Package: rsbml

Version: 2.38.0

Command: rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rsbml_2.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rsbml.buildbin-libdir

StartedAt: 2018-10-17 02:04:25 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:05:04 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 38.9 seconds

RetCode: 0

Status:  OK

PackageFile: rsbml_2.38.0.tgz

PackageFileSize: 1.191 MiB

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###
### Running command:
###
###   rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rsbml_2.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rsbml.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rsbml.buildbin-libdir rsbml_2.38.0.tar.gz'
>>>>>>> 

* installing *source* package ‘rsbml’ ...
checking for pkg-config... /usr/local/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... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin15.6.0
checking host system type... i386-apple-darwin15.6.0
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/local/bin/autoconf
checking for aclocal... /usr/local/bin/aclocal
checking for make... /usr/bin/make
checking for ar... /usr/bin/ar
checking for swig... /usr/local/bin/swig
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/local/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= 
                   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
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c StringMap.c -o StringMap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c check.c -o check.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c doc.c -o doc.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c dom.c -o dom.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c graph.c -o graph.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c io.c -o io.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c layoutWrappers.cpp -o layoutWrappers.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c mathml.c -o mathml.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/Cellar/libxml2/2.9.4_2/include/libxml2 -I/usr/local/Cellar/libsbml/5.11.4/include      -I/usr/local/include   -fPIC  -Wall -g -O2  -c simulate.c -o simulate.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -L/usr/local/Cellar/libsbml/5.11.4/lib -lsbml -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/rsbml.buildbin-libdir/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
* DONE (rsbml)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rsbml.buildbin-libdir/rsbml/libs//rsbml.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"