Question

kover installation problem: include could not find load file: GatbCore

0

Entering edit mode

7.3 years ago

hfan22 ▴ 40

Hi Alex or whoever could help:

operating system: Ubuntu 12.04.5 LTS (GNU/Linux 3.2.0-84-generic x86_64)

python version: 2.7.3

gcc (Ubuntu/Linaro 4.7.3-2ubuntu1~12.04) 4.7.3

GNU Fortran (Ubuntu/Linaro 4.6.4-1ubuntu1~12.04) 4.6.4

What I did:

Download kover

$ git clone https://github.com/aldro61/kover.git

Initiate virtual environment

$ cd kover

$ virtualenv venv

$ source venv/bin/activate

Prerequisites need to install myself

i. HDF5

Downloaded pre-build binary distributions Linux_2.6_CentOS_6_X86_64 from https://support.hdfgroup.org/HDF5/release/obtain5.html, copied things in bin, include and lib to kover/venv/bin, include or lib respectively.

ii. numpy and scipy

$ pip install numpy scipy

iii. Python development headers

$sudo apt-get install python-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
python-dev is already the newest version.

Install Kover. Note that only partial of the printscreen (I removed lines that don't seem to be relevant to the error such as copying stuff) are shown here in order to fit the 15000 characters limit.

$./install.sh

Installing setuptools.
Downloading https://pypi.python.org/packages/source/s/setuptools/setuptools-18.5.zip
Extracting in /tmp/tmp66V2oh
Now working in /tmp/tmp66V2oh/setuptools-18.5
Installing Setuptools
running install
running bdist_egg
running egg_info
writing requirements to setuptools.egg-info/requires.txt
writing setuptools.egg-info/PKG-INFO
writing top-level names to setuptools.egg-info/top_level.txt
writing dependency_links to setuptools.egg-info/dependency_links.txt
writing entry points to setuptools.egg-info/entry_points.txt
reading manifest file 'setuptools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'setuptools.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.7
copying easy_install.py -> build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/_markerlib
copying _markerlib/__init__.py -> build/lib.linux-x86_64-2.7/_markerlib
copying _markerlib/markers.py -> build/lib.linux-x86_64-2.7/_markerlib
creating build/lib.linux-x86_64-2.7/pkg_resources
copying pkg_resources/__init__.py -> build/lib.linux-x86_64-2.7/pkg_resources
creating build/lib.linux-x86_64-2.7/setuptools
copying setuptools/unicode_utils.py -> build/lib.linux-x86_64-2.7/setuptools
creating build/lib.linux-x86_64-2.7/setuptools/command
copying setuptools/command/install.py -> build/lib.linux-x86_64-2.7/setuptools/command
copying setuptools/script.tmpl -> build/lib.linux-x86_64-2.7/setuptools
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/_markerlib
copying build/lib.linux-x86_64-2.7/_markerlib/__init__.py -> build/bdist.linux-x86_64/egg/_markerlib
copying build/lib.linux-x86_64-2.7/_markerlib/markers.py -> build/bdist.linux-x86_64/egg/_markerlib
copying build/lib.linux-x86_64-2.7/easy_install.py -> build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/pkg_resources
copying build/lib.linux-x86_64-2.7/pkg_resources/__init__.py -> build/bdist.linux-x86_64/egg/pkg_resources
creating build/bdist.linux-x86_64/egg/pkg_resources/_vendor
copying build/lib.linux-x86_64-2.7/pkg_resources/_vendor/__init__.py -> build/bdist.linux-x86_64/egg/pkg_resources/_vendor
creating build/bdist.linux-x86_64/egg/pkg_resources/_vendor/packaging
copying build/lib.linux-x86_64-2.7/pkg_resources/_vendor/packaging/specifiers.py -> build/bdist.linux-x86_64/egg/pkg_resources/_vendor/packaging
byte-compiling build/bdist.linux-x86_64/egg/_markerlib/__init__.py to __init__.pyc
...
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying setuptools.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
...
creating dist
creating 'dist/setuptools-18.5-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing setuptools-18.5-py2.7.egg
Copying setuptools-18.5-py2.7.egg to /home/username/build/kover/venv/lib/python2.7/site-packages
Adding setuptools 18.5 to easy-install.pth file
Installing easy_install script to /home/username/build/kover/venv/bin
Installing easy_install-2.7 script to /home/username/build/kover/venv/bin

Installed /home/username/build/kover/venv/lib/python2.7/site-packages/setuptools-18.5-py2.7.egg
Processing dependencies for setuptools==18.5
Finished processing dependencies for setuptools==18.5
Building GATB tools
You need to run this command from the toplevel of the working tree.
You need to run this command from the toplevel of the working tree.
CMake Warning (dev) in CMakeLists.txt:
  Syntax Warning in cmake code at

    /home/username/build/kover/core/kover/dataset/tools/contigs_tools/CMakeLists.txt:108:42

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) in CMakeLists.txt:
  Syntax Warning in cmake code at

    /home/username/build/kover/core/kover/dataset/tools/contigs_tools/CMakeLists.txt:113:38

  Argument not separated from preceding token by whitespace.
This warning is for project developers.  Use -Wno-dev to suppress it.

-- The C compiler identification is GNU 4.7.3
-- The CXX compiler identification is GNU 4.7.3
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at CMakeLists.txt:49 (include):
  include could not find load file:

    GatbCore


-- Configuring incomplete, errors occurred!
See also "/home/username/build/kover/core/kover/dataset/tools/contigs_tools/build/CMakeFiles/CMakeOutput.log".
make: *** No targets specified and no makefile found.  Stop.
Installing Kover and its dependencies.
running install
running bdist_egg
running egg_info
creating kover.egg-info
writing requirements to kover.egg-info/requires.txt
writing kover.egg-info/PKG-INFO
writing top-level names to kover.egg-info/top_level.txt
writing dependency_links to kover.egg-info/dependency_links.txt
writing manifest file 'kover.egg-info/SOURCES.txt'
reading manifest file 'kover.egg-info/SOURCES.txt'
writing manifest file 'kover.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/kover
copying kover/__init__.py -> build/lib.linux-x86_64-2.7/kover
copying kover/utils.py -> build/lib.linux-x86_64-2.7/kover
creating build/lib.linux-x86_64-2.7/kover/dataset
copying kover/dataset/__init__.py -> build/lib.linux-x86_64-2.7/kover/dataset
copying kover/dataset/ds.py -> build/lib.linux-x86_64-2.7/kover/dataset
copying kover/dataset/split.py -> build/lib.linux-x86_64-2.7/kover/dataset
copying kover/dataset/create.py -> build/lib.linux-x86_64-2.7/kover/dataset
creating build/lib.linux-x86_64-2.7/kover/learning
copying kover/learning/experiment.py -> build/lib.linux-x86_64-2.7/kover/learning
copying kover/learning/__init__.py -> build/lib.linux-x86_64-2.7/kover/learning
creating build/lib.linux-x86_64-2.7/kover/dataset/tools
copying kover/dataset/tools/contigs_count.py -> build/lib.linux-x86_64-2.7/kover/dataset/tools
copying kover/dataset/tools/contigs_pack.py -> build/lib.linux-x86_64-2.7/kover/dataset/tools
copying kover/dataset/tools/__init__.py -> build/lib.linux-x86_64-2.7/kover/dataset/tools
creating build/lib.linux-x86_64-2.7/kover/learning/set_covering_machine
copying kover/learning/set_covering_machine/models.py -> build/lib.linux-x86_64-2.7/kover/learning/set_covering_machine
copying kover/learning/set_covering_machine/__init__.py -> build/lib.linux-x86_64-2.7/kover/learning/set_covering_machine
copying kover/learning/set_covering_machine/rules.py -> build/lib.linux-x86_64-2.7/kover/learning/set_covering_machine
copying kover/learning/set_covering_machine/scm.py -> build/lib.linux-x86_64-2.7/kover/learning/set_covering_machine
running build_ext
building 'kover/learning/set_covering_machine/popcount' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/kover
creating build/temp.linux-x86_64-2.7/kover/learning
creating build/temp.linux-x86_64-2.7/kover/learning/set_covering_machine
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -I/home/username/build/kover/venv/local/lib/python2.7/site-packages/numpy/core/include -c kover/learning/set_covering_machine/popcount.c -o build/temp.linux-x86_64-2.7/kover/learning/set_covering_machine/popcount.o -march=native
In file included from /usr/include/python2.7/numpy/ndarrayobject.h:26:0,
                 from /usr/include/python2.7/numpy/arrayobject.h:14,
                 from kover/learning/set_covering_machine/popcount.c:242:
/usr/include/python2.7/numpy/__multiarray_api.h:1532:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
In file included from /usr/include/python2.7/numpy/ufuncobject.h:152:0,
                 from kover/learning/set_covering_machine/popcount.c:243:
/usr/include/python2.7/numpy/__ufunc_api.h:226:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-x86_64-2.7/kover/learning/set_covering_machine/popcount.o -o build/lib.linux-x86_64-2.7/kover/learning/set_covering_machine/popcount.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/kover
copying build/lib.linux-x86_64-2.7/kover/__init__.py -> build/bdist.linux-x86_64/egg/kover
creating build/bdist.linux-x86_64/egg/kover/dataset
copying build/lib.linux-x86_64-2.7/kover/dataset/__init__.py -> build/bdist.linux-x86_64/egg/kover/dataset
creating build/bdist.linux-x86_64/egg/kover/dataset/tools
copying build/lib.linux-x86_64-2.7/kover/dataset/tools/contigs_count.py -> build/bdist.linux-x86_64/egg/kover/dataset/tools
...
byte-compiling build/bdist.linux-x86_64/egg/kover/__init__.py to __init__.pyc
...
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/kover/dataset/tools/contigs_tools
error: can't copy 'kover/dataset/tools/contigs_tools/build/bin/dsk2kover': doesn't exist or not a regular file
Cleaning up.
rm: cannot remove `dist': No such file or directory
Creating Kover executable.
Done.

As you can see it failed at:

CMake Error at CMakeLists.txt:49 (include):
  include could not find load file:

    GatbCore

Is it referring to this? https://github.com/GATB/gatb-core On their page it says Linux gcc 4.7 build failing. Is it why I'm failing as well? Btw there is no build folder under kover/core/kover/dataset/tools/contigs_tools/, therefore I did not find the CMakeOutput.log file.

Any help would be appreciated and thanks ahead.

Cheers,

Huan

kover • 3.1k views

ADD COMMENT • link updated 7.3 years ago by Alexandre Drouin ▴ 90 • written 7.3 years ago by hfan22 ▴ 40

0

Entering edit mode

Who is "Alex"?

ADD REPLY • link 7.3 years ago by Brian Bushnell 20k

0

Entering edit mode

The author of Kover.

ADD REPLY • link 7.3 years ago by hfan22 ▴ 40

0

Entering edit mode

Could you please add the "kover" tag to your post?

ADD REPLY • link 7.3 years ago by Alexandre Drouin ▴ 90

0

Entering edit mode

I thought I did! Isn't it besides the number of views?

ADD REPLY • link 7.3 years ago by hfan22 ▴ 40

0

Entering edit mode

You're right. Sorry about that!

ADD REPLY • link 7.3 years ago by Alexandre Drouin ▴ 90

score 2 · Accepted Answer · 2017-01-09

2

Entering edit mode

7.3 years ago

Alexandre Drouin ▴ 90

Hi Huan,

Try using:

git clone --recursive https://github.com/aldro61/kover.git

GATB is included as a submodule in Kover and when you don't use the "recursive" option, it doesn't get cloned. This is why the installer cannot find the GatbCore files.

Let me know if it works!

Alex

ADD COMMENT • link 7.3 years ago by Alexandre Drouin ▴ 90

1

Entering edit mode

Thanks Alex.

Yes that was exactly the problem. I was able to replicate the results from your example as well. Great documentation!

Cheers, Huan

ADD REPLY • link 7.3 years ago by hfan22 ▴ 40