Problems with new installation

[Develbold]

I'm trying to do a clean install. Running command

girderformindlogger build

from step3 produces the following error message:

/.../mindlogger-backend/girderformindlogger/init.py:42: SyntaxWarning: "is not" with a literal. Did you mean "!="?
if env is not 'localhost':
Traceback (most recent call last):
File "/.../backend/lib/python3.8/site-packages/cherrypy/lib/reprconf.py", line 213, in as_dict
value = unrepr(value)
File "/.../backend/lib/python3.8/site-packages/cherrypy/lib/reprconf.py", line 508, in unrepr
return b.build(obj)
File "/.../backend/lib/python3.8/site-packages/cherrypy/lib/reprconf.py", line 354, in build
raise TypeError('unrepr does not recognize %s' %
TypeError: unrepr does not recognize 'Constant'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/.../backend/bin/girderformindlogger", line 33, in
sys.exit(load_entry_point('girderformindlogger', 'console_scripts', 'girderformindlogger')())
File "/.../backend/bin/girderformindlogger", line 25, in importlib_load_entry_point
return next(matches).load()
File "/usr/lib/python3.8/importlib/metadata.py", line 77, in load
module = import_module(match.group('module'))
File "/usr/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 961, in _find_and_load_unlocked
File "", line 219, in _call_with_frames_removed
File "", line 1014, in _gcd_import
File "", line 991, in _find_and_load
File "", line 975, in _find_and_load_unlocked
File "", line 671, in _load_unlocked
File "", line 783, in exec_module
File "", line 219, in _call_with_frames_removed
File "/.../mindlogger-backend/girderformindlogger/init.py", line 34, in
config.loadConfig() # Populate the config info at import time
File "/.../mindlogger-backend/girderformindlogger/utility/config.py", line 54, in loadConfig
_loadConfigsByPrecedent()
File "/.../mindlogger-backend/girderformindlogger/utility/config.py", line 49, in _loadConfigsByPrecedent
_mergeConfig(curConfigPath)
File "/.../mindlogger-backend/girderformindlogger/utility/config.py", line 15, in _mergeConfig
cherrypy._cpconfig.merge(cherrypy.config, filename)
File "/.../backend/lib/python3.8/site-packages/cherrypy/_cpconfig.py", line 139, in merge
for section, value_map in reprconf.as_dict(other).items():
File "/.../backend/lib/python3.8/site-packages/cherrypy/lib/reprconf.py", line 46, in as_dict
config = Parser().dict_from_file(config)
File "/.../backend/lib/python3.8/site-packages/cherrypy/lib/reprconf.py", line 228, in dict_from_file
return self.as_dict()
File "/.../backend/lib/python3.8/site-packages/cherrypy/lib/reprconf.py", line 219, in as_dict
raise ValueError(msg, x.class.name, x.args)
ValueError: ('Config error in section: 'global', option: 'server.socket_host', value: '"127.0.0.1"'. Config values must be valid Python.', 'TypeError', ("unrepr does not recognize 'Constant'",))

what am I missing here?

[TheMightyMoe]

Sadly getting the same error message

[jj105]

could you try using python3.7?
I was having similar issue in the past when I was using python3.8.

[ristau-marc-auticon]

python 3.7 failed for me too after having had the same issues with 3.8

[jj105]

@devmrac could you show me your error message?

[TheMightyMoe]

@jj105 heres the error. After running the setupscript
pip install -e .
which is installing pandas it comes also to a numpy error: NUMPY_IMPORT_ARRAY_RETVAL
Maybe solved it last time with downgrading numpy, but i am not exactly sure
Output (reduced to the most nessecary):

Running setup.py install for pandas ... error
ERROR: Command errored out with exit status 1:
command: /home/ubuntu/girder_env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-07_0_j_n/pandas_32df6ba889094767a835d17f2ebcf3c6/setup.py'"'"'; file='"'"'/tmp/pip-install-07_0_j_n/pandas_32df6ba889094767a835d17f2ebcf3c6/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-6ktae7yf/install-record.txt --single-version-externally-managed --compile --install-headers /home/ubuntu/girder_env/include/site/python3.8/pandas
cwd: /tmp/pip-install-07_0_j_n/pandas_32df6ba889094767a835d17f2ebcf3c6/
Complete output (1731 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/pandas
[...]
In file included from pandas/_libs/tslibs/src/datetime/np_datetime.c:24:
/usr/include/python3.8/datetime.h:189:25: warning: ‘PyDateTimeAPI’ defined but not used [-Wunused-variable]
189 | static PyDateTime_CAPI *PyDateTimeAPI = NULL;
| ^~~~~~~~~~~~~
x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DNPY_NO_DEPRECATED_API=0 -Ipandas/_libs/src/klib -Ipandas/_libs/src -Ipandas/_libs/tslibs/src -Ipandas/_libs/tslibs -I/home/ubuntu/girder_env/lib/python3.8/site-packages/numpy/core/include -I/home/ubuntu/girder_env/include -I/usr/include/python3.8 -c pandas/_libs/tslibs/src/datetime/np_datetime_strings.c -o build/temp.linux-x86_64-3.8/pandas/_libs/tslibs/src/datetime/np_datetime_strings.o -Wno-unused-function
In file included from pandas/_libs/tslibs/src/datetime/np_datetime.h:25,
from pandas/_libs/tslibs/src/datetime/np_datetime_strings.c:37:
/usr/include/python3.8/datetime.h:189:25: warning: ‘PyDateTimeAPI’ defined but not used [-Wunused-variable]
189 | static PyDateTime_CAPI *PyDateTimeAPI = NULL;
| ^~~~~~~~~~~~~
[...]
pandas/_libs/internals.c: In function ‘__pyx_gb_6pandas_5_libs_9internals_8generator:
pandas/_libs/internals.c:9237:36: warning: ‘__pyx_t_23’ may be used uninitialized in this function [-Wmaybe-uninitialized]
9237 | __pyx_cur_scope-__pyx_t_9 = __pyx_t_23;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pandas/_libs/internals.c:8964:36: warning: ‘__pyx_t_11’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8964 | __pyx_cur_scope-__pyx_t_5 = __pyx_t_11;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pandas/_libs/internals.c:8961:36: warning: ‘__pyx_t_6’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8961 | __pyx_cur_scope-__pyx_t_4 = __pyx_t_6;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
pandas/_libs/internals.c:8966:36: warning: ‘__pyx_t_15’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8966 | __pyx_cur_scope-__pyx_t_8 = __pyx_t_15;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pandas/_libs/internals.c:8965:36: warning: ‘__pyx_t_12’ may be used uninitialized in this function [-Wmaybe-uninitialized]
8965 | __pyx_cur_scope-__pyx_t_7 = __pyx_t_12;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[...]
pandas/_libs/src/ujson/python/objToJSON.c:181:12: error: ‘NUMPY_IMPORT_ARRAY_RETVAL’ undeclared (first use in this function)
181 | return NUMPY_IMPORT_ARRAY_RETVAL;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
pandas/_libs/src/ujson/python/objToJSON.c:181:12: note: each undeclared identifier is reported only once for each function it appears in
pandas/_libs/src/ujson/python/objToJSON.c:182:1: warning: control reaches end of non-void function [-Wreturn-type]
182 | }
| ^
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

[jj105]

@TheMightyMoe did you try using python3.7?

[TheMightyMoe]

@jj105 see above
Waiting for a new release, as i heard there will be some

[jj105]

@TheMightyMoe
I rechecked your message think your above message is one from python3.8 not python3.7.
by the way, which OS are you using?

[TheMightyMoe]

@jj105
Oh It seems you are right (.../usr/include/python3.8/datetime.h:189:25: warning...) strange...
Because we uninstalled python 3.8 and installed python 3.8
We will check it. We are using Ubuntu Server

[WorldImpex]

@TheMightyMoe or Develbold - Do you require any further assistance?

[TheMightyMoe]

The problem is, that
sudo apt-get install pip
installes the newest Version of python pip (in my case 3.8) even if I remove python 3.8 with all its dependencies and install python 3.7. The command
sudo apt-get install python3.7-pip
unfortunately doesn't exist.

Does anyone have a solution or a hint to solve this?
Or is a new verion of mindlogger backend available?

[TheMightyMoe]

We tried it with installing a python3.7 version of pip using the script python3.7 get-pip.py installed using
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
So Pip was successfully installed without using python3.8 packaged but unfortunately this has not been the solution.
Here the full output:
ERROR: Command errored out with exit status 1: command: /usr/bin/python3.7 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-t4krda2_/psutil_0055b38908e445a59c0d66e01cd7045d/setup.py'"'"'; __file__='"'"'/tmp/pip-install-t4krda2_/psutil_0055b38908e445a59c0d66e01cd7045d/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-7n8g0cgs/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.7/psutil cwd: /tmp/pip-install-t4krda2_/psutil_0055b38908e445a59c0d66e01cd7045d/ Complete output (44 lines): running install running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/psutil copying psutil/_psosx.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_compat.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_psposix.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/__init__.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_common.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.7/psutil copying psutil/_psaix.py -> build/lib.linux-x86_64-3.7/psutil creating build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/__init__.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_process.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/runner.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/__main__.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_memory_leaks.py -> build/lib.linux-x86_64-3.7/psutil/tests copying psutil/tests/test_system.py -> build/lib.linux-x86_64-3.7/psutil/tests running build_ext building 'psutil._psutil_linux' extension creating build/temp.linux-x86_64-3.7 creating build/temp.linux-x86_64-3.7/psutil x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fdebug-prefix-map=/build/python3.7-uNfk84/python3.7-3.7.10=. -fstack-protector-strong -Wformat -Werror=format-security -g -fdebug-prefix-map=/build/python3.7-uNfk84/python3.7-3.7.10=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=566 -DPSUTIL_LINUX=1 -I/usr/include/python3.7m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.7/psutil/_psutil_common.o psutil/_psutil_common.c:9:10: fatal error: Python.h: No such file or directory 9 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Its a different error then the NUMPY Error from using python3.8

[WorldImpex]

@TheMightyMoe

Without having access to your environment it is hard to help further with your request

[TheMightyMoe]

@WorldImpex

Having you access to our mindlogger backend would not be possible, but we could organize a video call with screenshare.
Is this possible for you?

[WorldImpex]

Could you provide contact details @TheMightyMoe ?