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Package 266/319HostnameOS / ArchBUILDCHECKBUILD BIN
rsbml 2.2.1
Michael Lawrence
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/rsbml
Last Changed Rev: 39231 / Revision: 42512
Last Changed Date: 2009-04-29 15:36:12 -0700 (Wed, 29 Apr 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386 [ OK ] OK  OK 
Package: rsbml
Version: 2.2.1
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD build rsbml
StartedAt: 2009-10-20 16:07:04 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 16:07:44 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 40.1 seconds
RetCode: 0
Status: OK
PackageFile: rsbml_2.2.1.tar.gz
PackageFileSize: 510 KiB

Command output

* checking for file 'rsbml/DESCRIPTION' ... OK
* preparing 'rsbml':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* 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... awk
checking whether make sets $(MAKE)... yes
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
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/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
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c StringMap.c -o StringMap.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c check.c -o check.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c doc.c -o doc.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c dom.c -o dom.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c graph.c -o graph.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c init.c -o init.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c io.c -o io.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c mathml.c -o mathml.o
mathml.c: In function ‘rmathml_SEXP’:
mathml.c:56: warning: unused variable ‘closure’
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -I/usr/include/libxml2 -I/usr/local/include    -DLIBSBML3 -I/usr/local/include    -fPIC  -g -O2 -Wall -c simulate.c -o simulate.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rsbml.so StringMap.o check.o doc.o dom.o graph.o init.o io.o mathml.o simulate.o -L/usr/local/lib -lsbml -lstdc++ -lm -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
 >>> Building/Updating help pages for package 'rsbml'
     Formats: text html latex example 
  AlgebraicRule-class               text    html    latex
  AssignmentRule-class              text    html    latex
  BoundingBox-class                 text    html    latex
  CVTerm-class                      text    html    latex
  Compartment-class                 text    html    latex
  CompartmentGlyph-class            text    html    latex
  CompartmentType-class             text    html    latex
  CompartmentVolumeRule-class       text    html    latex
  Constraint-class                  text    html    latex
  CubicBezier-class                 text    html    latex
  Curve-class                       text    html    latex
  Delay-class                       text    html    latex
  Describable-class                 text    html    latex
  Dimensions-class                  text    html    latex
  Event-class                       text    html    latex
  EventAssignment-class             text    html    latex
  Experiment-class                  text    html    latex
  FunctionDefinition-class          text    html    latex
  GraphicalObject-class             text    html    latex
  InitialAssignment-class           text    html    latex
  KineticLaw-class                  text    html    latex
  Layout-class                      text    html    latex
  LineSegment-class                 text    html    latex
  Model-class                       text    html    latex
  ModelCreator-class                text    html    latex
  ModelHistory-class                text    html    latex
  ModifierSpeciesReference-class    text    html    latex
  Parameter-class                   text    html    latex
  ParameterRule-class               text    html    latex
  Point-class                       text    html    latex
  RateRule-class                    text    html    latex
  Reaction-class                    text    html    latex
  ReactionGlyph-class               text    html    latex
  Rule-class                        text    html    latex
  SBML-class                        text    html    latex   example
  SBMLDocument-class                text    html    latex   example
  SBMLProblem-class                 text    html    latex
  SBMLProblems-class                text    html    latex
  SBase-class                       text    html    latex
  SOSDesign-class                   text    html    latex
  SOSExperiment-class               text    html    latex
  SOSProtocol-class                 text    html    latex
  SOSResult-class                   text    html    latex
  SOSSubject-class                  text    html    latex
  SimpleSpeciesReference-class      text    html    latex
  Species-class                     text    html    latex
  SpeciesConcentrationRule-class    text    html    latex
  SpeciesGlyph-class                text    html    latex
  SpeciesReference-class            text    html    latex
  SpeciesReferenceGlyph-class       text    html    latex
  SpeciesType-class                 text    html    latex
  StoichiometryMath-class           text    html    latex
  TextGlyph-class                   text    html    latex
  Trigger-class                     text    html    latex
  Unit-class                        text    html    latex
  UnitDefinition-class              text    html    latex
  math                              text    html    latex
  read                              text    html    latex   example
** building package indices ...
* DONE (rsbml)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'rsbml_2.2.1.tar.gz'