it that way. Ubuntu currently is distributing graphviz 2.16.1 Do you have libgvc.so.3 on your system? Michael Thanks, Mark On Wed, May 7, 2008 at 12:14 AM, Michael Lawrence [EMAIL PROTECTED] wrote: On Tue, May 6, 2008 at 6:06 PM, Mark Kimpel [EMAIL PROTECTED] wrote: R crashed just after the warnings were issued, but ggobi kept running (if that makes sense). I am not sure if that makes sense; GGobi should exit when the R process does. I have Graphviz and Rgraphiz installed and use Rgraphviz regularly without a problem, so I'm not sure why it didn't load. Mark Which version of graphviz? I am not sure which version the Ubuntu binary expects, but this may be a binary compatibility issue. That said, I am not sure if the GraphLayout plugin is the reason for R crashing... On Tue, May 6, 2008 at 4:37 PM, Michael Lawrence [EMAIL PROTECTED] wrote: On Tue, May 6, 2008 at 10:32 AM, Mark Kimpel [EMAIL PROTECTED] wrote: I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive graph displays but R crashes. See my sessionInfo() and a short example below. Ggobi and rggobi installed without complaints. Mark sessionInfo() R version 2.7.0 Patched (2008-05-04 r45620) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rggobi_2.1.9 RGtk2_2.12.5-3 graph_1.18.0 loaded via a namespace (and not attached): [1] cluster_1.11.10 tools_2.7.0 a - matrix(rnorm(1000), nrow = 10) g - ggobi(a) ** (R:25146): CRITICAL **: Error on loading plugin library plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared object file: No such file or directory ** (R:25146): CRITICAL **: Error on loading plugin library plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared object file: No such file or directory ** (R:25146): CRITICAL **: can't locate required plugin routine addToToolsMenu in GraphLayout It's not clear to me - did R crash or did you just receive these warnings? These warnings are due to a missing graphviz, so the GraphLayout plugin fails to load. -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rggobi is crashing R-2.7.0
On Wed, May 7, 2008 at 11:40 AM, Mark Kimpel [EMAIL PROTECTED] wrote: Uninstalling and reinstalling ggobi via Synaptic solved the problem, at least for the demo data mtcars. Rotation works fine. No crashes on exit. Thanks for the good advice. I am pretty sure what Paul is referring to is the graphics device stuff. GGobi does not link against R anyway, so R would not be the problem here. The reason rebuilding GGobi fixed it, is that your GGobi binary was linked against an old version of graphviz. The new version broke binary compatibility, thus you needed to install a GGobi binary built against the new version. Mark On Wed, May 7, 2008 at 2:12 PM, Paul Johnson [EMAIL PROTECTED] wrote: On Tue, May 6, 2008 at 12:32 PM, Mark Kimpel [EMAIL PROTECTED] wrote: I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive graph displays but R crashes. See my sessionInfo() and a short example below. Ggobi and rggobi installed without complaints. Mark sessionInfo() R version 2.7.0 Patched (2008-05-04 r45620) x86_64-unknown-linux-gnu In the R 2.7 release notes, there is a comment about a change in the GUI libraries and it says that one must recompile everything that relies on R. If your R 2.7 was an upgrade, not a fresh install, it could explain why this is happening. If there's some old library or R package sitting around, it could account for this. The part that concerned me about the R release note is that they don't give a very clear guide on how far back in the toolchain we are supposed to go. Certainly, ggobi has to be rebuilt from scratch. But are any of the things on which ggobi depends needing recompliation as well. pj -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rggobi is crashing R-2.7.0
On Tue, May 6, 2008 at 10:32 AM, Mark Kimpel [EMAIL PROTECTED] wrote: I am running 64-bit Ubuntu 8.04 and when I invoke rggobi the interactive graph displays but R crashes. See my sessionInfo() and a short example below. Ggobi and rggobi installed without complaints. Mark sessionInfo() R version 2.7.0 Patched (2008-05-04 r45620) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rggobi_2.1.9 RGtk2_2.12.5-3 graph_1.18.0 loaded via a namespace (and not attached): [1] cluster_1.11.10 tools_2.7.0 a - matrix(rnorm(1000), nrow = 10) g - ggobi(a) ** (R:25146): CRITICAL **: Error on loading plugin library plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared object file: No such file or directory ** (R:25146): CRITICAL **: Error on loading plugin library plugins/GraphLayout/plugin.la: libgvc.so.3: cannot open shared object file: No such file or directory ** (R:25146): CRITICAL **: can't locate required plugin routine addToToolsMenu in GraphLayout It's not clear to me - did R crash or did you just receive these warnings? These warnings are due to a missing graphviz, so the GraphLayout plugin fails to load. -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Annoying bug in package cairoDevice
Sorry about this. cairoDevice 2.8 (just uploaded to CRAN) should fix this problem. On Tue, Apr 29, 2008 at 1:08 PM, Josh Gilbert [EMAIL PROTECTED] wrote: I sent this to R-Help and the listed maintainer of cairoDevice, I hope that was the right thing to do. For some reason, Cairo_png puts a box around a figure when you call plot.new. It looks like box was called with black and a transparent background. Example: library(cairoDevice) Cairo_png('cairo.png') plot.new() dev.off() null device 1 The boarder is narrow, so it's hard to see with a stand-alone image viewer. If you paste the png onto a white background it's quite clear. Admittedly, the default for par(bg) is transparent, par(bty) is o and par(col) is black. However, this behavior is not consistent with other devices (such as png in grDevices even if I set par(bg=white)). Also, Cairo_png draws the box even when par(bty=n). I just tested this on Debian with version 2.6 of cairoDevice. I've also observed this behavior on Windows and it's not a new problem. The only workaround I've found is to call Cairo_png() par(col=white) setHook(plot.new, function() par(col=black)) plot(...) As far as I'm concerned, this is a serious bug, it's a real problem when creating figures for publication. I'd like confirmation that this is, in fact, a bug as I haven't seen much documentation for standards for devices. I suspect that it's a shallow bug, but I've never seen the code for plot.new nor do_Cairo so my suspicion may be more hope than insight. Josh Gilbert Statistical Researcher Broad Institute Chemical Biology Program [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] GUI developement / Matlab
On Fri, Feb 29, 2008 at 6:45 AM, Antje [EMAIL PROTECTED] wrote: Hi there, I was wondering whether there are flexible packages available with which you can create user interfaces? (I've read about gWidgets!?) gWidgets provides an easy to use API for developing GUIs in R. It's an abstraction over several actual toolkit bindings (tcl/tk, RGtk2, and rJava/Swing). The best supported implementation is based on RGtk2. Depending on the level of control and features you require, you might have to resort to direct use of RGtk2, which is a complete low-level binding to the GTK+ toolkit. For example in Matlab you can even create stand alone applications. Is it also possible for R in the same extend? Of course it should be platform independent if possible... tcl/tk, GTK+, and Swing are all cross-platform toolkits used for developing stand-alone applications. Developing your GUI in gWidgets will allow the user to choose among those three. But for a true stand-alone application (without running R directly) you'll probably want to develop the application and its GUI in another language and then delegate to the R library for certain tasks. And then I would like to know from people who know R as well as Matlab. What would you see as advantages and disadvantages comparing both systems (from your personal needs). I've learned a little bit of R and I like the concept but I don't know much about Matlab. (I hope this question is not too off topic?) Thank you! Antje __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RGTK2 and glade on Windows - GUI newbie
That would be a good idea. I'm finishing up a much more comprehensive guide that will become available soon. Thanks for the suggestion, Michael 2008/2/14 Felix Andrews [EMAIL PROTECTED]: I just discovered a good introduction to the RGtk2 package: RShowDoc(overview2, package=RGtk2) I have been using RGtk2 for over a year without knowing about that, and struggling with the API documentation, so can I suggest that it be mentioned somewhere prominent? i.e. put it on the project web-page, and make it a vignette so that it appears on the CRAN package page. Cheers, Felix 2008/2/11 Felix Andrews [EMAIL PROTECTED]: Yes, a GUI based on GTK+ (with or without Glade) will work on Windows XP. If what you want to do is relatively straightforward (say, without any fancy formatting, or advanced event handling) then you should consider gWidgets. Look at the vignette in the gWidgets package. If you do decide to go with RGtk2 directly rather than gWidgets, look at demo(package=RGtk2). If you are using Glade, you might want to look at the source code for Rattle, which is a GUI built with Glade: see http://rattle.googlecode.com/ and http://datamining.togaware.com/survivor/Installation_Details.html (Another example is hydrosanity: http://hydrosanity.googlecode.com/) By the way, there is a special mailing list for GUI issues: https://stat.ethz.ch/mailman/listinfo/r-sig-gui Felix On Mon, Feb 11, 2008 at 9:52 PM, Anja Kraft [EMAIL PROTECTED] wrote: Hallo, I'd like to write a GUI (first choice with GTK+). I've surfed through the R- an Omegahat-Pages, because I'd like to use RGTK2, GTK 2.10.11 in combination with glade on Windows XP (perhaps later Unix, Mac). I've found a lot of different information. Because of the information I'm not sure, if this combination is running on Windows XP and I'm unsure how it works. Is there anyone, who has experience with this combination (if it works) and could tell me, where I could find something like a tutorial, how this combination is used together and how it works? Thank you very much, Anja Kraft __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Felix Andrews / $B0BJ!N)(B PhD candidate Integrated Catchment Assessment and Management Centre The Fenner School of Environment and Society The Australian National University (Building 48A), ACT 0200 Beijing Bag, Locked Bag 40, Kingston ACT 2604 http://www.neurofractal.org/felix/ 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 -- Felix Andrews / $B0BJ!N)(B PhD candidate Integrated Catchment Assessment and Management Centre The Fenner School of Environment and Society The Australian National University (Building 48A), ACT 0200 Beijing Bag, Locked Bag 40, Kingston ACT 2604 http://www.neurofractal.org/felix/ 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] gWidgets process management
On Feb 12, 2008 1:51 PM, Peter McMahan [EMAIL PROTECTED] wrote: Thanks, that's very helpful. Unfortunately Gtk2 is difficult to get running on a Mac, so I've been trying the gWidgetstcktk interface. It sounds like the behavior you're describing is exactly what I want, so it may just be a difference in the TGtk2 and tcltk event loops? In your example, can you think of a way to have a cancel button that would be able to kill reallySlowFunction() early? for the time being, I guess I'll just work on getting the gtk28 package from macports working... There are GTK+ binaries available that should work with the RGtk2 CRAN binary for the Mac. http://r.research.att.com/gtk2-runtime.dmg Thanks, Peter On Feb 12, 2008, at 1:31 PM, John Verzani wrote: Dear Peter, I think this issue has more to do with the event loop than gWidgets. I've cc'ed Michael Lawrence, who may be able to shed more light on this. Perhaps gIdleAdd from RGtk2 can work around this, but I didn't get anywhere. My understanding is that the event loop is preventing the console from being interactive, but not GTK events. So for instance, the GUI in the following example is responsive, during the execution, but the command line is not. library(gWidgets) options(guiToolkit=RGtk2) reallySlowFunction = function(n=20) { for(i in 1:n) { cat(z) Sys.sleep(1) } cat(\n) } w - gwindow(test) g - ggroup(cont=w, horizontal=FALSE) b - gbutton(click me, cont=g,handler = function(h,...) reallySlowFunction()) r - gradio(1:3, cont=g, handler = function(h,...) print(svalue(h $obj))) ## you can click the radio button and get a response, but not the console --John Hello, I'm trying to make a graphical interface for an R function I've written. A common use for the function is to call it with specific parameters, and then watch the output as it evolves. There's not necessarily a logical stopping point, so I usually use ctrl-C when I'm done to stop it. I've made a gWidgets interface to the function that gets some user info and then on a button click calls the function. The gWidgets window, however, seems to be frozen as long as the function is running, and the function output seems to be happening in the background in my R session, so ctrl-C (esc on the Mac GUI) does not work to stop it. I have to kill R entirely to stop the process. So after all that setup here is my question: Is there some way to have a gWidgets window interrupt a function that it has called via a widget handler? Thanks, Peter -- John Verzani CUNY/CSI Department of Mathematics [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need suggestions about GUI
On Jan 22, 2008 6:41 AM, ronggui [EMAIL PROTECTED] wrote: Thanks, John, Here is some code to show what I want to do. BTW, it seems there is a bug in svalue in gWidgetstcltk for gtext when using the drop=T argument. getsel - function(obj, toolkit, ...) { ### get the selected text from gtext getWidget - gWidgetstcltk:::getWidget if(tclvalue(tktag.ranges(getWidget(obj),sel)) != ) ### notice ### gWidgetstcltk's _svalue(drop=T)_ has bug. should add tclvalue to the above line. {val = tclvalue(tkget(getWidget(obj),sel.first,sel.last))} else val =#tclvalue(tkget(getWidget(obj),0.0,end)) val = unlist(strsplit(val,\n)) return(val) } get_index - function(obj, toolkit, ...) { ### get the selected text from gtext, return the index instead of text. getWidget - gWidgetstcltk:::getWidget if(tclvalue(tktag.ranges(getWidget(obj),sel)) != ){ val = strsplit(tclvalue(tktag.ranges(getWidget(obj), sel)), )[[1]]} else val =c(0,0) return(as.numeric(val)) } require(gWidgets) #initial parameters, storing the relavant information freecodes - c(node1,node2) n_coding - 0 node - character(1) chunk - character(1) begin - numeric(1) end - numeric(1) imported_file - readLines(file.path(R.home(),COPYING)) codepanel - gpanedgroup(container=gwindow(Code bar), horizontal = FALSE) addcode = gdroplist(freecodes,0,container=codepanel,editable=TRUE) addcodebutton - gbutton(Add new code,container=codepanel,handler=function(...) { if(svalue(addcode)!=) addcode[length(addcode)+1]-svalue(addcode) } ) ## allow the user to change the extant codes -- related to freecodes parameter updatecodes - gbutton(Update Codes,container=codepanel,handler=function(...) assign(freecodes,addcode[seq_len(length(addcode))],pos=1)) ## get the items in gdroplist, and push it to variable freecodes coding - gbutton( Coding ,container=codepanel,handler= function(...){ if (svalue(addcode)!= sel!=){ sel - paste(getsel(ed),collapse=\n) sel_index - get_index(ed) n_coding - n_coding + 1 node[n_coding] - svalue(addcode) chunk[n_coding] - sel begin[n_coding] - sel_index[1] end[n_coding] - sel_index[2] }} ) ## coding: get seleted text from gtext and link it to specific code/node. ed - gtext(con=T,width=500) # gtext svalue(ed) - imported_file # push it file to gtext # steps to using this toy: 1, enter new code names into the droplist box, for example node3, then click add new code 2, select specific code, for example node2. 3, select text chunk in the gtext, and click coding. repeat step 3 in coding process. 4, We can see what's been coded by inpecting variable of node,chunk. What I don't know how to do: 1, When I select specific code, and click some button (for example highligh), all the text chunk related to that code will be highlighted (through color or font style etc.) John might correct me, but I don't think that gWidgets supports this level of markup. You might try using tcltk or RGtk2 directly (eg the GtkTextView and GtkTextBuffer classes). It would be easy to get the index of a selection in the buffer. See the function gtkTextBufferGetSelectionBounds() in RGtk2. 2, I would like to arganize the codes like a tree. The code tree and reorganized by drag and drop. 3, In the coding buttong, how can I avoid using - in handler function. 2008/1/22, j verzani [EMAIL PROTECTED]: ronggui ronggui.huang at gmail.com writes: Thanks. gWidgets is quite good. However, I want to get the selection text chunk as well as the index, but the index arguments does not work for gtext. obj-gtext(cont=T) svalue(obj,drop=T) [1] cde svalue(obj,drop=T,index=T) [1] cde The svalue method has the index argument for the widgets where you might want to return the index or value such with a radio button group or combobox. For gtext, the drop argument when TRUE returns just the text selected by the mouse, otherwise the entire text buffer is returned. library(gWidgets) options(guiToolkit=RGtk2) obj = gtext(sadfsad,cont=T) svalue(obj) ## returns: sadfsad\n svalue(obj,drop=TRUE) ## returns ## now highlight some text svalue(obj,drop=TRUE) ## returns dfsa If you want to email me a bit more detail as to what you are trying to do, I can let you know if gWidgets can work for you. --John 2008/1/21, Gabor Grothendieck ggrothendieck at gmail.com: You can find examples of using tcltk here: http://www.sciviews.org/_rgui/tcltk/ Also the gwidgets package is a toolkit independent layer that can run on top of tcltk or RGtk and it is described with many examples here: http://wiener.math.csi.cuny.edu/pmg/gWidgets On Jan 21, 2008 4:02 AM, ronggui ronggui.huang at gmail.com wrote: What I want to do is: 1, creat a text box, insert
Re: [R] Graphics device storable in a variable
This is possible using the cairoDevice package and RGtk2. Turning an R graphic into a raw vector of bytes: library(cairoDevice) library(RGtk2) # create a pixmap and tell cairoDevice to draw to it pixmap - gdkPixmapNew(w=500, h=500, depth=24) asCairoDevice(pixmap) # make a dummy plot plot(1:10) # convert the pixmap to a pixbuf plot_pixbuf - gdkPixbufGetFromDrawable(NULL, pixmap, pixmap$getColormap(), 0, 0, 0, 0, 500, 500) # save the pixbuf to a raw vector buffer - gdkPixbufSaveToBufferv(plot_pixbuf, jpeg, character(0), character(0))$buffer ### Then you can send buffer to your database, or whatever. Replacing jpeg with png will probably produce png output. Michael On Nov 15, 2007 3:32 PM, Greg Snow [EMAIL PROTECTED] wrote: You might try looking at the tkrplot package, it uses win.metafile and captures the graphics device into a variable (which is then put into a tk lable, but you could probably do something else with it). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Josh Tolley Sent: Thursday, November 15, 2007 2:08 PM To: r-help@r-project.org Subject: [R] Graphics device storable in a variable I'm using R embedded in PostgreSQL (via PL/R), and would like to use it to create images. It works fine, except that I have to create every image in a file (owned by and only readable by the PostgreSQL server), and then use PostgreSQL to read from that file and return it to the client. It would be much nicer if I could plot images into an R variable (for instance, a matrix), and return that variable through the PostgreSQL client. Leaving aside the details of returning the data to PostgreSQL (which I realize are beyond the scope of this list), I envision R code along the lines of the following: # Create a png device, a handle to which is stored in myDevice myDevice - png.variable(height = 1280, width = 1024, bg = white) # Plot some data into the current device plot(myX, myY, col=red) # Finalize dev.off() # Print out the contents of myDevice myDevice ...and the data would print out just like any other matrix or class or whatever type myDevice actually is. So my question is does such a thing already exist? I know about piximage, but apparently I have to load image data from somewhere for it to work; I can't use plot(), etc. to create the piximage data. GDD would be a nice way to do it, because GD libraries are widely available for use with other languages I might use with PostgreSQL and PL/R (for instance, Perl would talk to PostgreSQL, call a PL/R function to use R to return an image, which Perl would then process further), but GDD requires temporary files as well, as far as I can see. Thanks for any help anyone can offer. -Josh / eggyknap __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] jEdit for R
On 10/26/07, John Thaden [EMAIL PROTECTED] wrote: Michael, Where can we read you document that includes various ideas going far beyond simply embedding R? What about Julian's opinion that Tinn-R is more stable and loads more quickly than jEdit? Can that be true in a Windows environment? Tinn-R probably loads faster, since it doesn't have the overhead of Java. As far as stability, I haven't used Tinn-R enough to compare. I use jEdit for my daily work, all day long, for the past 6 years, and I can't remember it ever crashing on me. -John Thaden On Thu, 25 Oct 2007 07:25:12, Michael Lawrence wrote: I think a better idea would be to make a jEdit plugin that embeds an R console component (perhaps the one from JGR, but the last I checked it was not embeddable, unfortunately). Anyway, it would be easy enough to roll your own by extending the existing jEdit Console plugin using JRI. I would have done that ages ago, but I'm still hoping that JGR could be leveraged in some way. In my opinion, jEdit has a very clean design (at both the UI and the API level) as do several of the important plugins (ie Console). One can actually run R inside the jEdit console, but it does not echo your commands, which hinders its usability. I haven't used Tinn-R much since it is not cross-platform. Also, I prefer to use the same editor for all my work, beyond R, and I'm not sure if Tinn-R would be up to that task (but as I've said I haven't used it much). If anyone wants to work with me on providing an R support plugin for jEdit, I'd be open to starting the project. I've already written a document with various ideas, which goes far beyond simply embedding R. The editor-centric mode of using R is obviously very popular and useful, but, at least in my opinion, no editor does a great job at it on all platforms. Michael On 10/24/07, Julian Burgos [EMAIL PROTECTED] wrote: Hi Rob, I used jEdit, but I'm not sure if there is a 'ctrl-R' option available. I eventually switched to Tinn-R, which is an editor customized for R (although it can be used for other languages) and does provide the connection to R you are looking for. Also (I think) loads faster and it is more stable than jEdit. Julian threshold wrote: Hi, I just installed jEdit but have no clue, whether I can run my code a'la ctrl-R directly from jEdit script, or should source it from R command line, after saving it first in jEdit. thanks for any help, rob [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD build not excluding .svn
Thanks for the help. I looked into it further and noticed that the src/RGtk2 directory was actually a symlink. The perl find() does not follow symlinks, as invoked, but tar, as invoked, does. Thus, when the tar/untar effectively copies the files, there is a mismatch with the exclude paths. Is there some reason why the exclude paths cannot be calculated on the untar'd version rather than the original package directory? If this sounds reasonable, I'll submit a patch. Thanks, Michael On 10/1/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: It does this via an exclude list which it uses to remove files from a staged build. Printing out the exclude list (at ca line 232) should be informative. One possibility is simply that there is a permissions issue in deleting that directory. On Sun, 30 Sep 2007, Michael Lawrence wrote: Hi, In my package RGtk2, there's a directory called 'src/RGtk2' that contains, like all the other directories in the package, a '.svn' directory. It seems that R CMD build is somehow missing that one '.svn' in 'src/RGtk2', even though it excludes all the other instances of '.svn'. I've tried putting 'src/RGtk2/.svn' into the .Rbuildignore, but it does not have any effect. I've also looked into the R CMD build script, but I can't find where this problem might occur (but then again, perl is not exactly my thing). Perhaps it has something to do with having a directory with the same name as the package under the 'src' directory? Pretty unlikely. Thanks for the help, Michael [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R CMD build not excluding .svn
Hi, In my package RGtk2, there's a directory called 'src/RGtk2' that contains, like all the other directories in the package, a '.svn' directory. It seems that R CMD build is somehow missing that one '.svn' in 'src/RGtk2', even though it excludes all the other instances of '.svn'. I've tried putting 'src/RGtk2/.svn' into the .Rbuildignore, but it does not have any effect. I've also looked into the R CMD build script, but I can't find where this problem might occur (but then again, perl is not exactly my thing). Perhaps it has something to do with having a directory with the same name as the package under the 'src' directory? Thanks for the help, Michael [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cairo on windows
On 9/27/07, Moisan Yves [EMAIL PROTECTED] wrote: My experience is that cairoDevice is a lot slower than Cairo, especially on Windows, and about equally flaky. If you see how many layers are involved with Cairo on Windows you will not be surprised. Actually, I ended up trying to load deviceCairo simply because it was the only other package with the string Cairo in it besides Cairo itself ;-). I suspected some interaction between the two libraries (deviceCairo and Cairo) so that's why I tried to load it hoping it would solve the flakiness of the CairoWin display. My guess is the problem is due to an older version of GTK+. Although cairoDevice only requires GTK+ 2.8.x (which is probably what you have installed), the Windows binary of cairoDevice on CRAN is probably built against GTK+ 2.10.x, just like RGtk2. I've added a feature to cairoDevice and RGtk2 recently that will automatically try to install the latest binary of GTK+ on Mac and Windows when loading the library fails. That said, I'd really like to merge cairoDevice (specifically the RGtk2-embedding feature) with the Cairo package. Having one less package to maintain would be nice. If all you need is semi-transparency support I suggest you try R 2.6.0 RC which supports it in the windows() device. Thanx for the tip. Yves Moisan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.