Re: Java help for beast needed
Le 6/6/12 8:28 AM, Olivier Sallou a écrit :
>
> Le 6/5/12 4:56 PM, Andreas Tille a écrit :
>> Hi,
>>
>> after now having all preconditions for beast packaged in Debian upstream
>> had release a new version meanwhile. I was quite optimistic but now I
>> was running into Java detail problems:
>>
>>
>> compile-all:
>> [mkdir] Created dir: /home/tillea/debian-maintain/repack/beast/beast-mcmc-1.7.2/build
>> [javac] /home/tillea/debian-maintain/repack/beast/beast-mcmc-1.7.2/build.xml:67: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
>> [javac] Compiling 1875 source files to /home/tillea/debian-maintain/repack/beast/beast-mcmc-1.7.2/build
>> [javac] /home/tillea/debian-maintain/repack/beast/beast-mcmc-1.7.2/src/dr/app/beagle/evomodel/sitemodel/EpochBranchSubstitutionModel.java:463: cannot find symbol
>> [javac] symbol : method convolveTransitionMatrices(int[],int[],int[],int)
>> [javac] location: interface beagle.Beagle
>> [javac] beagle.convolveTransitionMatrices(firstConvolutionBuffers, // A
>> [javac] ^
>> [javac] Note: Some input files use or override a deprecated API.
>> [javac] Note: Recompile with -Xlint:deprecation for details.
>> [javac] Note: Some input files use unchecked or unsafe operations.
>> [javac] Note: Recompile with -Xlint:unchecked for details.
>> [javac] 1 error
>>
>>
>> Any idea? (You can get the upstream source tarball via
> After a look, it appears that beagle package (beagle/beagle.java) does
> not provide method
>
> convolveTransitionMatrices
>
>
> So I think there is a version issue between beagle and beast-mcmc use of
> beagle (too recent or not recent enough)
> Olivier
It is available is Beast 1.1, you should upgrade package first... :-(
Olivier
>> uscan --verbose --force-depends
>>
>> )
>>
>> Kind regards
>>
>> Andreas.
>>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
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