############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rsbml ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘rsbml’ ... ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for LIBSBML... 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... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu 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++ -std=gnu++17 accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++ -std=gnu++17... 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... 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... checking for SUNDIALS Library... checking correct functioning of SUNDIALS... no: CFLAGS=-g -O2 -pg -Wno-unknown-pragmas -Wall -ansi -std=iso9899:1990 LDFLAGS=-L/usr/local/lib 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 ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c StringMap.c -o StringMap.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c check.c -o check.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c doc.c -o doc.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c dom.c -o dom.o dom.c: In function ‘rsbml_build_dom_line_segment’: dom.c:687:12: warning: comparison between ‘SBMLTypeCode_t’ and ‘enum ’ [-Wenum-compare] 687 | if (type == SBML_LAYOUT_CUBICBEZIER) { | ^~ dom.c:693:19: warning: comparison between ‘SBMLTypeCode_t’ and ‘enum ’ [-Wenum-compare] 693 | } else if (type == SBML_LAYOUT_LINESEGMENT) | ^~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c graph.c -o graph.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c io.c -o io.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c layoutWrappers.cpp -o layoutWrappers.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c mathml.c -o mathml.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -c simulate.c -o simulate.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o layoutWrappers.o mathml.o simulate.o -lsbml -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-rsbml/00new/rsbml/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rsbml)