search

mdozmorov / genome_runner

Academic Free License v3.0
0 stars 3 forks source link

setup_cg.sh installation issues #104

Closed mdozmorov closed 9 years ago

mdozmorov commented 9 years ago

When everything is installed from .deb packages, there are numerous errors. So, we are back to installing python packages through apt-get.

When installing main GR as 'sudo python setup.py install', that is, as a package, OLD interface shows up! Same when installing in developer mode.

When installing main GR as 'sudo python setup.py install develop -d /usr/local/lib/python2.7/dist-packages/', that is, in developer mode, error arises, below. Cured by removing 'install_requires' section from 'setup.py':

int exp (void); ^ _configtest.o: In function main': /tmp/easy_install-JSD6vn/numpy-1.9.2/_configtest.c:6: undefined reference toexp' collect2: error: ld returned 1 exit status _configtest.o: In function main': /tmp/easy_install-JSD6vn/numpy-1.9.2/_configtest.c:6: undefined reference toexp' collect2: error: ld returned 1 exit status _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ [enabled by default] int exp (void); ^ _configtest.c:1:20: fatal error: Python.h: No such file or directory

include 

                ^

compilation terminated. _configtest.c:1:20: fatal error: Python.h: No such file or directory

include 

                ^

compilation terminated. Traceback (most recent call last): File "setup.py", line 36, in "redis == 2.10.0" File "/usr/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 73, in run File "build/bdist.linux-x86_64/egg/setuptools/command/install.py", line 101, in do_egg_install File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 358, in run File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 574, in easy_install File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 625, in install_item File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 671, in process_distribution File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 563, in resolve entry = dist.location File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 801, in best_match

File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 813, in obtain

File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 593, in easy_install File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 623, in install_item File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 809, in install_eggs File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 1015, in build_and_install File "build/bdist.linux-x86_64/egg/setuptools/command/easy_install.py", line 1000, in run_setup File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 50, in run_setup File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 100, in run File "build/bdist.linux-x86_64/egg/setuptools/sandbox.py", line 52, in File "setup.py", line 251, in

File "setup.py", line 243, in setup_package

File "/tmp/easy_install-JSD6vn/numpy-1.9.2/numpy/distutils/core.py", line 169, in setup File "/usr/lib/python2.7/distutils/core.py", line 151, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "build/bdist.linux-x86_64/egg/setuptools/command/bdist_egg.py", line 177, in run File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/easy_install-JSD6vn/numpy-1.9.2/numpy/distutils/command/egg_info.py", line 10, in run File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/easy_install-JSD6vn/numpy-1.9.2/numpy/distutils/command/build_src.py", line 153, in run File "/tmp/easy_install-JSD6vn/numpy-1.9.2/numpy/distutils/command/build_src.py", line 170, in build_sources File "/tmp/easy_install-JSD6vn/numpy-1.9.2/numpy/distutils/command/build_src.py", line 329, in build_extension_sources File "/tmp/easy_install-JSD6vn/numpy-1.9.2/numpy/distutils/command/build_src.py", line 386, in generate_sources File "numpy/core/setup.py", line 432, in generate_config_h

File "numpy/core/setup.py", line 42, in check_types

File "numpy/core/setup.py", line 293, in check_types

SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

mdozmorov commented 9 years ago

dbcreator_encode is not installed as a module.