Re: [Rd] R CMD check error with the GNU Scientific Library

You'll need something like : PKG_LIBS=-lgsl -lgslcblas in your Makevars. This is from package gsl (on CRAN). Of course! That makes sense 'cause I was already compiling using MAKEFLAGS="CFLAGS=-g -O0" R CMD SHLIB sharka.c -lgsl -lgslcblas and including the above line in Makevars has done the

[Rd] R CMD check error with the GNU Scientific Library

iles and in Makevars they have "PKG_CFLAGS = -I./gsl". I have copied this approach, but wonder if using the standard "R CMD build myPackage" "R CMD check myPackage" needs modifying in some way? All hints or ideas welcome. Thanks David -- David Pleydell UMR BG

Re: [Rd] enabling core dumps

... If I launch gdb this way I don't have any means to navigate through previously executed gdb lines using M-p and M-n, but following a (gdb) run or (gdb) continue I can use M-p and M-n to recall previous R commands If I launch gdb in other ways M-p and M-n function as expected. I suppose there

Re: [Rd] enabling core dumps

usually what happens is (# meant to be a comment char) % R -d gdb -f test.R gdb> run ...segfault happens, breaks into gdb gdb> bt # print the backtrace gdb> up # move up the stack, to get to 'your' frame gdb> l # show source listing, use -O0 compiler flag, see gdb> help dir gdb> print some

Re: [Rd] Strange behaviour with global variable in C

To answer my own question... I have two copies of my program 1) a working copy stored in $PROJECT/analysis/c 2) a packaged copy stored in $PROJECT/analysis/myPackage_1.0.2.tar.gz I have been running a script which does the following library(myPackage) load(myData) detach("package:myPackge") dy

[Rd] Strange behaviour with global variable in C

I understand global variables can be a bad idea, but even so I would like to understand what is going on here... ### DESCRIPTION OF PROGRAM ### ...I have a strange bug on a global variable in some C code which I am compiling using $ MAKEFLAGS="CFLAGS=-g -O0" R CMD SHLIB myProgram.c the global v

Re: [Rd] Building R package with .c sub-routine files

Create a file named Makevars in the same directory and put the following line in it: OBJECTS=file1.o Then R CMD SHLIB will only compile file1.c. Kjell Great, that's done the job nicely. Many thanks David __ R-devel@r-project.org mailing list htt

[Rd] Building R package with .c sub-routine files

Lets say I have two source files file1.c and file2.c The latter just contains sub-routines to be used by the first. i.e. in file1.c I have the line #include "file2.c" Let's say "R CMD SHLIB file1.c" runs perfectly and I want to include the code in a package, "R CMD build" also runs fine but R

Re: [Rd] Unexpected behaviour of "next line" in gdb

Looking through the archives I found this thread http://tolstoy.newcastle.edu.au/R/e4/devel/08/02/0347.html and so I tried MAKEFLAGS="CFLAGS=-g -O" R CMD SHLIB ... and this worked great. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mail

[Rd] Unexpected behaviour of "next line" in gdb

nd the expected next line). So to me it looks like there is still a gdb ~ optimisation conflict. Does this mean I have to have a copy of R compiled from source using the -O0 flag too? thanks David -- David Pleydell UMR BGPI CIRAD TA A-54/K Campus International de Baillarguet 34398 MONTPELLIE

Re: [Rd] enabling core dumps

usually what happens is (# meant to be a comment char) % R -d gdb -f test.R gdb> run ...segfault happens, breaks into gdb gdb> bt # print the backtrace gdb> up # move up the stack, to get to 'your' frame gdb> l # show source listing, use -O0 compiler flag, see gdb> help dir gdb> print some

Re: [Rd] enabling core dumps

To answer my own question. My mistake was that "ulimit -c unlimited" applies to the current bash session only. I had used this call in a bash *shell* buffer in emacs but this was unable to affect R processes started in emacs with C-u M-x R, hence no core files. Running the buggy code from R start

Re: [Rd] enabling core dumps

not really answering your question, but I find it more useful to R -d gdb or R -d gdb -f test.R where test.R reproduces the bug in some minimal code. A variant is R -d valgrind -f test.R if the memory problem is not easy to spot. Thanks for your reply Martin Yes, I have used that route

Re: [Rd] enabling core dumps

ght need to configure next? thanks David -- David Pleydell UMR BGPI CIRAD TA A-54/K Campus International de Baillarguet 34398 MONTPELLIER CEDEX 5 FRANCE Tel: +33 4 99 62 48 65 - Secrétariat : +33 4 99 62 48 21 Fax : +33 4 99 62 48 22 http://umr-bgpi.cirad.fr/trombinoscope/pleydell_d.htm https:

[Rd] enabling core dumps

2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 1 I am running Ubuntu jaunty on a laptop. Any ideas as to what I might need to configure next? thanks David -- David Pleydell UMR BGPI CIRAD TA A-54/K Campus International de Ba

Re: [Rd] Cannot make 3 different R installations for 3 different valgrind-instrumentation levels

^^-- this is really bad form - you should never build/compile software as root. The location of the build directory is irrelevant so use /tmp or you home or something like that ... (usualy the fastest disk ;)) OK, thanks for the tip, although I don't understand the configure - make - insta

Re: [Rd] Cannot make 3 different R installations for 3 different valgrind-instrumentation levels

is suspect installing to seperate _vg0, _vg1 and _vg2 directories could be the problem. I'll retry and post the results. Well, the following script didn't work cd /usr/local/lib sudo mkdir R cd /usr/local/lib/R sudo /usr/local/src/R-2.9.2/configure --enable-memory-profiling --with-valgrind-inst

Re: [Rd] Cannot make 3 different R installations for 3 different valgrind-instrumentation levels

You're confusing rhome and arch - the above makes no sense. Let rhome alone and you should be fine. (And make sure you're not building in the source tree - you should be using something like mkdir obj_vg0 && cd obj_vg0 && ../R-2.9.1/configure ...) Thanks Simon. I'd already tried various var

[Rd] Cannot make 3 different R installations for 3 different valgrind-instrumentation levels

"R Installation and Administration", section 2.5 "Sub-architectures" describes calling specific builds of R using the call "R --arch=name". I am trying to build and install three versions of R-2.9.1, each configured with a different valgrind-instrumentation level ("Writing R Extensions", section 4.