Re: [SOSlib-discuss] SOSlib Windows build

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I've added "WIN32;_DEBUG;_WINDOWS;_USRDLL;SBML_ODESOLVER_EXPORTS" as 
defines 
and get a bit farther.  I am still unclear on how the exports work in 
Windows...

Thanks

John

On Mon, 11 Jun 2007, Rainer Machne wrote:

> Hi John,
>
>
> The log file contains two errors:
>
> ASTIndexNameNode.cpp:79: error: function `int ASTNode_isIndexName(ASTNode_t*)' 
> definition is marked dllimport.
>
> ASTIndexNameNode.cpp:87: error: function `unsigned int 
> ASTNode_isSetIndex(ASTNode_t*)' definition is marked dllimport
>
> Unfortunately we have no knowledge here about the dll import/export in 
> Windows.
>
> However, the file src/sbmlsolver/exportdefs.h is important for that.
>
> The "marked as dllimport" probably comes from the definition of 
> SBML_ODESOLVER_API, which was introduced for such import/export issues by 
> Andrew. It is supposed to indicate functions that are exported, i.e. that 
> should be available for calling applications which use SOSlib as a libary.
>
> Both functions, ASTNode_isIndexName and ASTNode_isSetIndex, have this prefix.
>
> In exportsdefs.h:
>
> #ifdef WIN32
> #ifdef SBML_ODESOLVER_EXPORTS
> #define SBML_ODESOLVER_API __declspec(dllexport)
> #else
> #define SBML_ODESOLVER_API __declspec(dllimport)
> #endif
> #else
> #define SBML_ODESOLVER_API
> #endif
>
> So this prefix can have two values, one for export, one for import. Now, I 
> guess we only need to find out what that means :) and when/how to set 
> SBML_ODESOLVER_EXPORTS.
>
> Andrew's comment in exportdefs.h says:
>
> /* The following ifdef block is the standard way of creating macros
> which make exporting from a DLL simpler. All files within this DLL are
> compiled with the SBML_ODESOLVER_EXPORTS symbol defined on the command
> line. this symbol should not be defined on any project that uses this
> DLL. This way any other project whose source files include this file
> see SBML_ODESOLVER_API functions as being imported from a DLL, whereas
> this DLL sees symbols defined with this macro as being exported. */
>
> The symbol is also mentioned in the Win32 VisualC++ folder, in the (main?) 
> project file
> Win32/SBML_odeSolver/SBML_odeSolver/SBML_odeSolver.vcproj:
>
> PreprocessorDefinitions="WIN32;_DEBUG;_WINDOWS;_USRDLL;SBML_ODESOLVER_EXPORTS"
>
>
> Maybe it suffices to  define it on commandline (to 1 e.g.)? So the compiler 
> knows that the functions are being exported??
>
> However, I wonder if it is an (alphabetical) accident of the make process, 
> that this error occurs in our only C++ functions in ASTIndexNameNode.cpp, or 
> whether the problem is really C++-specific and import/export related.
> The code in this file imports and modifies the libSBML Abstract Syntax Tree 
> class (AST, contains math equations).
>
> Rainer
>
>
> John Legato wrote:
>> Hi Rainer,
>> 
>> We are attempting a build under mingw using the precompiled distribution of 
>> libsbml 2.3.4 (we tried to build it from source under mingw and it failed 
>> with dll export errors). We are getting dllexport errors with soslib as 
>> well. I've attached the log of the build. Do you have any insights?
>> 
>> Thanks
>> 
>> John
>> 
>>
>>  On Wed, 6 Jun 2007, Rainer Machne wrote:
>> 
>>> Hi John,
>>> 
>>> The windows/Visual C++ files (Win32 directory in source code distribution) 
>>> where made by Andrew Finney and unfortunately we have so far not found the 
>>> time to get into it and keep the windows branch up-to-date or even 
>>> understand how it works on Windows. Unfortunately Andrew is no longer 
>>> active. Christoph and James are currently at the SBML hackathon and Andrew 
>>> will be there. So maybe they can help you from there!
>>> 
>>> It is definitely something we need to understand and repair for the next 
>>> release:  installing from source under Cygwin or MinGW (have you tried 
>>> Akira's instructions for MinGW at 
>>> http://www.tbi.univie.ac.at/~raim/odeSolver/doc/installWin.html#src ?)
>>> and as a Visual C++ project.
>>> 
>>> Rainer
>>> 
>>> John Legato wrote:
>>> 
>>>> Hi Rainer,
>>>> 
>>>> We are still attempting to get a windows based DLL of soslib to use with 
>>>> Java bindings. I was wondering if you could suggest what might be the best 
>>>> route. We've tried Cygwin but got hung up on a link issue with libsbml 
>>>> which the Xerces rearranging the link flags to put -lsbml before -lxerces 
>>>> was suggested by the Xerces folks. This worked for the examples but using 
>>>> the same options building SOSlib was unsuccessful.
>>>> 
>>>> I am in the process of attempting the Visual C++ route to build a native 
>>>> library. I can successfully build WinCVODE but other modules fail due to 
>>>> missing header files. For example kinsol.h is missing, I know it's in the 
>>>> sundials distribution but it doesn't seem to be included in the sundials 
>>>> headers included with SOSlib. Do I need to build sundials from source on 
>>>> Windows to get a successful build?
>>>> 
>>>> I've tried to use SWIG with the prebuilt distribution for Windows but I 
>>>> can't seem to find the header files for SOSlib. release.zip appears to 
>>>> only include the DLLs without headers. I am also confused regarding the 
>>>> DLL names under windows. Under Linux we have libODES.a, under windows I 
>>>> see SBML_odeSolver.dll and WinCVODE.dll. Has SOSlib been split up 
>>>> differently under Windows? Is there a roadmap somewhere to the Windows 
>>>> build? I see a readme on the web but I am missing a few steps.
>>>> 
>>>> Thanks
>>>> 
>>>> John
>>>> 
>>>> 
>>>> ---
>>>> Contractor
>>> 
>> 
>> ---
>> Contractor
>> 
>> 
>> ------------------------------------------------------------------------
>> 
>> tar xzf SBML_odeSolver-1.6.0.tar.gz
>> cd SBML_odeSolver-1.6.0; \
>> export LDFLAGS="-L/home/jlegato/SOSlibSWIG/xerces/lib 
>> -L/home/jlegato/SOSlibSWIG/libsbml2_3_4/lib 
>> -L/home/jlegato/SOSlibSWIG/sundials/lib" && ./configure 
>> LDFLAGS="-L/home/jlegato/SOSlibSWIG/xerces/lib 
>> -L/home/jlegato/SOSlibSWIG/libsbml2_3_4/lib 
>> -L/home/jlegato/SOSlibSWIG/sundials/lib" 
>> --prefix=/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0_installed 
>> -with-sundials=/home/jlegato/SOSlibSWIG/sundials-2.1.1 
>> --with-libsbml=/home/jlegato/SOSlibSWIG/libsbml2_3_4 && \
>> patch src/Makefile ../SBML_so.patch && make 
>> LDFLAGS="-L/home/jlegato/SOSlibSWIG/xerces/lib 
>> -L/home/jlegato/SOSlibSWIG/libsbml2_3_4/lib 
>> -L/home/jlegato/SOSlibSWIG/sundials/lib ";make install
>> checking for a BSD-compatible install... /bin/install -c
>> checking whether build environment is sane... yes
>> checking for gawk... gawk
>> checking whether make sets $(MAKE)... yes
>> checking build system type... i686-pc-mingw32
>> checking host system type... i686-pc-mingw32
>> checking for g++... g++
>> checking for C++ compiler default output file name... a.exe
>> checking whether the C++ compiler works... yes
>> checking whether we are cross compiling... no
>> checking for suffix of executables... .exe
>> 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 ANSI C... none needed
>> checking dependency style of gcc... gcc3
>> checking how to run the C preprocessor... gcc -E
>> checking for ranlib... ranlib
>> checking for a BSD-compatible install... /bin/install -c
>> checking whether make sets $(MAKE)... (cached) yes
>> checking for autoconf... /bin/autoconf
>> checking for aclocal... /bin/aclocal
>> checking for make... /bin/make
>> checking for ar... /mingw/bin/ar
>> checking for swig... /usr/local/bin/swig
>> checking for perl... /bin/perl
>> checking for SBML Library Version... expr: syntax error
>> expr: syntax error
>> expr: syntax error
>> ./configure: test: -eq: unary operator expected
>> configure: found SBML Library Version ./configure: test: =: unary operator 
>> expected
>> checking correct functioning of SBML... yes
>> ./configure: test: -eq: unary operator expected
>> checking correct functioning of SUNDIALS CVODE... yes
>> checking for GRACE Library headers... checking for GRACE Library... checking 
>> correct functioning of GRACE... no:
>>                    CFLAGS=-g -O2 
>> LDFLAGS=-L/home/jlegato/SOSlibSWIG/xerces/lib 
>> -L/home/jlegato/SOSlibSWIG/libsbml2_3_4/lib 
>> -L/home/jlegato/SOSlibSWIG/sundials/lib                    LIBS= Can not 
>> link to GRACE Library!
>> odeSolver will be installed without XMGrace functionality
>> checking for dot... no
>> configure: found Graphviz Library Version ./configure: test: -ge: unary 
>> operator expected
>> installed version of graphviz is too old!
>> disabling graphviz functionality!!!!!!!!!
>> ./configure: test: -ge: unary operator expected
>> ./configure: =no: command not found
>> ./configure: test: =: unary operator expected
>> :
>>                    CFLAGS=-g -O2
>>                    LDFLAGS=-L/home/jlegato/SOSlibSWIG/xerces/lib 
>> -L/home/jlegato/SOSlibSWIG/libsbml2_3_4/lib 
>> -L/home/jlegato/SOSlibSWIG/sundials/lib
>>                    LIBS=
>> Can not link to GRAPHVIZ Library
>> odeSolver will be installed without Graphviz functionality
>> ./configure: test: =: unary operator expected
>> checking for isnan in -lm... yes
>> checking for egrep... grep -E
>> checking for ANSI C header files... yes
>> checking for sys/types.h... yes
>> checking for sys/stat.h... yes
>> checking for stdlib.h... yes
>> checking for string.h... yes
>> checking for memory.h... yes
>> checking for strings.h... yes
>> checking for inttypes.h... yes
>> checking for stdint.h... yes
>> checking for unistd.h... yes
>> checking errno.h usability... yes
>> checking errno.h presence... yes
>> checking for errno.h... yes
>> checking math.h usability... yes
>> checking math.h presence... yes
>> checking for math.h... yes
>> checking whether byte ordering is bigendian... no
>> checking for an ANSI C-conforming const... yes
>> checking for size_t... yes
>> configure: creating ./config.status
>> config.status: creating ./Makefile
>> config.status: creating examples/Makefile
>> config.status: creating odeSolver/Makefile
>> config.status: creating src/Makefile
>> config.status: creating src/libODES.pc
>> config.status: creating bindings/Makefile
>> config.status: creating bindings/swig/Makefile
>> config.status: creating bindings/perl/Makefile
>> config.status: creating bindings/perl/Makefile.PL
>> config.status: creating src/sbmlsolver/config.h
>> config.status: executing depfiles commands
>> ./configure: test: !=: unary operator expected
>> 
>> Build Settings for SBML_odeSolver v1.6.0:
>> ----------------------------------
>>   host type            =   shared lib extension =   install dir          = 
>> /home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0_installed
>>   CC                   = gcc
>>   CFLAGS               =   LDFLAGS              =   LIBS                 = 
>> -lm   SBML Library         = yes
>>        CFLAGS          = -I/home/jlegato/SOSlibSWIG/libsbml2_3_4/include 
>> -I/home/jlegato/SOSlibSWIG/libsbml2_3_4/include/sbml
>>        LDFLAGS         = -L/home/jlegato/SOSlibSWIG/libsbml2_3_4/lib
>>        LIBS            = -lsbml
>> SUNDIALS Library         = yes
>>        CFLAGS          = -I/home/jlegato/SOSlibSWIG/sundials-2.1.1/include
>>        LDFLAGS         = -L/home/jlegato/SOSlibSWIG/sundials-2.1.1/lib
>>        LIBS            = -lsundials_kinsol -lsundials_cvodes 
>> -lsundials_cvode -lsundials_nvecserial -lsundials_shared
>>   GRACE                = no
>> XMGRACE functionality will NOT be installed!
>>   GRAPHVIZ             = no
>> GRAPHVIZ functionality will NOT be installed!
>> 
>> NOTE:
>>      Unfortunately the current version of the SBML ODE Solver
>>      only works with the libSBML version >= 2.3.2. 
>> patching file `src/Makefile'
>> make[1]: Entering directory `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0'
>> Making all in src
>> make[2]: Entering directory 
>> `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0/src'
>> if g++ -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver 
>> -I/home/jlegato/SOSlibSWIG/sundials-2.1.1/include 
>> -I/home/jlegato/SOSlibSWIG/libsbml2_3_4/include 
>> -I/home/jlegato/SOSlibSWIG/libsbml2_3_4/include/sbml -I.    -g -O2 -MT 
>> ASTIndexNameNode.o -MD -MP -MF ".deps/ASTIndexNameNode.Tpo" -c -o 
>> ASTIndexNameNode.o ASTIndexNameNode.cpp; \
>> then mv -f ".deps/ASTIndexNameNode.Tpo" ".deps/ASTIndexNameNode.Po"; else rm 
>> -f ".deps/ASTIndexNameNode.Tpo"; exit 1; fi
>> ASTIndexNameNode.cpp:79: error: function `int 
>> ASTNode_isIndexName(ASTNode_t*)' definition is marked dllimport.
>> 
>> ASTIndexNameNode.cpp:87: error: function `unsigned int 
>> ASTNode_isSetIndex(ASTNode_t*)' definition is marked dllimport.
>> 
>> make[2]: *** [ASTIndexNameNode.o] Error 1
>> make[2]: Leaving directory 
>> `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0/src'
>> make[1]: *** [all-recursive] Error 1
>> make[1]: Leaving directory `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0'
>> make[1]: Entering directory `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0'
>> Making install in src
>> make[2]: Entering directory 
>> `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0/src'
>> if g++ -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver 
>> -I/home/jlegato/SOSlibSWIG/sundials-2.1.1/include 
>> -I/home/jlegato/SOSlibSWIG/libsbml2_3_4/include 
>> -I/home/jlegato/SOSlibSWIG/libsbml2_3_4/include/sbml -I.    -g -O2 -MT 
>> ASTIndexNameNode.o -MD -MP -MF ".deps/ASTIndexNameNode.Tpo" -c -o 
>> ASTIndexNameNode.o ASTIndexNameNode.cpp; \
>> then mv -f ".deps/ASTIndexNameNode.Tpo" ".deps/ASTIndexNameNode.Po"; else rm 
>> -f ".deps/ASTIndexNameNode.Tpo"; exit 1; fi
>> ASTIndexNameNode.cpp:79: error: function `int 
>> ASTNode_isIndexName(ASTNode_t*)' definition is marked dllimport.
>> 
>> ASTIndexNameNode.cpp:87: error: function `unsigned int 
>> ASTNode_isSetIndex(ASTNode_t*)' definition is marked dllimport.
>> 
>> make[2]: *** [ASTIndexNameNode.o] Error 1
>> make[2]: Leaving directory 
>> `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0/src'
>> make[1]: *** [install-recursive] Error 1
>> make[1]: Leaving directory `/home/jlegato/SOSlibSWIG/SBML_odeSolver-1.6.0'
>> make: *** [soslib] Error 2
>

---
Contractor