Question: rsbml: can not link to SUNDIALS
0
gravatar for ivo
3.6 years ago by
ivo0
ivo0 wrote:

Hi,

My System: Linux debian testing amd64

sundials 2.6.2, libsbml 5.13, graphviz 2.38.0,, R 3.3.0, biocgenerics 0.18.0, biocgraph 1.50.0

I try to install rsbml 3.3 with sundials support, but this fails, although sundials is installed:

dpkg -l "*sundials*" | grep ^i | awk '{print $2}'
libsundials-arkode1
libsundials-cvode1
libsundials-cvodes2
libsundials-ida2
libsundials-idas0
libsundials-kinsol1
libsundials-nvecpthreads0
libsundials-nvecserial0
libsundials-serial
libsundials-serial-dev

the full configure message is:

ivo@orm/local/home/ivo/src/sbos/R/rsbml/rsbml-3.3]./configure
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML3... yes
configure: === Begin local SOSLib build ===
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking whether gcc accepts -fpic... yes
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for autoconf... /usr/bin/autoconf
checking for aclocal... /usr/bin/aclocal
checking for make... /usr/bin/make
checking for ar... /usr/bin/ar
checking for swig... /usr/bin/swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for SBML... yes
checking for correct functioning of SBML... yes
checking for SUNDIALS Library headers... yes
checking for SUNDIALS Library... checking correct functioning of SUNDIALS... no:
                   CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 -I/usr/include
                   LDFLAGS= 
                   LIBS= -lm -lstdc++
configure: error: Can not link to SUNDIALS Library
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars

 

How do you test for SUNDIALS? Is my version simply too new for rsbml?

Best,

 

Ivo

 

rsbml • 479 views
ADD COMMENTlink written 3.6 years ago by ivo0

Yea, SOSLib is getting a bit long in the tooth. You could check its config.log to see how the test is failing. 

ADD REPLYlink written 3.6 years ago by Michael Lawrence11k
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