Re: Cmake help needed (Was: Unresolved ${java:Depends} (Was: IGV))
On 10/24/18 11:08 AM, Olivier Sallou wrote:
> On 10/24/18 10:56 AM, Olivier Sallou wrote:
>> On 10/24/18 9:51 AM, Andreas Tille wrote:
>>> On Wed, Oct 24, 2018 at 09:13:51AM +0200, Olivier Sallou wrote:
>>>>> PS: Do you have some free resources to check the cmake issue with gatb-core?
>>>> which issue ? Have not seen related mail.
>>> https://lists.debian.org/debian-med/2018/10/msg00073.html
>>> says:
>>> since a long time there are new versions of discosnp and minia which
>>> Build-Depend from gatb-core. Gatb-core is packaged and includes the
>>> cmake information - but it is not found by discosnp and minia.
>>>
>>> Just try to build discosnp or minia from Git and you see that
>>> it fails to detect gatb-core despite the package is installed.
>>>
>>>> I can try, but I am not really a cmake expert...
>>> If nobody else can help I could ask on debian-mentors.
>> I had a quick look.
>>
>> 1) in minia, ... there is a need to patch the CMakeLists.txt cmake
>> module path to have:
>>
>>
>> -SET (CMAKE_MODULE_PATH ${GATB_CORE_HOME}/cmake)
>>
>> +SET (CMAKE_MODULE_PATH /usr/lib/x86_64-linux-gnu/cmake)
>>
>> I don't know how to manage arch related path here (x86_64)....
>>
>>
>> with this it finds the gatbcore cmake module.
>>
>> However, this does not work (fails later on) because it looks for gatb
>> source files in some local sub directories (GatbCore.cmake)
>>
>> the gatbcore.cmake expects to find all gatb source code in specific sub
>> dir and copy those files to compile them with current software.....
>>
>> This is not what we want in debian, as we only want to link against library.
>>
>>
>> So I think that this module should not be loaded, and cmake for minia
>> etc... be modified to link against gatb lib (don't know yet how)
> at least for minia, code tries to use some gatb third party code
> (gatb-core/thirdparty/json)
>
> so gatb core may need to add in its -dev includes those thridparty code
> headers too.....
even with local patching to use missing gatdb thridparty includes, code
fails to compile, I think it expects a specific version of gatb-core as
failures are link to invalid number of arguments (given vs expected,
type conversions etc....
So i think that minia source code does not match gatb-core debian one,
and fixing it may need quite a lot patches in minia etc...
Else, minia should ship with its source code the expected gatdb code and
be linked against it... :-(
>
>
>>
>>> Kind regards
>>>
>>> Andreas.
>>>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
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