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Geophysical Inversion and Modeling Library :earth_africa:
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Problem building pygimli with python3.5 #38

Closed kodaz1 closed 8 years ago

kodaz1 commented 8 years ago

hello, I'm trying to build pygimli with python3.5 cause i upgrade my system to ubuntu16.04 LTS which is using python3.5 instead of python3.4 on ubuntu14.04 on a 64 bits system .

After installing all the dependencies the same error occurs when i use the build script curl -Ls install.pygimli.org | bash or when i run step buy step the building process as you explain it in the documentation. I mainly notice these lines: CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:178 (include): include could not find load file: /usr/share/llvm/cmake/LLVMExports.cmake Call Stack (most recent call first): CMakeLists.txt:64 (find_package) CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:181 (include): include could not find load file: /usr/share/llvm/cmake/LLVM-Config.cmake Call Stack (most recent call first): CMakeLists.txt:64 (find_package) CMake Error at src/CMakeLists.txt:46 (llvm_map_components_to_libnames): Unknown CMake command "llvm_map_components_to_libnames".

*\ Please tell me who you are. Run git config --global user.email "you@example.com" git config --global user.name "Your Name" to set your account's default identity. Omit --global to set the identity only in this repository. fatal: unable to auto-detect email address (got 'fadisaac@gnutrip.(none)')

~/gimli/thirdParty/src ~/gimli/thirdParty abort: couldn't find mercurial libraries in [/usr/bin /usr/lib/python35.zip /usr/lib/python3.5 /usr/lib/python3.5/plat-x86_64-linux-gnu /usr/lib/python3.5/lib-dynload /home/fadisaac/.local/lib/python3.5/site-packages /usr/local/lib/python3.5/dist-packages /usr/lib/python3/dist-packages](check your install and PYTHONPATH)

Sorry to disturb you but do you have any idea on what is happening if you have a little time to look at the problem.

Thank you for your help the logfile is in attachment. log.txt

carsten-forty2 commented 8 years ago

hello,

there are 2 problems .. the first is that you cannot build castXML
(which we need to generate the python bindings) due a possible wrong
or uncomplete llvm installation on your ubuntu. Second seems that the
git update fails to fetch pygccxml and pyplusplus.

The second problem seems easy to solve by removing the
thirdParty/src/pygccxml and thirdParty/src/pyplusplus

The first is castXML or ubuntu related, you can either use an old
castxml binary (if you still have) or take a look at there issuetracker:

https://github.com/CastXML/CastXML/issues/53

e.g.: Please make sure the libclang-3.8-dev package is installed.

Hope this helps ..

Quoting kodaz1 notifications@github.com:

hello, I'm trying to build pygimli with python3.5 cause i upgrade my
system to ubuntu16.04 LTS which is using python3.5 instead of
python3.4 on ubuntu14.04 on a 64 bits system .

After installing all the dependencies the same error occurs when i
use the build script curl -Ls install.pygimli.org | bash or when i run step buy step the building process as you explain it
in the documentation. I mainly notice these lines: CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:178 (include): include could not find load file: /usr/share/llvm/cmake/LLVMExports.cmake Call Stack (most recent call first): CMakeLists.txt:64 (find_package) CMake Error at /usr/share/llvm-3.8/cmake/LLVMConfig.cmake:181 (include): include could not find load file: /usr/share/llvm/cmake/LLVM-Config.cmake Call Stack (most recent call first): CMakeLists.txt:64 (find_package) CMake Error at src/CMakeLists.txt:46 (llvm_map_components_to_libnames): Unknown CMake command "llvm_map_components_to_libnames".

*\ Please tell me who you are. Run git config --global user.email "you@example.com" git config --global user.name "Your Name" to set your account's default identity. Omit --global to set the identity only in this repository. fatal: unable to auto-detect email address (got 'fadisaac@gnutrip.(none)')

~/gimli/thirdParty/src ~/gimli/thirdParty abort: couldn't find mercurial libraries in [/usr/bin
/usr/lib/python35.zip /usr/lib/python3.5
/usr/lib/python3.5/plat-x86_64-linux-gnu
/usr/lib/python3.5/lib-dynload
/home/fadisaac/.local/lib/python3.5/site-packages
/usr/local/lib/python3.5/dist-packages /usr/lib/python3/dist-packages](check your install and PYTHONPATH)

Sorry to disturb you but do you have any idea on what is happening
if you have a little time to look at the problem.

Thank you for your help the logfile is in attachment. log.txt


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kodaz1 commented 8 years ago

Hello , Thank you for your help . libclang3.8-dev was already installed but it doesn't work. I try to install all packages referring to clang3.8 or llvm3.8 but i still can't build castxml . Perhaps it's an idea to downgrade to clang3.7 and llvm 3.7.

kodaz1 commented 8 years ago

Hello Carsten, castxml have been compiled and build after downgrading clang3.8 and llvm3.8 to clang3.7 and llvm 3.7 and changing the python priority (python2.7 to python3.5) using: update-alternatives --config python It seems that the problem was due to a Debian packaging bug in clang3.8 : https://github.com/CastXML/CastXML/issues/58 But pygccxml and pyplusplus still doesn't compile and the same error occurs even when i try with python3.4: abort: couldn't find mercurial libraries in /usr/bin /usr/lib/python35.zip /usr/lib/python3.5 /usr/lib/python3.5/plat-x86_64-linux-gnu /usr/lib/python3.5/lib-dynload /home/fadisaac/.local/lib/python3.5/site-packages /usr/local/lib/python3.5/dist-packages /usr/lib/python3/dist-packages

I have tried to add to the pythonpath, the path to the mercurial libs : /usr/lib/python2.7/dist-packages/mercurial but it doesn't work I have copied the mercurial libs into /usr/lib/python3.5/mercurial before retrying and i got the following error : Traceback (most recent call last): File "/usr/bin/hg", line 41, in mercurial.util.setbinary(fp) File "/usr/lib/python3.5/mercurial/demandimport.py", line 130, in getattribute self._load() File "/usr/lib/python3.5/mercurial/demandimport.py", line 96, in _load mod = _hgextimport(_import, head, globals, locals, None, level) File "/usr/lib/python3.5/mercurial/demandimport.py", line 53, in _hgextimport return importfunc(name, globals, _args, *_kwargs) ..... You can find the complete logfile in attachment. thank you for your help log1.txt

carsten-forty2 commented 8 years ago

Do you have mercurial installed?

does a

hg --version

works?

pygccxml and pyplusplus does not need to be compiled .. both will just
be cloned from there respective locations with git(pygccxml) and
mercurial(pyplusplus

Quoting kodaz1 notifications@github.com:

Hello Carsten, castxml have been compiled and build after downgrading clang3.8 and
llvm3.8 to clang3.7 and llvm 3.7 and changing the python priority
(python2.7 to python3.5) using: update-alternatives --config python It seems that the problem was due to a Debian packaging bug in
clang3.8 : https://github.com/CastXML/CastXML/issues/58 But pygccxml and pyplusplus still doesn't compile and the same error
occurs even when i try with python3.4: abort: couldn't find mercurial libraries in /usr/bin
/usr/lib/python35.zip /usr/lib/python3.5
/usr/lib/python3.5/plat-x86_64-linux-gnu
/usr/lib/python3.5/lib-dynload
/home/fadisaac/.local/lib/python3.5/site-packages
/usr/local/lib/python3.5/dist-packages /usr/lib/python3/dist-packages

I have tried to add to the pythonpath, the path to the mercurial libs : /usr/lib/python2.7/dist-packages/mercurial but it doesn't work I have copied the mercurial libs into /usr/lib/python3.5/mercurial
before retrying and i got the following error : Traceback (most recent call last): File "/usr/bin/hg", line 41, in mercurial.util.setbinary(fp) File "/usr/lib/python3.5/mercurial/demandimport.py", line 130, in
getattribute self._load() File "/usr/lib/python3.5/mercurial/demandimport.py", line 96, in _load mod = _hgextimport(_import, head, globals, locals, None, level) File "/usr/lib/python3.5/mercurial/demandimport.py", line 53, in
_hgextimport return importfunc(name, globals, _args, *_kwargs) ..... You can find the complete logfile in attachment. thank you for your help log1.txt


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kodaz1 commented 8 years ago

hello Yes mercurial is already installed and the libraries are in , /usr/lib/python2.7/dist-packages/mercurial

carsten-forty2 commented 8 years ago

I know nothing about mercurial and python .. the question is if

hg clone https://bitbucket.org/ompl/pyplusplus

works?

Quoting kodaz1 notifications@github.com:

hello Yes mercurial is already installed and the libraries are in , /usr/lib/python2.7/dist-packages/mercurial


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kodaz1 commented 8 years ago

Sorry i haven't seen your answer
yes hg works fine

carsten-forty2 commented 8 years ago

the latest log states that the hg command fails .. is your problem solved now?

kodaz1 commented 8 years ago

2016-05-09 14:34 GMT+02:00 carsten-forty2 notifications@github.com: Hello Carsten I was finally able to install pygimli with the anaconda suite a few days ago. That solved the problem. Thank you for your support. Sorry but i still need your help for BERT . I wrote mails in order to be allow to download and install it. Please, can you help me for that. I 'm on Xubuntu 16.04 / 64 bits

Best regards

2016-05-09 14:34 GMT+02:00 carsten-forty2 notifications@github.com:

the latest log states that the hg command fails .. is your problem solved now?

the latest log states that the hg command fails .. is your problem solved now?

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carsten-forty2 commented 8 years ago

For BERT related question please see: https://gitlab.com/resistivity-net/bert

You probably need an account there so I can add you into the BERT user list.

Best regards, Carsten

florian-wagner commented 8 years ago

We don't have a bert package in anaconda yet, but if @carsten-forty2 and @halbmy are okay with it, I can quickly compile one for you, so that you are able to do a quick conda install -c gimli bert.

kodaz1 commented 8 years ago

2016-05-23 15:16 GMT+02:00 Florian Wagner notifications@github.com:

We don't have a bert package in anaconda yet, but if @carsten-forty2 https://github.com/carsten-forty2 and @halbmy https://github.com/halbmy are okay with it, I can quickly compile one for you, so that you are able to do a quick conda install -c gimli bert.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/gimli-org/gimli/issues/38#issuecomment-220976982

kodaz1 commented 8 years ago

Sorry florian , I'm confused, I called you Carsten.

2016-05-23 15:38 GMT+02:00 Tenten Ten mapuke@gmail.com:

hello Carsten, I'm waiting for there answer thank you very much for your proposition. I'll give you the feedback as soon as they give me an answer.

2016-05-23 15:16 GMT+02:00 Florian Wagner notifications@github.com:

We don't have a bert package in anaconda yet, but if @carsten-forty2 https://github.com/carsten-forty2 and @halbmy https://github.com/halbmy are okay with it, I can quickly compile one for you, so that you are able to do a quick conda install -c gimli bert.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/gimli-org/gimli/issues/38#issuecomment-220976982

kodaz1 commented 8 years ago

2016-05-23 15:38 GMT+02:00 Tenten Ten mapuke@gmail.com:

hello Carsten, I'm waiting for there answer thank you very much for your proposition. I'll give you the feedback as soon as they give me an answer.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/gimli-org/gimli/issues/38#issuecomment-220976982

carsten-forty2 commented 8 years ago

This issue tracker here is only GIMLi related.

There is a different location for the BERT Project. https://gitlab.com/resistivity-net/bert/

Until now you need to register at http://gitlab.com/ and we need to invite you to the BERT community.

Please write me a PM or an email with your gitlab account name.