[R] R crashes when loading library/package; Windows, Cygwin
Dear list members, This is a question is about building an R package under windows and cygwin. Please bear with me. I have a package in R that compiles well on my stationary computer (WINDOWS NT, R 1.8.1 and prior), and the resulting (package_version).zip file works well there. It contains an R script file and a C file. After installing tools to build the package on my laptop, the package builds successfully in the sense that both (a)rcmd build -binary -docs=normal cultosaurus and (b) R CMD BUILD -binary -docs=normal cultosaurus will successfully create a zipfile. (R version and compiler version below). When I install the package from the local zip file, R seems happy and says package 'cultosaurus' successfully unpacked and MD5 sums checked updating HTML package descriptions Trying to load the library, however, causes R to freeze for 10 seconds or so, without giving any message and then exit (Exit 5). A subset of this package with the C source file removed will successfully build, and successfully load. Then of course there will be an error saying C entry point ... not in load table Therefore the DLL seems to be causing this problem. Any hints or advice would be highly appreciated. Thanks in advance, Sixten version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor2.1 year 2005 month12 day 20 svn rev 36812 language R $ gcc -v Reading specs from /usr/lib/gcc/i686-pc-cygwin/3.4.4/specs Configured with: /gcc/gcc-3.4.4/gcc-3.4.4-1/configure --verbose --prefix=/usr -- exec-prefix=/usr --sysconfdir=/etc --libdir=/usr/lib --libexecdir=/usr/lib --man dir=/usr/share/man --infodir=/usr/share/info --enable-languages=c,ada,c++,d,f77, java,objc --enable-nls --without-included-gettext --enable-version-specific-runt ime-libs --without-x --enable-libgcj --disable-java-awt --with-system-zlib --ena ble-interpreter --disable-libgcj-debug --enable-threads=posix --enable-java-gc=b oehm --disable-win32-registry --enable-sjlj-exceptions --enable-hash-synchroniza tion --enable-libstdcxx-debug : (reconfigured) Thread model: posix gcc version 3.4.4 (cygming special) (gdc 0.12, using dmd 0.125) $ perl -v This is perl, v5.8.8 built for MSWin32-x86-multi-thread (with 21 registered patches, see perl -V for more detail) Copyright 1987-2006, Larry Wall Binary build 816 [255195] provided by ActiveState http://www.ActiveState.com Built Mar 1 2006 18:00:52 Output from building the package.__ $ make rcmd build -binary -docs=normal cultosaurus * checking for file 'cultosaurus/DESCRIPTION' ... OK * preparing 'cultosaurus': * checking DESCRIPTION meta-information ... OK * cleaning src * checking whether 'INDEX' is up-to-date ... OK * removing junk files * checking for LF line-endings in source files * checking for empty directories WARNING: directory cultosaurus/data is empty * building binary distribution WARNING * some HTML links may not be found installing R.css in c:/DOCUME~1/Sixten/LOKALA~1/Temp/Rinst.432 Using auto-selected zip options '' /bin/sh: latex: command not found /bin/sh: latex: command not found /bin/sh: latex: command not found -- Making package cultosaurus /bin/sh: latex: command not found adding build stamp to DESCRIPTION /bin/sh: latex: command not found /bin/sh: latex: command not found making DLL ... /bin/sh: latex: command not found /bin/sh: latex: command not found /bin/sh: latex: command not found making erectus.d from erectus.c gcc -Ic:/program/R/R-2.2.1/include -Wall -O2 -c erectus.c -o erectus.o ar cr cultosaurus.a erectus.o ranlib cultosaurus.a windres --include-dir c:/program/R/R-2.2.1/include -i cultosaurus_res.rc -o cul tosaurus_res.o gcc --shared -s -o cultosaurus.dll cultosaurus.def cultosaurus.a cultosaurus_r es.o -Lc:/program/R/R-2.2.1/src/gnuwin32 -lg2c -lR ... DLL made installing DLL /bin/sh: latex: command not found installing R files /bin/sh: latex: command not found /bin/sh: latex: command not found installing man source files installing indices installing help Building/Updating help pages for package 'cultosaurus' Formats: text html latex example sygehus texthtmllatex example missing link(s): ~~fun~~ /bin/sh: latex: command not found adding MD5 sums packaged installation of package 'cultosaurus' as cultosaurus_0.1.zip * DONE (cultosaurus) $ Sixten Borg IHE Box 2127 S-220 02 Lund Sweden tel: +46 46 32 91 07 fax:+46 46 12 16 04 Kommer man inte upp före klockan fyra på morgonen, så vaknar man inte på hela dan. www.ihe.se *** Note: The information contained in this message and attachments may be privileged and confidential and protected from
Re: [R] R seems to stall after several hours on a long series of analyses... where to start?
Hi,
I saw something similar, when I had R to look in a file every half minute if
there was a request to do something, and if so, do that something and empty the
file. (This was my way of testing if I coud do an interactive web page, somehow
I managed to get the web page to write the requests to the file that R would
look in. R would update a graph that was visible on that same web page).
Anyway, this ran smoothly for while (40 minutes I think), then it just stopped.
When I examined the situation, R suddenly woke up and continued its task as if
nothing had happened (which was quite correct).
My amateur interpretation was that the system put R to sleep since it appeared
to be inactive according to the system. When I swithed to R, it became
interactive and was given CPU time again.
Maybe this gives some inspiration to solve the problem. The system was Windows
NT, R version 1.8, I think.
Kind regards.
Sixten
David L. Van Brunt, Ph.D. [EMAIL PROTECTED] 2005-11-07 16:09
Great suggestions, all.
I do have a timer in there, and it looks like the time to complete a loop is
not increasing as it goes. From your comments, I take it that suggests there
is not a memory leak. I could try scripting the loop from the shell, rather
than R, to see if that works, but will do that as a last resort as it will
require a good deal of re-writing (the loop follows some setup code that
builds a pretty large data set... the loop then slaps several new columns on
a copy of that data set, and analyses that...)
I'll still try the other platform as well, see if the same problem occurs
there.
On 11/7/05, jim holtman [EMAIL PROTECTED] wrote:
Here is some code that I use to track the progress of my scripts. This
will print out the total cpu time and the memory that is being used. You
call it with 'my.stats(message)' to print out message on the console.
Also, have you profiled your code to see where the time is being spent?
Can you break it up into multiple runs so that you can start with a fresh
version of memory?
==script===
my.stats - local({
# local variables to hold the last times
# first two variables are the elasped and CPU times from the last report
lastTime - lastCPU - 0
function(text = stats, reset=F)
{
procTime - proc.time()[1:3] # get current metrics
if (reset){ # setup to mark timing from this point
lastTime - procTime[3]
lastCPU - procTime[1] + procTime[2]
} else {
cat(text, -,sys.call(sys.parent())[[1]], : ,
round((procTime[1] + procTime[2]) - lastCPU,1),
round(procTime[3] - lastTime,1), , procTime,
: , round(memory.size()/2.^20., 1.), MB\n)
invisible(flush.console()) # force a write to the console
}
}
})
= here is some sample output=
my.stats(reset=TRUE) # reset counters
x - runif(1e6) # generate 1M random numbers
my.stats('random')
random - my.stats : 0.3 31.8 96.17 11.7 230474.9 : 69.5 MB
y - x*x+sqrt(x) # just come calculation
my.stats('calc')
calc - my.stats : 0.7 71.2 96.52 11.74 230514.3 : 92.4 MB
You can see that memory is growing. The first number is the CPU time and
the second (in ) is the elapsed time.
HTH
On 11/7/05, David L. Van Brunt, Ph.D. [EMAIL PROTECTED] wrote:
Not sure where to even start on this I'm hoping there's some
debugging I
can do...
I have a loop that cycles through several different data sets (same
structure, different info), performing randomForest growth and
predictions... saving out the predictions for later study...
I get about 5 hours in (9%... of the planned iterations.. yikes!) and R
just
freezes.
This happens in interactive and batch mode execution (I can see from the
.Rout file that it gets about 9% through in Batch mode, and about 6%
if in
interactive mode... does that suggest memory problems?)
I'm thinking of re-executing this same code on a different platform to
see
if that's the issue (currently using OS X)... any other suggestions on
where
to look, or what to try to get more information?
Sorry so vague... it's a LOT of code, runs fine without error for many
iterations, so I didn't think the problem was syntax...
--
---
David L. Van Brunt, Ph.D.
mailto: [EMAIL PROTECTED]
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Jim Holtman
Cincinnati, OH
+1 513 247 0281
What the problem you are trying to solve?
--
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David L. Van Brunt, Ph.D.
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Sv: [R] Using locator() to digitise
Hi, Splus allows pasting a graphics object into the plotting window, which makes it possible to do what you describe below. Now I use R which doesn't seem to allow pasting the picture into the graphics window, so I copy the graph onto a transparency sheet, and stick it onto my screen using tape. The coordinates need to be converted to make sense (as you describe). My methodology with the transparency has a stoneage appearance, but it works quite well, if I may say so myself. I have written down some notes that describes what I did, but it's in Swedish so I guess it's not of much help. Kind regards, Sixten. Ted Harding [EMAIL PROTECTED] 2005-03-20 17:09 Hi Folks, I'm contemplating using locator() to digitise external graphics. To set context, I would be using X11 display on Linux. To pre-empt the obvious comment: I've found on the R site the suggestion to use the 'pixmap' package. I've tried this, and it works; but it involves building a big R object (the internal pixmap representation), and this chokes my somewhat puny laptop (e.g. it can take about 1 minute to draw the graphic inside a plot area using addlogo(), with mucho swappo, and subsequently working knee-deep in treacle). The following idea would be a lot slicker. For examples: I have something like a) A scatterplot of data printed in a journal (but the data values are not available; b) A contour map (on paper) of a region. So, I can scan the document, and obtain a file in some graphics format (jpeg, pbm or png, say). Now: an idea which I find attractive is to be able to overlay an R plot with axes onto a display of the graphics file (produced as an X window by any suitable program such as 'xv' or 'display') so that (if the overlay were possible) clicking on the points of the graphic would in fact be clicking on the R plot and, via locator(), generate the R-plot coordinates of the mouse clicks which would correspond to the selected points on the graphic. Provided the coordinate system of the R plot were properly related to the graphic, the results would be a digitisation of the selected points on the graphic. What seems to be needed for this idea to work is that the R-plot should be displayed in an X11() device whose background was completely transparent, so that when moved over the (independently generated) display of the graphic the latter would be visible (but locator() would still be working on the R-plot itself). Window resizing could look after the correspondence between graphic coordinates and R-plot coordinates. The R plot itself could be empty (apart from coordinate axes) or could contain helper elements such as grid lines, circles (e.g. I want to digitise graphics points within a certain circle), etc. Helper elements could be added to the R-plot by subsequent 'lines' or 'points' commands (e.g. I identify two points on the graphic, R-plot the line joining them, and then pick off graphic-points which lie on the R-line). So this question is really about producing a bare R plot on, as it were, a virtual acrylic transparency. It's certainly possible to do such a thing in X: e.g. the cute xteddy is in fact a picture of a bear on a completely transparent rectangular background, though you'd never know by looking! Any comments? With thanks, and best wishes to all, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 20-Mar-05 Time: 16:09:11 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Advice on good programming practice, lexical scope
In An Introduction to R (See R help menu), there is an example of a function 'open.account' that makes use of the lexical scope in R. I have a set of functions that can be used to output R tables and graphics into a single report document. (I am aware that several tools can do this already). While reorganizing my code, I realize that I can collect my functions in a list, in the style of 'open.account' above. This will result in a list containing data and operations on those data. The data is for example the file name of the report. This also results in a rather large object instead of a set of rather small functions and a list of data. Writing a package of these functions (or this object containing functions), would require documentation of each function. The style that I see in the R help is that the functions are not enclosed like this in a list. I like the idea of having the functions collected in a single list, but I think the documentation might be messy. Any ideas, opinions, anyone? Thanks in advance, Sixten. Example: myreport - report(filename=report.rtf) my.report$add.table(my.data.frame, Table of ...) plot(runif(10)) my.report$add.picture(Plot of ...) or... r - report(filename=report.rtf) r - add.table(r, my.data.frame, Table of...) plot(runit(10)) r - add.picture(r, Plot of...) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Simulation from a model fitted by survreg.
Dear list, I would like to simulate individual survival times from a model that has been fitted using the survreg procedure (library survival). Output shown below. My plan is to extract the shape and scale arguments for use with rweibull() since my error terms are assumed to be Weibull, but it does not make any sense. The mean survival time is easy to predict, but I would like to simulate individual survival times. I am probably missing something completely obvious. Any hints or advice are appreciated. Thanks Sixten summary(mod1) Call: survreg(formula = Surv(tid, study$first.event.death) ~ regim + age + stadium2, data = study, dist = weibull) Value Std. Error zp (Intercept) 11.6005 0.7539 15.387 2.01e-53 regimposto -0.1350 0.1558 -0.867 3.86e-01 age -0.0362 0.0102 -3.533 4.11e-04 stadium2ii -0.0526 0.2794 -0.188 8.51e-01 Log(scale) -0.5148 0.1116 -4.615 3.93e-06 Scale= 0.598 Weibull distribution Loglik(model)= -680.7 Loglik(intercept only)= -689.2 Chisq= 16.87 on 3 degrees of freedom, p= 0.00075 Number of Newton-Raphson Iterations: 8 n=1183 (4 observations deleted due to missing) version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor8.1 year 2003 month11 day 21 language R __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R 1.9.0, special characters in variable names.
Hello all, I upgraded from R 1.8.1 to 1.9.0 (Windows XP), and spotted an odd thing. The last three letters in the Swedish alphabet are å, ä and ö. (In case they don't show correctly: they are a with a ring, a with two dots, and o with two dots (HTML: aring; auml; ouml;). When I use these as variable names in a data.frame, odd things happen: In R 1.8.1, å (aring;) doesn't work while the others do. In R 1.9.0, ö (ouml;) doesn't work while the others do. Please find examples below. It would be nice if all three could be used in variable names. At least in Sweden :-) Thanks... Sixten. # # R 1.9.0: ö is renamed to X. # data.frame(a=1, å=2, ä=3, ö=4) a å ä X. 1 1 2 3 4 version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.0 year 2004 month04 day 12 language R # # R 1.8.1: å is renamed to X. # data.frame(a=1, å=2, ä=3, ö=4) a X. ä ö 1 1 2 3 4 version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor8.1 year 2003 month11 day 21 language R # __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Summary [R] R 1.9.0, special characters in variable names.
Summary: The locale setting in the operating system seems to be involved in what confused me a little bit. Thank you all for your help, especially the suggested work-around data.frame(..., check.names=F) which works very well. A mystery still to be solved is why two versions of R, running on the same machine on the same time, behaves differently. Please do not respond to this on the list. I very much welcome you not to respond at all. Sixten. Prof Brian Ripley [EMAIL PROTECTED] 2004-06-24 10:20:55 Can we stop blaming R for things which are not its fault, especially as that has already been pointed out twice this morning? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Extracting the survival function estimate from a survreg object.
Hello all,
I want to extract the survival function estimate from a model fitted by survreg().
Using predict.survreg(..., type=quantile, p=seq(0,1,0.001)), gives the quantiles,
which
I managed to turn around into a survival function estimate (Prob{T t} as function of
t).
Is there a more straightforward way of doing this? I have had difficulties using
pweibull() with
the coefficients reported by summary(survreg object).
I am enclosing an outline of my code for reference if anyone is interested.
Thanks in advance,
Sixten
-
sure - survreg(formula = Surv(time, dead) ~ age + group + sex, data = modb)
nd - data.frame(
age=50,
group=factor(A, levels=c(A, B, C)),
sex=factor(M, levels=c(F, M)))
y - seq(0, 1, 0.001)
#
# For a range of p-values, predict the quantiles.
#
sufu - list(
y=1-y,
x=predict.survreg(sure, nd, type=quantile, p=y)
)
#
# Find the p value for each t, by locating the last quantile no larger than t.
# The pairs (t,p) forms a step function.
#
sufu2 - list(
x=0:14,
y=unlist(lapply(0:14,function(x){rev(sufu$y[sufu$x=x])[1]}))
)
# Looks ok?
plot(sufu, type=s, xlim=c(0,20))
points(sufu2, pch=20, col=blue)
#EOF#
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Ang: [R] How to write efficient R code
Hej Lennart, I would like to add one thing: Often, there already exists an R function that solves the problem at hand. Instead of writing your own function, search the help files [apropos(), help.search()]. What I some times find difficult though, is guessing what key words will produce relevant search hits... Mvh Sixten [EMAIL PROTECTED] 2004-02-17 15:36:12 I have been lurking in this list a while and searching in the archives to find out how one learns to write fast R code. One solution seems to be to write part of the code not in R but in C. However after finding a benchmark article (http://www.sciviews.org/other/benchmark.htm) I have been more interested in making the R code itself more efficient. I would like to find more info about this. I have tried to mail the contact person for the benchmark, but I have so recieved no reply. I am not an R programmer (or statistican) so I do not know R well. I am looking for some advice about writing fast R code. What about the different data types for example? Is there some good place to start to look for more info about this? Thanks for any pointers Lennart __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (no subject)
Hello, I have trouble converting a character string to a R object. Let me describe this by an example; dim(a) [1] 270 14 dim(a) NULL names(a) [1] Var1 Var2 Var3 Var4 Var5 Var6 Var7 Var8 Var9 [10] Var10 Var11 Var12 Var13 Var14 names(a) NULL I realise that the character string lacks both a dimension and any column names; my question is how to make R understand that I look for the object a when I write a. Like a type cast in C; (R data.frame) a for those familiar with C. The underlying reason for this is that I am writing a script that imports several datasets. The file names of the datasets contain the '_' character which forces me to construct a valid dataset name for each file. Although I can do this by hand, I would like to know if there is any solution to my first approach. Thanks in advance, Sixten Sixten Borg IHE Box 2127 S-220 02 Lund Sweden tel: +46 46 32 91 07 fax:+46 46 12 16 04 www.ihe.se *** Note: The information contained in this message and attachments may be privileged and confidential and protected from disclosure. If the reader of this message is not the intended recipient you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately by replying to the message and deleting it from your computer. Thank you. IHE __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
