similar to: how do I tell configure where to find Java? [Broadcast]

Dear R-help, I'm trying to build R-2.4.0 on our Opteron-based Scyld cluster. The system has gcj (the GNU Java compiler, part of GCC) stuff in /usr/bin. When I installed jdk 1.5.08, the install script placed it in /usr/java (I didn't have a choice, as the script didn't offer that option). Now when I run configure in R-2.4.0, it finds gcj, which is not what I want to use. Is there a

Having difficulties getting rJava to install on my Debian Squeeze box. Perused the R-help list and tried some things that have worked for others but not for me. Below is the output of my attempted build, R CMD javareconf -e, and sessionInfo(). Note I tried the R CMD javareconf also as root, restarted R after each of these, all no help. * Installing *source* package ?rJava? ... checking for

As ever, I learn from this: I didn't know apt-file. Got it, installed it, used it: root at DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-file search jni.h android-libnativehelper-dev: /usr/include/android/nativehelper/jni.h android-platform-frameworks-native-headers: /usr/include/android/android/asset_manager_jni.h android-platform-frameworks-native-headers:

Dear R-help, Has anyone tried running R on a Beowulf-type cluster? I can get R to run in batch (using R CMD BATCH) on a cluster, but am wondering if it is possible to get an interactive R session on a compute node. Right now, if I run: beorun --nolocal R I just get the R start-up message and back to the shell prompt. If I try bpsh 0 R I can get R started (but the R prompt does not

Dear R-help, This one is probably a piece of cake for regexp masters. I'd like to split a character vector (for simplicity, say of length one for now) that contains fields that are delimited by arbitrary number of white spaces (e.g., " a b c "). How do I get the character vector that contain the fields? In the example I gave, I've tried: > strsplit(" a b c

Dear DevelopeRs, I'd like to ask those who develop R packages with compiled code to please try avoiding dependency on GCC (gcc/g77/gfortran/g++) specific features in the code, for the simple reason that there are non-GCC compilers out there that might choke on such features. I found this out back when I was trying to build R-2.3.0-to-be on our dual Opteron based Scyld cluster. Because the

Hi All, While attempting to build R-patched using the Portland Group compiler suite on our dual Opteron 250 box running Scyld 29cz5 (based on RH, kernel 2.4.29), I get: make[5]: Leaving directory `/home/andy/Rbuild/R221-pgi/src/library/tools/src' make[5]: Entering directory `/home/andy/Rbuild/R221-pgi/src/library/tools/src' pgcc -I../../../../include -I/include -I/include/CC -fpic

Hi, I met a problem when I binding JAVA. 1. download xapian-bindings-0.9.10.tar.gz to my local. 2. unzip binding file. 3. input ./configure --with-java in cygwin. 4 give me error: checking for java... /cygdrive/c/Program Files/Java/jdk1.5.0_11/bin/java checking for javac... /cygdrive/c/Program Files/Java/jdk1.5.0_11/bin/javac checking for jar... /cygdrive/c/Program Files/Java/jdk1.5.0_11/bin/jar

Dear all, I installed the amd64 cran2deb [1] JGR binaries on a fresh Debian testing, and JGR is missbehaving. When JGR starts up, one core of the CPU goes to 100% and stays there, even though I am keeping it idle and not performing any operation. I tried JGR with both sun-java6-jdk and openjdk-6-jdk, debian-liv:/home/liviu# update-alternatives --config java There are 4 choices for the alternative

Dear R-help, Has anyone notice the problem that, on Windows (NT and XP), when printing a graph using the "File -> Print..." menu in the graphics window to print the graph, that line width seemed to be ignored in the printed output? For example, if I make a plot with plot(1:10, type="l", lwd=5), it looks right on screen, but when printed out using the menu, it looks like

Dear R-help, I was bitten by the behavior of all() when given logical(0): It is TRUE! (And any(logical(0)) is FALSE.) Wouldn't it be better to return logical(0) in both cases? The problem surfaced because some un-named individual called randomForest(x, y, xtest, ytest,...), and gave y as a two-level factor, but ytest as just numeric vector. I thought I check for that in my code by testing

Dear R-help: Has anyone tried using R on the the AMD Opteron in either 64- or 32-bit mode? If so, any good/bad experiences, comments, etc? We are considering getting this hardware, and would like to know if R can run smoothly on such a beast. Any comment much appreciated. Best, Andy Andy Liaw, PhD Biometrics Research PO Box 2000, RY33-300 Merck Research Labs Rahway, NJ

Morning All: Having problems installing this one into my R setup and wondered if anyone on the list had the same problem and found a workable solution. First to the system particulars: OS is the Hardy Heron edition of Ubuntu Linux R version is 2.13.1 Java installation is sun-java6 Next up is the result of javareconf: R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.5.0

Hi all, I am new to Xapian and want to use it with Java. In order to do that I tried to compile the Java bindings. I set XAPIAN_CONFIG and invoked "configure". However "./configure --with-java" exits with an error. Point of failure: checking for jni.h... no checking for jni.h in /usr/lib/jvm/java-1.5.0-sun/include... no checking for jni.h in

Hi all, i'm trying to install JGR on linux (see bottom), but it runs into errors. The bottom of the sequence below shows "JavaJD could not be found" Any suggestion, please? $ sudo apt-get install sun-java6-jdk $ sudo update-alternatives --config java There are 5 alternatives which provide `java'. Selection Alternative ----------------------------------------------- 1

Dear R-devel, Has anyone played with this? http://www.amd.com/us-en/Processors/DevelopWithAMD/0,,30_2252_2282,00.html <http://www.amd.com/us-en/Processors/DevelopWithAMD/0,,30_2252_2282,00.html> . I'll probably give it a shot... Best, Andy Andy Liaw, PhD Biometrics Research PO Box 2000, RY33-300 Merck Research Labs Rahway, NJ 07065 mailto:andy_liaw@merck.com

Dear R-devel, [I'm not sure if this is appropriate for R-devel. If not, I'm more than happy to move it to R-help.] As those of you who saw my post on R-help know, I've been trying to build R-patched on a dual Opteron box running Scyld Beowulf, using the PGI 6.1 compilers. The build went fine, but I couldn't get it to pass make check-all. Jennifer Lai, who reported success with

Morning All: Having problems installing this one into my R setup and wondered if anyone on the list had the same problem and found a workable solution. First to the system particulars: OS is the Hardy Heron edition of Ubuntu Linux R version is 2.13.1 Java installation is sun-java6 Next up is the result of javareconf: R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.5.0

Dear R-help, I've encounter what seems to me a strange problem with "names<-". Suppose I define the function: fun <- function(x, f) { m <- tapply(x, f, mean) ans <- x - m[match(f, unique(f))] names(ans) <- names(x) ans } which subtract out the means of `x' grouped by `f' (which is the same as, e.g., resid(lm(x~f)) if `f' is a factor).

Installing rJava fails consistently, whether installed via the command line as below, or through "install.packages( 'rJava' )", and whether 0.84 or 0.85 is used, with the message :- "checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to