Re: Cmake help needed (Was: Unresolved ${java:Depends} (Was: IGV))
On 10/24/18 1:12 PM, Andreas Tille wrote:
> On Wed, Oct 24, 2018 at 01:03:50PM +0200, Olivier Sallou wrote:
>> On 10/24/18 11:49 AM, Andreas Tille wrote:
>>> On Wed, Oct 24, 2018 at 11:37:34AM +0200, Olivier Sallou wrote:
>>>>> 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... :-(
>>> Hmmmm, if I remember correctly you know the authors. Would you mind
>>> asking them about this issue?
>> code is not managed locally anymore, so no local contact anymore :-(
>>
>> but I remember that indeed tools based on gatb were close to specific
>> gatb versions (maybe was not stable enough at some time....)
>>
>> cmake code from gatb explicitly specifies that gatb code should be in
>> sub dir of tool that needs to be linked against.
> Hmmmm, anyway - I'd love if we could find a (hopefully clean) way to
> update discosnp and minia to the latest upstream versions. Its probably
> not good to lag heavily behind upstream.
minia 3.2 needs a gatb-core more recent than code in 1.4.1
the minia code do some calls to gatbcore functions with different number
of parameters.
Means gatbcore ABI has been modified since, though no new release was done.
example:
in core v1.4.1, src/gatb/bcalm2/bglue_algo.hpp, line ~137 , we have
this definition
void bglue(gatb::core::tools::storage::impl::Storage* storage,
std::string prefix,
int kmerSize,
int nb_threads,
bool verbose
);
}}}}
with 5 arguments, ut minia calls it with 6 argiments:
so minia depends on an unreleased gatb core ......
methods switched to 6 arguments ~9 month ago, but gatb has not been
released since Dec 2017.....
Remaining option is to include the gatb-core source code from minia
(etc...) and compile code with this one.
In minia git repo, gatbcore is in thridparty dir as a sub module.
>
> 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)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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