rsbml 2.26.0
Michael Lawrence
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/rsbml | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | [ OK ] | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf rsbml.buildbin-libdir && mkdir rsbml.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rsbml_2.26.0.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_2.26.0.tar.gz'
>>>>>>>
* installing *source* package ‘rsbml’ ...
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... 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-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
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/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... 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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c StringMap.c -o StringMap.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c check.c -o check.o
In file included from check.c:1:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from check.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c doc.c -o doc.o
In file included from doc.c:1:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from doc.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
doc.c: In function ‘rsbml_build_doc_simple_species_reference’:
doc.c:453: warning: unused variable ‘tmp’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c dom.c -o dom.o
In file included from dom.c:1:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from dom.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c graph.c -o graph.o
In file included from graph.c:1:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from graph.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c init.c -o init.o
In file included from init.c:1:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from init.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c io.c -o io.o
In file included from io.c:1:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from io.c:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c layoutWrappers.cpp -o layoutWrappers.o
In file included from layoutWrappers.cpp:1:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from layoutWrappers.cpp:1:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c mathml.c -o mathml.o
In file included from mathml.c:3:
rsbml.h:8:1: warning: "USE_LAYOUT" redefined
In file included from /usr/local/include/sbml/common/libsbml-config.h:66,
from /usr/local/include/sbml/common/sbmlfwd.h:45,
from /usr/local/include/sbml/SBMLTypes.h:37,
from rsbml.h:1,
from mathml.c:3:
/usr/local/include/sbml/common/libsbml-config-common.h:93:1: warning: this is the location of the previous definition
mathml.c: In function ‘rmathml_SEXP’:
mathml.c:56: warning: unused variable ‘closure’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include/libxml2 -I/usr/local/include -DLIBSBML3 -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c simulate.c -o simulate.o
llvm-g++-4.2 -arch x86_64 -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 -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/lib -lpthread -licucore -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/rsbml.buildbin-libdir/rsbml/libs
** R
** inst
** preparing 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/3.2/Resources/lib/libgcc_s.1.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/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/3.2/Resources/lib/libreadline.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"