[gmx-developers] libxml2 detection problem (bug?)

[Christoph Junghans]

The libraries needed for static linking are already in
PC_LIBXML_STATIC_LIBRARIES if libxml was detected via pkg-config.
However, to make it more bullet-proof it might be useful to add libm
and libz if the linking fails.

Christoph


2014-07-02 13:43 GMT-06:00 Roland Schulz <roland at utk.edu>:
> Hi,
>
> static libraries don't pull in dependencies automatically. Thus this error.
> We could
> 1) Skip the check whether we can link the library (check_library_exists) if
> the library is static. Then if the library which was found is not OK (e.g.
> 32bit instead of 64bit, or host instead of Phi) then the user will only get
> a error at the end of the build.
> 2) Do the same as we do in FindFFTW and manually add the dependencies before
> check_library_exists:
>   if (HAVE_LIBM)
>     #adding MATH_LIBRARIES here to allow static libs, this does not harm us
> as we are anyway using it
>     set(CMAKE_REQUIRED_LIBRARIES m)
>   endif ()
>
> Roland
>
>
>
>
> On Wed, Jul 2, 2014 at 3:35 PM, Szilárd Páll <pall.szilard at gmail.com> wrote:
>>
>> Hi,
>>
>> I'm having trouble getting libxml2 detection pass with
>> -DGMX_PREFER_STATIC_LIBS=ON with 5.0 release.
>>
>> I keep getting:
>> -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.a (found version
>> "2.7.8")
>> -- Looking for xmlTextWriterEndAttribute in
>> /usr/lib/x86_64-linux-gnu/libxml2.a
>> -- Looking for xmlTextWriterEndAttribute in
>> /usr/lib/x86_64-linux-gnu/libxml2.a - not found
>>
>> even though:
>> nm -g /usr/lib/x86_64-linux-gnu/libxml2.a | grep -i
>> xmlTextWriterEndAttribute
>> 0000000000001090 T xmlTextWriterEndAttribute
>>
>> It looks like the trouble is caused by some linking order issue
>> because I see this in the CMakeError.log:
>>
>> /usr/bin/gcc-4.8  -Wno-maybe-uninitialized -Wextra
>> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer
>> -arith -Wall -Wno-unused -Wunused-value -Wunused-parameter
>> -DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
>>     CMakeFiles/cmTryCompileExec3409173216.dir/CheckFunctionExists.c.o
>> -o cmTryCompileExec3409173216 -rdynamic
>>  -Wl,-Bstatic -lxml2 -Wl,-Bdynamic
>>
>> /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/libxml2.a(xmlIO.o):
>> In function `xmlGzfileOpenW':
>> (.text+0x253): undefined reference to `gzdopen'
>>
>> /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/libxml2.a(xmlIO.o):
>> In function `xmlGzfileOpenW':
>> (.text+0x285): undefined reference to `gzopen64'
>>
>> /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/libxml2.a(xmlIO.o):
>> In function `xmlFreeZMemBuff':
>> (.text+0x2f8): undefined reference to `deflateEnd'
>>
>> /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/libxml2.a(xmlIO.o):
>> In function `xmlGzfileClose':
>> (.text+0x995): undefined reference to `gzclose'
>>
>> ... and so one with all kinds of libz and even math.h functions listed.
>>
>> Any idea what's going on?
>>
>> Cheers,
>> --
>> Szilárd
>> --
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>
>
>
>
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-- 
Christoph Junghans
Web: http://www.compphys.de