Simon Penel
2007-Apr-06 13:09 UTC
[Rd] getConnection is not found in R depending on the Linux flavour (RedHat or Debian) - dyn.load problems
Hello R developers,
I am working on the "seqinr" package and I encounter a tricky problem
using a C
function.
We defined a C fonction called "getzlibsock" which is dedicated to
compressed
socket connections. This function is using the R internal C function
called "getConnection(int)" in order to get information about the
socket
previously opened with the dedicated R functions.
The program works fine on several platform:
-Unix (SunOS),
-MacOS and
-Linux (some).
However, on Linux, an error occurs depending on the installation.
I tried to play with the Makevars file by specifing lots of path and
library
without succees
On Red Hat Linux it works fine, but on Debian the dynamic library can
not be
loaded:
Library is working fine with Linux Red Hat:
---------------------------------------------------------
R.2.4.0
Linux ccali24 2.4.21-32.0.1.ELsmp #1 SMP Wed May 25 15:42:26 CDT 2005
i686 i686 i386 GNU/Linux
RedHat
gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-52)
Reading specs from /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/specs
Configured with:
../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--disable-checking --with-system-zlib --enable-__cxa_atexit
--host=i386-redhat-linux
Thread model: posix
Compiling the dynamic library:
Makevars:
PKG_CFLAGS = -ansi -DUSE_TYPE_CHECKING_STRICT
R CMD SHLIB -o test.so *.c
gcc -I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2
-std=gnu99 -c alignment.c -o alignment.o
gcc -I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2
-std=gnu99 -c getzlibsock.c -o getzlibsock.o
gcc -I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2
-std=gnu99 -c kaks.c -o kaks.o
gcc -I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2
-std=gnu99 -c util.c -o util.o
gcc -I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/afs/in2p3.fr/home/throng/biometr/R_dir/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2
-std=gnu99 -c zsockr.c -o zsockr.o
gcc -shared -L/usr/local/lib -o test.so alignment.o getzlibsock.o kaks.o
util.o zsockr.o
Note that the dll libR.so is not asked not the path to the dll
Loading the dynamic library:
R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> dyn.load("test.so")
>
Problem in library with Linux Debian
--------------------------------------------------
( both binary distribution of R and version builded from sources):
a) with the binary version
R version 2.4.1 (2006-12-18)
This the binary distribution obtained via apt-get
Linux pcstef 2.6.15-1-686-smp #2 SMP Mon Mar 6 15:34:50 UTC 2006 i686
GNU/Linux
Debian
gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)
Configured with:
../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang
--prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib
--without-included-gettext --enable-threads=posix --enable-nls
--program-suffix=-4.1 --enable-__cxa_atexit --enable-clocale=gnu
--enable-libstdcxx-debug --enable-mpfr --with-tune=i686
--enable-checking=release i486-linux-gnu
Thread model: posix
Compiling the dynamic library:
Makevars:
PKG_CFLAGS = -ansi -DUSE_TYPE_CHECKING_STRICT
PKG_LIBS = -lR -lz
rm *o
R CMD SHLIB -o test.so *.c
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -ansi
-DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c alignment.c -o alignment.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -ansi
-DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c getzlibsock.c -o getzlibsock.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -ansi
-DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c kaks.c -o kaks.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -ansi
-DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c util.c -o util.o
gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -ansi
-DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c zsockr.c -o zsockr.o
gcc -std=gnu99 -shared -o test.so alignment.o getzlibsock.o kaks.o
util.o zsockr.o -lR -lz -L/usr/lib/R/lib -lR
Loading the dynamic library:
....
> dyn.load("test.so")
Erreur dans dyn.load(x, as.logical(local), as.logical(now)) :
impossible de charger la biblioth?que partag?e
'/home/simon/seqinr_in2p3/seqinr/src/test.so':
/home/simon/seqinr_in2p3/seqinr/src/test.so: undefined symbol:
getConnection
>
....
However the dll libR.so exists in the "/usr/lib/R/lib" path:
ls /usr/lib/R/lib
libRlapack.so libR.so
But the libR.so does not seems to contain getConnection:
grep getConnection /usr/lib/R/lib/libR.so give no answer
Moreover libR.so can not be read by nm:
nm: /usr/lib/R/lib/libR.so: aucun symbole
b) with the sources
I was thus wondering if the problem was due to a incompatibility between
the binary
version of R I get via apt-get and the dynamic library I compiled with the
current gcc.
I try with the R installed from sources
../../../R-install_R-2.4.1/bin/R CMD SHLIB -o test.so *.c
gcc-4.1 -std=gnu99 -I/home/simon/R-install_R-2.4.1//lib/R/include
-I/home/simon/R-install_R-2.4.1//lib/R/include -I/usr/local/include
-ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c alignment.c -o alignment.o
gcc-4.1 -std=gnu99 -I/home/simon/R-install_R-2.4.1//lib/R/include
-I/home/simon/R-install_R-2.4.1//lib/R/include -I/usr/local/include
-ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c getzlibsock.c -o
getzlibsock.o
gcc-4.1 -std=gnu99 -I/home/simon/R-install_R-2.4.1//lib/R/include
-I/home/simon/R-install_R-2.4.1//lib/R/include -I/usr/local/include
-ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c kaks.c -o kaks.o
gcc-4.1 -std=gnu99 -I/home/simon/R-install_R-2.4.1//lib/R/include
-I/home/simon/R-install_R-2.4.1//lib/R/include -I/usr/local/include
-ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c util.c -o util.o
gcc-4.1 -std=gnu99 -I/home/simon/R-install_R-2.4.1//lib/R/include
-I/home/simon/R-install_R-2.4.1//lib/R/include -I/usr/local/include
-ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c zsockr.c -o zsockr.o
gcc-4.1 -std=gnu99 -shared -L/usr/local/lib -o test.so alignment.o
getzlibsock.o kaks.o util.o zsockr.o -lR -lz
-L/home/simon/R-install_R-2.4.1//lib/R/lib -lR
Loading the dynamic library:
~/seqinr_in2p3/seqinr/src$
../../../R-install_R-2.4.1/bin/R
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
...
> dyn.load("test.so")
Erreur dans dyn.load(x, as.logical(local), as.logical(now)) :
impossible de charger la biblioth?que partag?e
'/home/simon/seqinr_in2p3/seqinr/src/test.so':
/home/simon/seqinr_in2p3/seqinr/src/test.so: undefined symbol:
getConnection
>
...
In this case the path still contains
/home/simon/R-install_R-2.4.1//lib/R/lib
where the R ldd can be found:
ls /home/simon/R-install_R-2.4.1//lib/R/lib
libRblas.so libRlapack.so libR.so
and libR.so contains getConnection:
nm /home/simon/R-install_R-2.4.1//lib/R/lib/libR.so |grep getConnection
00052990 t getConnection
00052240 t getConnection_no_err
I was wondering if the problem was a difference between R-2.4.1 and
R.2.4.0 but I
think this not the case because it is possible to compile and load the
dll test.so on Linux
Red Hat with the R-devel version as well as the R-2.4.0., and it works
fine as well on the MacOS
R-2.4.1.:
Library is working fine with MacOS:
-----------------------------------------------
R-2.4.1
Darwin chobits.univ-lyon1.fr 8.8.0 Darwin Kernel Version 8.8.0: Fri Sep
8 17:18:57 PDT 2006; root:xnu-792.12.6.obj~1/RELEASE_PPC Power Macintosh
powerpc
gcc: Target: i686-apple-darwin8
Configured with: ../gcc-4.0.3/configure --prefix=/usr/local/gcc4.0
--disable-checking --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/
--build=i686-apple-darwin8 --program-prefix=powerpc-apple-darwin8-
--host=powerpc-apple-darwin8 --target=i686-apple-darwin8 --with-sysroot=
--enable-languages=c,c++,f95,objc
Thread model: posix
gcc version 4.0.3
R CMD SHLIB -o test.o *.c
gcc-4.0 -arch ppc -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fPIC -g -O2 -c
alignment.c -o alignment.o
gcc-4.0 -arch ppc -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fPIC -g -O2 -c
getzlibsock.c -o getzlibsock.o
gcc-4.0 -arch ppc -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fPIC -g -O2 -c
kaks.c -o kaks.o
gcc-4.0 -arch ppc -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fPIC -g -O2 -c
util.c -o util.o
gcc-4.0 -arch ppc -std=gnu99
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/ppc
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fPIC -g -O2 -c
zsockr.c -o zsockr.o
gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl -single_module
-multiply_defined suppress -L/usr/local/lib -o test.o alignment.o
getzlibsock.o kaks.o util.o zsockr.o
-L/Library/Frameworks/R.framework/Resources/lib/ppc -lR -dylib_file
libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/ppc/libRblas.dylib
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
....
> dyn.load("test.o")
>
>
R Installation problem?
-------------------------------
I was wondering if it the way in which R is configured? I installed R on
the Linux Debian with these options ./configure --prefix
/home/simon/R-install_R-2.4.1/ --without-dataentry --without-x
--disable-dataentry --enable-R-shlib --enable-static
--with-recommended-packages CC=gcc-4.1
I noticed as well that concerning the Debian Linux installations ,I
had problem when the libR.so was required during compilation of my
sources ( -lR option). I try a new installation of R with the folowing
options:
./configure --prefix=/home/simon/R-2.4.1_otherinstall/install/
--without-dataentry --without-x --disable-dataentry --enable-static
--with-recommended-packages
When compiling my sources I get:
rm *o
../../../R-2.4.1_otherinstall/install/bin/R CMD SHLIB -o test.o *.c
gcc -std=gnu99 -I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c
alignment.c -o alignment.o
gcc -std=gnu99 -I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c
getzlibsock.c -o getzlibsock.o
gcc -std=gnu99 -I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c
kaks.c -o kaks.o
gcc -std=gnu99 -I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c
util.c -o util.o
gcc -std=gnu99 -I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/home/simon/R-2.4.1_otherinstall/install//lib/R/include
-I/usr/local/include -ansi -DUSE_TYPE_CHECKING_STRICT -fpic -g -O2 -c
zsockr.c -o zsockr.o
gcc -std=gnu99 -shared -L/usr/local/lib -o test.o alignment.o
getzlibsock.o kaks.o util.o zsockr.o
But the problem still occurs:
../../../R-2.4.1_otherinstall/install/bin/R
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
...
> dyn.load("test.o")
Erreur dans dyn.load(x, as.logical(local), as.logical(now)) :
impossible de charger la biblioth?que partag?e
'/home/simon/seqinr_in2p3/seqinr/src/test.o':
/home/simon/seqinr_in2p3/seqinr/src/test.o: undefined symbol:
getConnection
>
Finally I tried as well on Windows and the function "getConnection"
was
not found at the compilation step.....
Thanks very much for any help!!
Simon
--
Simon Penel
Laboratoire de Biometrie et Biologie Evolutive
Bat 711 - CNRS UMR 5558 - Universite Lyon 1
43 bd du 11 novembre 1918 69622 Villeurbanne Cedex
Tel: 04 72 43 29 04 Fax: 04 72 43 13 88
http://pbil.univ-lyon1.fr/members/penel
Prof Brian Ripley
2007-Apr-07 07:52 UTC
[Rd] getConnection is not found in R depending on the Linux flavour (RedHat or Debian) - dyn.load problems
getConnection is not part of the API, so it is not intended to be visible to your code. The code reads /* internal, not the same as R function getConnection */ attribute_hidden Rconnection getConnection(int n) and 'internal' and 'attribute_hidden' should have been enough of a clue! On many OSes it is noticeably more efficient not to export unneeded entry points from DLLs, so we do not do so where the OS supplies (simple) facilities to do so. There are severe warnings in 'Writing R Extensions' about making use of entry points not in the API. There are medium-term plans to change the internal structure of connections to make use of features not in R when they were designed (weak references and finalizers), so this will definitely remain non-API. On Fri, 6 Apr 2007, Simon Penel wrote:> > Hello R developers, > > I am working on the "seqinr" package and I encounter a tricky problem > using a C function. > > We defined a C fonction called "getzlibsock" which is dedicated to > compressed > socket connections. This function is using the R internal C function > called "getConnection(int)" in order to get information about the socket > previously opened with the dedicated R functions. > > The program works fine on several platform: > -Unix (SunOS), > -MacOS and > -Linux (some). > However, on Linux, an error occurs depending on the installation.[...] -- Brian D. Ripley, ripley at 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, UK Fax: +44 1865 272595