Re: [Rd] unable to load shared library: undefined symbol
This is nothing to do with R: you need to seek help from whoever you are 'wroking' for. You don't have any libraries on your link command, but you do have include directories: please get your supervisor to explain how linking works and what to do to link against 'symphony'. (Are you confusing -L and -l?) On Fri, 20 Jul 2007, Ctagz wrote: > > Hi all, > > I'm a summer University research student and I've been wroking on writing a > package, Rsoam, to integrate R with Platform's symphony software to allow > for distributed computing. When I "R CMD check" the package, I get the > following error when trying to load the Rsoam.so after building Rsoam.cpp: > > * checking whether the package can be loaded ... ERROR > Loading required package: snow > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library '/root/Rsoam.Rcheck/Rsoam/libs/Rsoam.so': > /root/Rsoam.Rcheck/Rsoam/libs/Rsoam.so: undefined symbol: > _ZTIN4soam13SoamExceptionE > Error in library(Rsoam) : .First.lib failed for 'Rsoam' > Error in dyn.unload(x) : dynamic/shared library > '/root/Rsoam.Rcheck/Rsoam/libs/Rsoam.so' was not loaded > >My Makevars file consists of: > > PKG_CPPFLAGS = -I/opt/symphonyDE/3.1/src -I/opt/symphonyDE/3.1/include > -DGCC34 -Wall -DLINUX -Wno-deprecated > PKG_LIBS = -L/opt/symphonyDE/3.1/src -L/opt/symphonyDE/3.1/include > -L/opt/symphonyDE/3.1/linux2.6-glibc2.3-x86/lib -LsampleCommon -Lsoambase > -Lsoamapi > >and 00install.out has the following g++ build: > > g++ -I/usr/lib/R/include -I/usr/lib/R/include -I/opt/symphonyDE/3.1/src > -I/opt/symphonyDE/3.1/include -DGCC34 -Wall -DLINUX -Wno-deprecated > -I/usr/local/include-fpic -O2 -g -c Rsoam9.cpp -o Rsoam9.o > g++ -shared -Wl,-O1 -o Rsoam.so Rsoam9.o -L/opt/symphonyDE/3.1/src > -L/opt/symphonyDE/3.1/include > -L/opt/symphonyDE/3.1/linux2.6-glibc2.3-x86/lib -LsampleCommon -Lsoambase > -Lsoamapi -L/usr/lib/R/lib -lR > > I thought I'd written the Makevars to a sufficient degree, but I guess that > may not actually be the case. I understand that you guys are probably not > familiar with symphony, but I was hoping if someone could tell me what slips > through when I'm building this shared library? > > -Jon > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] triax.points() from package plotrix
Dear developers from package plotrix,
the function triax.points() from package plotrix does not draw any
points, because of internal setting in triax.points() {points(...,
type="l")}.
I add a new option in triax.points()
point.type = "l",
So the user can choose which type of points should be drawn.
May be other users already found this defect.
best whishes
Andreas Plank
--- 8< ###
triax.points <- function (x,
show.legend = FALSE,
label.points = FALSE,
point.labels = NULL,
col.symbols = par("fg"),
pch = par("pch"),
bg.symbols = par("bg"),
cc.axes = FALSE,
point.type = "l", # new add
...
)
{
if (dev.cur() == 1)
stop("Cannot add points unless the triax.frame has been drawn")
if (missing(x))
stop("Usage: triax.points(x,...)\n\twhere x is a 3 column array
of proportions or percentages")
if (!is.matrix(x) && !is.data.frame(x))
stop("x must be a matrix or data frame with at least 3 columns
and one row.")
if (any(x > 1) || any(x < 0)) {
if (any(x < 0))
stop("All proportions must be between zero and one.")
if (any(x > 100))
stop("All percentages must be between zero and 100.")
x <- x/100
}
if (any(abs(rowSums(x) - 1) > 0.01))
warning("At least one set of proportions does not equal one.")
sin60 <- sin(pi/3)
if (cc.axes) {
ypos <- x[, 3] * sin60
xpos <- x[, 1] + x[, 3] * 0.5
}
else {
ypos <- x[, 3] * sin60
xpos <- 1 - (x[, 1] + x[, 3] * 0.5)
}
nobs <- dim(x)[1]
if (is.null(point.labels))
point.labels <- rownames(x)
if (label.points)
thigmophobe.labels(xpos, ypos, point.labels)
if (show.legend) {
legend(0.16 - 0.02 * max(nchar(point.labels)), 0.75 +
0.04 * length(point.labels), legend = point.labels,
pch = pch, col = col.symbols)
}
points(x = xpos, y = ypos, pch = pch, col = col.symbols,
bg = bg.symbols, type = point.type, ...)
invisible(list(x = xpos, y = ypos))
}
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[Rd] Bug in dev.print ? (PR#9801)
Ladies and Gentlemen,
the following piece of code causes an annoying error:
> aa <- structure(list(BG = c(24, 16, 61, 30, 37, 33, 13, 4, -34,
+ 10, 33, 41, 6, 32, 39, 37, 36, -17, 60, 35, 22, 21, 29, 52,
+ 41, 62, -26, 30, -33, 27, 34, 28, 36, 29, -12, 38, 34, 32,
+ 40, 36, 39, 31, 19, 55, 28, 40, 38, 39, -31, 64, -22, 41,
+ 37, -33, 18, 31, 1, -33, 28, 36, -22), Kont = c(4, 7, 3,
+ 4, 6, 3, 4, 7, 7, 7, 2, 3, 4, 3, 3, 6, 3, 2, 6, 6, 4, 3,
+ 3, 4, 6, 4, 2, 1, 2, 4, 6, 6, 3, 4, 7, 6, 3, 6, 6, 6, 6,
+ 2, 7, 6, 4, 3, 6, 4, 5, 6, 7, 6, 3, 7, 7, 4, 4, 5, 6, 2,
+ 2), Jan = c(25, 31, -4, 15, 13, 12, 32, 20, 30, 30, 18, 1,
+ 30, 15, 8, 16, 7, 27, -3, 15, 20, 26, 18, -15, 8, -36, 25,
+ 19, 27, 18, 17, 21, 15, 9, 25, 14, 19, 19, 11, 17, 15, 18,
+ 21, -3, 19, 4, 14, 2, 32, 2, 29, 12, 13, 29, 30, 8, 30, 26,
+ 21, 15, 31), Feb = c(28, 31, -1, 16, 14, 14, 33, 19, 28,
+ 29, 18, 2, 32, 16, 7, 17, 8, 26, -3, 15, 21, 26, 20, -9,
+ 9, -29, 25, 21, 28, 21, 18, 21, 16, 10, 27, 16, 18, 18, 13,
+ 18, 15, 21, 23, -4, 24, 5, 15, 6, 30, 2, 30, 13, 15, 26,
+ 30, 11, 31, 28, 21, 17, 30), Mrz = c(30, 31, -1, 19, 17,
+ 19, 35, 19, 26, 30, 20, 9, 32, 21, 14, 19, 12, 27, 2, 18,
+ 23, 26, 23, 1, 12, -10, 24, 23, 27, 25, 20, 23, 23, 13, 26,
+ 18, 19, 20, 16, 19, 18, 24, 25, 3, 30, 9, 17, 12, 32, 4,
+ 30, 15, 17, 26, 30, 14, 32, 25, 23, 20, 29), Apr = c(35,
+ 31, 5, 21, 20, 23, 36, 19, 22, 30, 20, 16, 32, 25, 15, 21,
+ 14, 26, 9, 20, 26, 28, 26, 7, 16, 3, 22, 27, 24, 28, 22,
+ 23, 25, 16, 24, 20, 19, 20, 18, 22, 20, 24, 27, 12, 37, 14,
+ 20, 21, 25, 6, 29, 18, 17, 23, 30, 18, 32, 23, 23, 22, 26),
+ Mai = c(40, 32, 12, 27, 26, 26, 34, 19, 18, 31, 22, 21, 32,
+ 29, 22, 23, 22, 24, 16, 24, 30, 28, 30, 16, 22, 13, 19,
+ 32, 20, 27, 27, 24, 33, 20, 21, 22, 21, 21, 23, 25, 25,
+ 29, 26, 19, 40, 21, 24, 27, 23, 9, 26, 24, 20, 19, 31,
+ 24, 32, 20, 24, 28, 24), Jun = c(41, 32, 17, 33, 30,
+ 29, 34, 18, 16, 31, 25, 26, 31, 32, 27, 26, 28, 20, 20,
+ 27, 32, 29, 32, 23, 27, 21, 17, 35, 18, 29, 31, 26, 38,
+ 23, 18, 27, 22, 23, 31, 29, 29, 34, 25, 23, 39, 28, 28,
+ 30, 19, 12, 26, 28, 22, 15, 31, 27, 31, 17, 25, 32, 22),
+ Jul = c(42, 33, 19, 35, 33, 30, 34, 18, 14, 32, 26, 29, 31,
+ 36, 32, 29, 28, 21, 24, 30, 33, 30, 34, 23, 30, 26, 17,
+ 35, 18, 28, 33, 27, 39, 22, 19, 29, 25, 25, 34, 32, 32,
+ 37, 24, 25, 36, 29, 30, 32, 18, 14, 25, 29, 22, 15, 32,
+ 32, 31, 17, 28, 34, 21), Aug = c(43, 33, 17, 35, 33,
+ 31, 34, 18, 16, 32, 27, 28, 30, 35, 30, 29, 26, 23, 21,
+ 30, 32, 31, 34, 20, 29, 21, 20, 35, 18, 28, 33, 28, 39,
+ 21, 18, 30, 25, 26, 33, 31, 32, 37, 24, 22, 34, 29, 29,
+ 31, 19, 14, 26, 29, 22, 17, 32, 31, 31, 19, 28, 34, 24),
+ Sep = c(43, 33, 13, 32, 29, 28, 33, 18, 19, 33, 26, 25, 31,
+ 32, 26, 26, 24, 28, 17, 27, 31, 30, 32, 16, 25, 11, 23,
+ 34, 19, 28, 31, 28, 34, 20, 19, 28, 25, 26, 28, 28, 29,
+ 33, 23, 17, 35, 24, 27, 27, 20, 11, 26, 26, 24, 18, 32,
+ 29, 31, 22, 28, 29, 28), Okt = c(37, 32, 5, 27, 24, 23,
+ 32, 18, 21, 32, 24, 17, 31, 25, 17, 23, 17, 29, 9, 24,
+ 29, 29, 27, 5, 20, -5, 25, 29, 21, 26, 27, 26, 27, 17,
+ 20, 22, 22, 24, 21, 24, 25, 28, 23, 9, 33, 18, 25, 19,
+ 22, 6, 27, 22, 21, 22, 32, 23, 32, 21, 27, 27, 31), Nov = c(31,
+ 32, -2, 21, 18, 18, 32, 19, 25, 32, 21, 10, 31, 19, 11,
+ 19, 11, 27, 2, 20, 26, 28, 21, -5, 15, -24, 25, 25, 25,
+ 23, 23, 25, 19, 12, 22, 17, 21, 21, 13, 20, 18, 23, 22,
+ 0, 28, 13, 19, 10, 28, 4, 27, 17, 17, 26, 31, 17, 31,
+ 23, 25, 20, 31), Dez = c(27, 32, -4, 16, 14, 11, 31,
+ 19, 29, 30, 19, 2, 31, 14, 7, 17, 7, 27, 0, 16, 22, 27,
+ 16, -13, 10, -35, 25, 20, 26, 21, 18, 22, 14, 9, 23,
+ 14, 19, 20, 11, 17, 16, 20, 22, -3, 23, 6, 17, 3, 30,
+ 3, 29, 14, 15, 29, 31, 10, 30, 26, 23, 18, 33)), .Names = c("BG",
+ "Kont", "Jan", "Feb", "Mrz", "Apr", "Mai", "Jun", "Jul",
+ "Aug", "Sep", "Okt", "Nov", "Dez"), row.names = c("Abu
Dhabi ",
+ "Acapulco ", "Anchorage ",
"Antalya ",
+ "Athen ", "Atlanta ",
"Bangkok ",
+ "Bogota", "BuenosAires ",
"Caracas ",
+ "Casablanca", "Chicago ",
"ColomboSriLanka ",
+ "Dallas", "Denver",
"FaroAlgarve ",
+ "GrandCanyonArizona", "Harare",
"Helsinki ",
+ "HeraklionKreta", "Hongkong ",
"Honolulu ",
+ "Houston ", "Irkutsk ",
"Istanbul ",
+ "JakutskNordostsibirien", "Johannesburg ",
"Kairo ",
+ "Kapstadt
Re: [Rd] Bug in dev.print ? (PR#9801)
[EMAIL PROTECTED] wrote:
> Ladies and Gentlemen,
>
> the following piece of code causes an annoying error:
>
>
> > aa <- structure(list(BG = c(24, 16, 61, 30, 37, 33, 13, 4, -34,
> + 10, 33, 41, 6, 32, 39, 37, 36, -17, 60, 35, 22, 21, 29, 52,
> + 41, 62, -26, 30, -33, 27, 34, 28, 36, 29, -12, 38, 34, 32,
> + 40, 36, 39, 31, 19, 55, 28, 40, 38, 39, -31, 64, -22, 41,
> + 37, -33, 18, 31, 1, -33, 28, 36, -22), Kont = c(4, 7, 3,
> + 4, 6, 3, 4, 7, 7, 7, 2, 3, 4, 3, 3, 6, 3, 2, 6, 6, 4, 3,
> + 3, 4, 6, 4, 2, 1, 2, 4, 6, 6, 3, 4, 7, 6, 3, 6, 6, 6, 6,
> + 2, 7, 6, 4, 3, 6, 4, 5, 6, 7, 6, 3, 7, 7, 4, 4, 5, 6, 2,
> + 2), Jan = c(25, 31, -4, 15, 13, 12, 32, 20, 30, 30, 18, 1,
> + 30, 15, 8, 16, 7, 27, -3, 15, 20, 26, 18, -15, 8, -36, 25,
> + 19, 27, 18, 17, 21, 15, 9, 25, 14, 19, 19, 11, 17, 15, 18,
> + 21, -3, 19, 4, 14, 2, 32, 2, 29, 12, 13, 29, 30, 8, 30, 26,
> + 21, 15, 31), Feb = c(28, 31, -1, 16, 14, 14, 33, 19, 28,
> + 29, 18, 2, 32, 16, 7, 17, 8, 26, -3, 15, 21, 26, 20, -9,
> + 9, -29, 25, 21, 28, 21, 18, 21, 16, 10, 27, 16, 18, 18, 13,
> + 18, 15, 21, 23, -4, 24, 5, 15, 6, 30, 2, 30, 13, 15, 26,
> + 30, 11, 31, 28, 21, 17, 30), Mrz = c(30, 31, -1, 19, 17,
> + 19, 35, 19, 26, 30, 20, 9, 32, 21, 14, 19, 12, 27, 2, 18,
> + 23, 26, 23, 1, 12, -10, 24, 23, 27, 25, 20, 23, 23, 13, 26,
> + 18, 19, 20, 16, 19, 18, 24, 25, 3, 30, 9, 17, 12, 32, 4,
> + 30, 15, 17, 26, 30, 14, 32, 25, 23, 20, 29), Apr = c(35,
> + 31, 5, 21, 20, 23, 36, 19, 22, 30, 20, 16, 32, 25, 15, 21,
> + 14, 26, 9, 20, 26, 28, 26, 7, 16, 3, 22, 27, 24, 28, 22,
> + 23, 25, 16, 24, 20, 19, 20, 18, 22, 20, 24, 27, 12, 37, 14,
> + 20, 21, 25, 6, 29, 18, 17, 23, 30, 18, 32, 23, 23, 22, 26),
> + Mai = c(40, 32, 12, 27, 26, 26, 34, 19, 18, 31, 22, 21, 32,
> + 29, 22, 23, 22, 24, 16, 24, 30, 28, 30, 16, 22, 13, 19,
> + 32, 20, 27, 27, 24, 33, 20, 21, 22, 21, 21, 23, 25, 25,
> + 29, 26, 19, 40, 21, 24, 27, 23, 9, 26, 24, 20, 19, 31,
> + 24, 32, 20, 24, 28, 24), Jun = c(41, 32, 17, 33, 30,
> + 29, 34, 18, 16, 31, 25, 26, 31, 32, 27, 26, 28, 20, 20,
> + 27, 32, 29, 32, 23, 27, 21, 17, 35, 18, 29, 31, 26, 38,
> + 23, 18, 27, 22, 23, 31, 29, 29, 34, 25, 23, 39, 28, 28,
> + 30, 19, 12, 26, 28, 22, 15, 31, 27, 31, 17, 25, 32, 22),
> + Jul = c(42, 33, 19, 35, 33, 30, 34, 18, 14, 32, 26, 29, 31,
> + 36, 32, 29, 28, 21, 24, 30, 33, 30, 34, 23, 30, 26, 17,
> + 35, 18, 28, 33, 27, 39, 22, 19, 29, 25, 25, 34, 32, 32,
> + 37, 24, 25, 36, 29, 30, 32, 18, 14, 25, 29, 22, 15, 32,
> + 32, 31, 17, 28, 34, 21), Aug = c(43, 33, 17, 35, 33,
> + 31, 34, 18, 16, 32, 27, 28, 30, 35, 30, 29, 26, 23, 21,
> + 30, 32, 31, 34, 20, 29, 21, 20, 35, 18, 28, 33, 28, 39,
> + 21, 18, 30, 25, 26, 33, 31, 32, 37, 24, 22, 34, 29, 29,
> + 31, 19, 14, 26, 29, 22, 17, 32, 31, 31, 19, 28, 34, 24),
> + Sep = c(43, 33, 13, 32, 29, 28, 33, 18, 19, 33, 26, 25, 31,
> + 32, 26, 26, 24, 28, 17, 27, 31, 30, 32, 16, 25, 11, 23,
> + 34, 19, 28, 31, 28, 34, 20, 19, 28, 25, 26, 28, 28, 29,
> + 33, 23, 17, 35, 24, 27, 27, 20, 11, 26, 26, 24, 18, 32,
> + 29, 31, 22, 28, 29, 28), Okt = c(37, 32, 5, 27, 24, 23,
> + 32, 18, 21, 32, 24, 17, 31, 25, 17, 23, 17, 29, 9, 24,
> + 29, 29, 27, 5, 20, -5, 25, 29, 21, 26, 27, 26, 27, 17,
> + 20, 22, 22, 24, 21, 24, 25, 28, 23, 9, 33, 18, 25, 19,
> + 22, 6, 27, 22, 21, 22, 32, 23, 32, 21, 27, 27, 31), Nov = c(31,
> + 32, -2, 21, 18, 18, 32, 19, 25, 32, 21, 10, 31, 19, 11,
> + 19, 11, 27, 2, 20, 26, 28, 21, -5, 15, -24, 25, 25, 25,
> + 23, 23, 25, 19, 12, 22, 17, 21, 21, 13, 20, 18, 23, 22,
> + 0, 28, 13, 19, 10, 28, 4, 27, 17, 17, 26, 31, 17, 31,
> + 23, 25, 20, 31), Dez = c(27, 32, -4, 16, 14, 11, 31,
> + 19, 29, 30, 19, 2, 31, 14, 7, 17, 7, 27, 0, 16, 22, 27,
> + 16, -13, 10, -35, 25, 20, 26, 21, 18, 22, 14, 9, 23,
> + 14, 19, 20, 11, 17, 16, 20, 22, -3, 23, 6, 17, 3, 30,
> + 3, 29, 14, 15, 29, 31, 10, 30, 26, 23, 18, 33)), .Names = c("BG",
> + "Kont", "Jan", "Feb", "Mrz", "Apr", "Mai", "Jun", "Jul",
> + "Aug", "Sep", "Okt", "Nov", "Dez"), row.names = c("Abu
> Dhabi ",
> + "Acapulco ", "Anchorage ",
> "Antalya ",
> + "Athen ", "Atlanta ",
> "Bangkok ",
> + "Bogota", "BuenosAires ",
> "Caracas ",
> + "Casablanca", "Chicago ",
> "ColomboSriLanka ",
> + "Dallas", "Denver",
> "FaroAlgarve ",
> + "GrandCanyonArizona", "Harare",
> "Helsinki ",
> + "HeraklionKreta", "Hongkong ",
> "Honolulu ",
> +
[Rd] X11() dies in remote background
this is not a problem with R but a request for related advice.
i am trying to run a lengthy batch job from my home.
the OS is ...
Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 01:05:37 CEST
2003 i686 athlon i386 GNU/Linux
i start the job and put it in the background. while i am connected, all is
well. eventually my ISP shuts down the connection if i do not do any
input. then:
Boxplots of G intensitiesError in X11(paste("png::", filename, sep = ""),
width, height, pointsize, :
unable to start device PNG
Calls: doPlot -> qcBeadLevel -> png
In addition: Warning message:
In png(filename, width = 640, height = 480) :
unable to open connection to X11 display ''
Execution halted
is it possible to have X11() succeed when there is no real display to connect
to?
R version 2.6.0 Under development (unstable) (2007-06-29 r42093)
i686-pc-linux-gnu
locale:
LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
attached base packages:
[1] grid tools stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] beadarray_1.5.3beadarraySNP_1.3.7 quantsmooth_1.3.0 lodplot_1.1
[5] quantreg_4.06 SparseM_0.73 affy_1.13.9affyio_1.3.1
[9] geneplotter_1.13.4 lattice_0.15-11annotate_1.13.3Biobase_1.13.19
[13] limma_2.9.5
loaded via a namespace (and not attached):
[1] KernSmooth_2.22-20 RColorBrewer_0.2-3 rcompgen_0.1-13
---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
[EMAIL PROTECTED]
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Re: [Rd] triax.points() from package plotrix
Remarks, bug reports and feature requests on contributed packages should
go to the corresponding package maintainer (CCing). Note that several
developers of the > 1000 CRAN R packages do not read this mailing list.
Thank you,
Uwe Ligges
Andreas Plank wrote:
> Dear developers from package plotrix,
>
> the function triax.points() from package plotrix does not draw any
> points, because of internal setting in triax.points() {points(...,
> type="l")}.
> I add a new option in triax.points()
> point.type = "l",
> So the user can choose which type of points should be drawn.
> May be other users already found this defect.
>
> best whishes
> Andreas Plank
>
> --- 8< ###
> triax.points <- function (x,
> show.legend = FALSE,
> label.points = FALSE,
> point.labels = NULL,
> col.symbols = par("fg"),
> pch = par("pch"),
> bg.symbols = par("bg"),
> cc.axes = FALSE,
> point.type = "l", # new add
>...
> )
> {
> if (dev.cur() == 1)
> stop("Cannot add points unless the triax.frame has been drawn")
> if (missing(x))
> stop("Usage: triax.points(x,...)\n\twhere x is a 3 column array
> of proportions or percentages")
> if (!is.matrix(x) && !is.data.frame(x))
> stop("x must be a matrix or data frame with at least 3 columns
> and one row.")
> if (any(x > 1) || any(x < 0)) {
> if (any(x < 0))
> stop("All proportions must be between zero and one.")
> if (any(x > 100))
> stop("All percentages must be between zero and 100.")
> x <- x/100
> }
> if (any(abs(rowSums(x) - 1) > 0.01))
> warning("At least one set of proportions does not equal one.")
> sin60 <- sin(pi/3)
> if (cc.axes) {
> ypos <- x[, 3] * sin60
> xpos <- x[, 1] + x[, 3] * 0.5
> }
> else {
> ypos <- x[, 3] * sin60
> xpos <- 1 - (x[, 1] + x[, 3] * 0.5)
> }
> nobs <- dim(x)[1]
> if (is.null(point.labels))
> point.labels <- rownames(x)
> if (label.points)
> thigmophobe.labels(xpos, ypos, point.labels)
> if (show.legend) {
> legend(0.16 - 0.02 * max(nchar(point.labels)), 0.75 +
> 0.04 * length(point.labels), legend = point.labels,
> pch = pch, col = col.symbols)
> }
> points(x = xpos, y = ypos, pch = pch, col = col.symbols,
> bg = bg.symbols, type = point.type, ...)
> invisible(list(x = xpos, y = ypos))
> }
>
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Re: [Rd] X11() dies in remote background
I use a display on an Xvfb server:
Xvfb :5 -screen 0 1280x1024x24 &
setenv DISPLAY :5
You do most likely need a non-default depth (on my machine the default is
12 bits), and it is possible you may need to deal with authentication
issues.
On Sat, 21 Jul 2007, Vincent Carey 525-2265 wrote:
>
> this is not a problem with R but a request for related advice.
>
> i am trying to run a lengthy batch job from my home.
>
> the OS is ...
> Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 01:05:37 CEST
> 2003 i686 athlon i386 GNU/Linux
>
> i start the job and put it in the background. while i am connected, all is
> well. eventually my ISP shuts down the connection if i do not do any
> input. then:
>
>
> Boxplots of G intensitiesError in X11(paste("png::", filename, sep = ""),
> width, height, pointsize, :
> unable to start device PNG
> Calls: doPlot -> qcBeadLevel -> png
> In addition: Warning message:
> In png(filename, width = 640, height = 480) :
> unable to open connection to X11 display ''
> Execution halted
>
> is it possible to have X11() succeed when there is no real display to connect
> to?
>
> R version 2.6.0 Under development (unstable) (2007-06-29 r42093)
> i686-pc-linux-gnu
>
> locale:
> LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid tools stats graphics grDevices utils datasets
> [8] methods base
>
> other attached packages:
> [1] beadarray_1.5.3beadarraySNP_1.3.7 quantsmooth_1.3.0 lodplot_1.1
> [5] quantreg_4.06 SparseM_0.73 affy_1.13.9affyio_1.3.1
> [9] geneplotter_1.13.4 lattice_0.15-11annotate_1.13.3Biobase_1.13.19
> [13] limma_2.9.5
>
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.22-20 RColorBrewer_0.2-3 rcompgen_0.1-13
>
>
> ---
> Vince Carey, PhD
> Assoc. Prof Med (Biostatistics)
> Harvard Medical School
> Channing Laboratory - ph 6175252265 fa 6177311541
> 181 Longwood Ave Boston MA 02115 USA
> [EMAIL PROTECTED]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] X11() dies in remote background
Vincent Carey 525-2265 <[EMAIL PROTECTED]> writes: > this is not a problem with R but a request for related advice. > > i am trying to run a lengthy batch job from my home. > > the OS is ... > Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 01:05:37 CEST > 2003 i686 athlon i386 GNU/Linux > > i start the job and put it in the background. while i am connected, all is > well. eventually my ISP shuts down the connection if i do not do any > input. One thing you might try is using screen. The screen program lets you multiplex terminals in a single window, but the feature you want here is that it allows you to detach and reattach to a session. So you could start a screen session at work or home, start something running, detach, and then come back later and attach to see how things are going. However, screen may further complicate your desire to use X11(), but perhaps with Xvfb run from the screen session things will work. Do all of the graphics devices require access to X11()? I thought you could use pdf() for example, without X11() but I'm not certain. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] X11() dies in remote background
> Vincent Carey 525-2265 <[EMAIL PROTECTED]> writes: > > > this is not a problem with R but a request for related advice. > > > > i am trying to run a lengthy batch job from my home. > > > > the OS is ... > > Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 01:05:37 > > CEST > > 2003 i686 athlon i386 GNU/Linux > > > > i start the job and put it in the background. while i am connected, all is > > well. eventually my ISP shuts down the connection if i do not do any > > input. > > One thing you might try is using screen. The screen program lets you > multiplex terminals in a single window, but the feature you want here > is that it allows you to detach and reattach to a session. So you > could start a screen session at work or home, start something running, > detach, and then come back later and attach to see how things are going. > > However, screen may further complicate your desire to use X11(), but > perhaps with Xvfb run from the screen session things will work. Do > all of the graphics devices require access to X11()? I thought you > could use pdf() for example, without X11() but I'm not certain. it looks like pdf() would work. but ... qcBeadLevel runs png() ... and the ultimate desire seems to be to have images that will load nicely in a browser in html. admittedly i could hack qcBeadLevel to run pdf and then imagemagick the results into png. so far it looks like Xvfb will do the trick if i can authenticate properly. and so far, that is out of my hands. it seems i can get the ISP to refrain from timing me out if i print to screen from the process with some frequency. but i don't know if that will work indefinitely __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] X11() dies in remote background
Won't ServerAliveInterval 60 in /etc/ssh_config do the job of keeping your connection alive? And wouldn't it be more appropriate if bitmap() was used instead? b On Jul 21, 2007, at 12:23 PM, Vincent Carey 525-2265 wrote: > >> Vincent Carey 525-2265 <[EMAIL PROTECTED]> writes: >> >>> this is not a problem with R but a request for related advice. >>> >>> i am trying to run a lengthy batch job from my home. >>> >>> the OS is ... >>> Linux jedi.bwh.harvard.edu 2.4.22-openmosix1smp #1 SMP Fri Sep 5 >>> 01:05:37 CEST >>> 2003 i686 athlon i386 GNU/Linux >>> >>> i start the job and put it in the background. while i am >>> connected, all is >>> well. eventually my ISP shuts down the connection if i do not do >>> any >>> input. >> >> One thing you might try is using screen. The screen program lets you >> multiplex terminals in a single window, but the feature you want here >> is that it allows you to detach and reattach to a session. So you >> could start a screen session at work or home, start something >> running, >> detach, and then come back later and attach to see how things are >> going. >> >> However, screen may further complicate your desire to use X11(), but >> perhaps with Xvfb run from the screen session things will work. Do >> all of the graphics devices require access to X11()? I thought you >> could use pdf() for example, without X11() but I'm not certain. > > it looks like pdf() would work. but ... qcBeadLevel runs png() ... > and the ultimate desire seems to be to have images that will load > nicely in a browser in html. admittedly i could hack qcBeadLevel > to run pdf and then imagemagick the results into png. > > so far it looks like Xvfb will do the trick if i can authenticate > properly. and so far, that is out of my hands. > > it seems i can get the ISP to refrain from timing me out if i > print to screen from the process with some frequency. but i don't > know if > that will work indefinitely > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] dict package: dictionary data structure for R
Hi all, The dict package provides a dictionary (hashtable) data structure much like R's built-in environment objects, but with the following differences: - The Dict class can be subclassed. - Four different hashing functions are implemented and the user can specify which to use when creating an instance. I'm sending this here as opposed to R-packages because this package will only be of interest to developers and because I'd like to get feedback from a slightly smaller community before either putting it on CRAN or retiring it to /dev/null. The design makes it fairly easy to add additional hashing functions, although currently this must be done in C. If nothing else, this package should be useful for evaluating hashing functions (see the vignette for some examples). Source: R-2.6.x: http://userprimary.net/software/dict_0.1.0.tar.gz R-2.5.x: http://userprimary.net/software/dict_0.0.4.tar.gz Windows binary: R-2.5.x: http://userprimary.net/software/dict_0.0.4.zip + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] dict package: dictionary data structure for R
Although the proto package is not particularly aimed at hashing note that it covers some of the same ground and also is based on a well thought out object model (known as object-based programming or prototype programming). Here is an example where we create two proto objects (which could be regarded as hash tables) in which q is a child of p and so inherits a: library(proto) p <- proto(a = 1, b = 2) q <- p$proto(c = 3) q$a # 1 On 7/21/07, Seth Falcon <[EMAIL PROTECTED]> wrote: > Hi all, > > The dict package provides a dictionary (hashtable) data > structure much like R's built-in environment objects, but with the > following differences: > > - The Dict class can be subclassed. > > - Four different hashing functions are implemented and the user can >specify which to use when creating an instance. > > I'm sending this here as opposed to R-packages because this package > will only be of interest to developers and because I'd like to get > feedback from a slightly smaller community before either putting it on > CRAN or retiring it to /dev/null. > > The design makes it fairly easy to add additional hashing functions, > although currently this must be done in C. If nothing else, this > package should be useful for evaluating hashing functions (see the > vignette for some examples). > > Source: > R-2.6.x: http://userprimary.net/software/dict_0.1.0.tar.gz > R-2.5.x: http://userprimary.net/software/dict_0.0.4.tar.gz > > Windows binary: > R-2.5.x: http://userprimary.net/software/dict_0.0.4.zip > > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center > http://bioconductor.org > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] dict package: dictionary data structure for R
"Gabor Grothendieck" <[EMAIL PROTECTED]> writes:
> Although the proto package is not particularly aimed at hashing note
> that it covers some of the same ground and also is based on a well
> thought out object model (known as object-based programming
> or prototype programming).
Interesting. The dict package differs from proto in that it _is_
aimed at hashing and:
- It is S4 based
- It does not use R's environment objects to implement its
hashtables (proto uses environments).
In Bioconductor, we have many hashtables where the key is an
Affymetrix probeset ID. These look sort of like "1000_at". It turns
out that the algorithm used by R's environments is not very good at
hashing these values. The dict package lets you investigate this:
library("dict")
keys2 = paste(seq(1000, length=13000), "at", sep="_")
# here, hash.alg=0L corresponds to the hashing function used by R's
# environments. I know, a name would be better.
> summary(as.integer(table(hashCodes(keys=keys2, hash.alg=0L, size=2^14
Min. 1st Qu. MedianMean 3rd Qu.Max.
80011001500162520252700
# hash.alg=1L is djb2 from here: http://www.cse.yorku.ca/~oz/hash.html
> summary(as.integer(table(hashCodes(keys=keys2, hash.alg=1L, size=2^14
Min. 1st Qu. MedianMean 3rd Qu.Max.
1.000 1.000 2.000 1.648 2.000 4.000
# and this is what we see with an environment:
> e = new.env(hash=T, size=2^14)
> for (k in keys2) e[[k]] = k
> summary(env.profile(e)$counts)
Min. 1st Qu.Median Mean 3rd Qu. Max.
0.0.0.0.79350. 2700.
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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