rsbml 2.32.0
Michael Lawrence
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/rsbml | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | 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_2.32.0.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_2.32.0.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 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-darwin13.4.0
checking host system type... i386-apple-darwin13.4.0
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... 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/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c StringMap.c -o StringMap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c check.c -o check.o
In file included from check.c:1:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c doc.c -o doc.o
In file included from doc.c:1:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
doc.c:453:8: warning: unused variable 'tmp' [-Wunused-variable]
SEXP tmp = GET_SLOT(r_simple_species_reference, install("species"));
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c dom.c -o dom.o
In file included from dom.c:1:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
dom.c:792:12: warning: comparison of constant 'SBML_LAYOUT_CUBICBEZIER' (102) with expression of type 'SBMLTypeCode_t' is always false [-Wtautological-constant-out-of-range-compare]
if (type == SBML_LAYOUT_CUBICBEZIER) {
˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
dom.c:798:19: warning: comparison of constant 'SBML_LAYOUT_LINESEGMENT' (107) with expression of type 'SBMLTypeCode_t' is always false [-Wtautological-constant-out-of-range-compare]
} else if (type == SBML_LAYOUT_LINESEGMENT)
˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c graph.c -o graph.o
In file included from graph.c:1:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
In file included from init.c:1:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c io.c -o io.o
In file included from io.c:1:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c layoutWrappers.cpp -o layoutWrappers.o
In file included from layoutWrappers.cpp:1:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
In file included from layoutWrappers.cpp:1:
./rsbml.h:76:11: warning: struct 'LayoutModelPlugin' was previously declared as a class [-Wmismatched-tags]
typedef struct LayoutModelPlugin LayoutModelPlugin_t;
^
/usr/local/include/sbml/packages/layout/extension/LayoutModelPlugin.h:59:22: note: previous use is here
class LIBSBML_EXTERN LayoutModelPlugin : public SBasePlugin
^
./rsbml.h:76:11: note: did you mean class here?
typedef struct LayoutModelPlugin LayoutModelPlugin_t;
^˜˜˜˜˜
class
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c mathml.c -o mathml.o
In file included from mathml.c:3:
./rsbml.h:8:9: warning: 'USE_LAYOUT' macro redefined
#define USE_LAYOUT LIBSBML_HAS_PACKAGE_LAYOUT
^
/usr/local/include/sbml/common/libsbml-config-common.h:93:9: note: previous definition is here
#define USE_LAYOUT 1
^
mathml.c:56:12: warning: unused variable 'closure' [-Wunused-variable]
SEXP closure, pargs;
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/include/libxml2 -DLIBSBML3 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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/lib -lz -lbz2 -lsbml -lstdc++ -lm -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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/3.3/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/3.3/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/3.3/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/3.3/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/3.3/Resources/lib/libquadmath.0.dylib" "rsbml.buildbin-libdir/rsbml/libs//rsbml.so"