################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL rsbml###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘rsbml’ ...** this is package ‘rsbml’ version ‘2.68.0’** using staged installationchecking for pkg-config... /usr/bin/pkg-configchecking pkg-config is at least version 0.9.0... yeschecking for LIBSBML... yesconfigure: === Begin local SOSLib build ===checking for a BSD-compatible install... /usr/bin/install -cchecking whether build environment is sane... yeschecking for a thread-safe mkdir -p... /usr/bin/mkdir -pchecking for gawk... gawkchecking whether make sets $(MAKE)... yeschecking build system type... x86_64-unknown-linux-gnuchecking host system type... x86_64-unknown-linux-gnuchecking for C++ compiler default output file name... a.outchecking whether the C++ compiler works... yeschecking whether we are cross compiling... nochecking for suffix of executables... checking for suffix of object files... ochecking whether we are using the GNU C++ compiler... yeschecking whether g++ -std=gnu++17 accepts -g... yeschecking for style of include used by make... GNUchecking dependency style of g++ -std=gnu++17... gcc3checking for gcc... gcc -std=gnu2xchecking whether we are using the GNU C compiler... yeschecking whether gcc -std=gnu2x accepts -g... yeschecking for gcc -std=gnu2x option to accept ISO C89... none neededchecking dependency style of gcc -std=gnu2x... gcc3checking whether gcc -std=gnu2x accepts -fpic... yeschecking how to run the C preprocessor... gcc -std=gnu2x -Echecking for ranlib... ranlibchecking for a BSD-compatible install... /usr/bin/install -cchecking whether make sets $(MAKE)... (cached) yeschecking for autoconf... /usr/bin/autoconfchecking for aclocal... /usr/bin/aclocalchecking for make... /usr/bin/makechecking for ar... /usr/bin/archecking for swig... swigchecking for perl... /usr/bin/perlchecking for pkg-config... /usr/bin/pkg-configchecking pkg-config is at least version 0.9.0... yeschecking for SBML... yeschecking for correct functioning of SBML... yeschecking 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 Libraryconfigure: === End local SOSLib build ===configure: creating ./config.statusconfig.status: creating src/Makevars** libsusing 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 -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c StringMap.c -o StringMap.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c check.c -o check.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doc.c -o doc.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c dom.c -o dom.odom.c: In function ‘rsbml_build_dom_line_segment’:dom.c:687:12: warning: comparison between ‘SBMLTypeCode_t’ and ‘enum <anonymous>’ [-Wenum-compare] 687 | if (type == SBML_LAYOUT_CUBICBEZIER) { | ^~dom.c:693:19: warning: comparison between ‘SBMLTypeCode_t’ and ‘enum <anonymous>’ [-Wenum-compare] 693 | } else if (type == SBML_LAYOUT_LINESEGMENT) | ^~gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c graph.c -o graph.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init.c -o init.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c io.c -o io.og++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c layoutWrappers.cpp -o layoutWrappers.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c mathml.c -o mathml.ogcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c simulate.c -o simulate.og++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-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)