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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL rsbml
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘rsbml’ ...
** this is package ‘rsbml’ version ‘2.67.0’
** 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 -std=gnu2x
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu2x accepts -g... yes
checking for gcc -std=gnu2x option to accept ISO C89... none needed
checking dependency style of gcc -std=gnu2x... gcc3
checking whether gcc -std=gnu2x accepts -fpic... yes
checking how to run the C preprocessor... gcc -std=gnu2x -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 -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.o
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 check.c -o check.o
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 doc.c -o doc.o
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 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 <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.o
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 init.c -o init.o
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 io.c -o io.o
g++ -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.o
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 mathml.c -o mathml.o
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 simulate.c -o simulate.o
g++ -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 -lR
installing 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)