`pip install` fails with Python 3.7 #132

ghost · 2018-09-05T23:22:39Z

Unable to install with python3.7.

$ pip install line_profiler --user
Collecting line_profiler
  Using cached https://files.pythonhosted.org/packages/14/fc/ecf4e238bb601ff829068e5a72cd1bd67b0ee0ae379db172eb6a0779c6b6/line_profiler-2.1.2.tar.gz
Requirement already satisfied: IPython>=0.13 in /home/taha/.local/lib/python3.7/site-packages (from line_profiler) (6.5.0)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (4.6.0)
Requirement already satisfied: pickleshare in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (0.7.4)
Requirement already satisfied: jedi>=0.10 in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (0.12.1)
Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.15 in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (1.0.15)
Requirement already satisfied: setuptools>=18.5 in /usr/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (40.2.0)
Requirement already satisfied: pygments in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (2.2.0)
Requirement already satisfied: traitlets>=4.2 in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (4.3.2)
Requirement already satisfied: backcall in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (0.1.0)
Requirement already satisfied: decorator in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (4.3.0)
Requirement already satisfied: simplegeneric>0.8 in /home/taha/.local/lib/python3.7/site-packages (from IPython>=0.13->line_profiler) (0.8.1)
Requirement already satisfied: ptyprocess>=0.5 in /home/taha/.local/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->IPython>=0.13->line_profiler) (0.6.0)
Requirement already satisfied: parso>=0.3.0 in /home/taha/.local/lib/python3.7/site-packages (from jedi>=0.10->IPython>=0.13->line_profiler) (0.3.1)
Requirement already satisfied: wcwidth in /home/taha/.local/lib/python3.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.15->IPython>=0.13->line_profiler) (0.1.7)
Requirement already satisfied: six>=1.9.0 in /usr/lib/python3.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.15->IPython>=0.13->line_profiler) (1.11.0)
Requirement already satisfied: ipython-genutils in /home/taha/.local/lib/python3.7/site-packages (from traitlets>=4.2->IPython>=0.13->line_profiler) (0.2.0)
Installing collected packages: line-profiler
  Running setup.py install for line-profiler ... error
    Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ob2zmt46/line-profiler/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-p1lprqxu/install-record.txt --single-version-externally-managed --compile --user --prefix=:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    copying line_profiler.py -> build/lib.linux-x86_64-3.7
    copying kernprof.py -> build/lib.linux-x86_64-3.7
    copying line_profiler_py35.py -> build/lib.linux-x86_64-3.7
    running build_ext
    skipping '_line_profiler.c' Cython extension (up-to-date)
    building '_line_profiler' extension
    creating build/temp.linux-x86_64-3.7
    gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -flto -fuse-linker-plugin -ffat-lto-objects -flto-partition=none -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -fPIC -I/usr/include/python3.7m -c _line_profiler.c -o build/temp.linux-x86_64-3.7/_line_profiler.o
    _line_profiler.c: In function ‘__Pyx__ExceptionSave’:
    _line_profiler.c:7890:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
         *type = tstate->exc_type;
                         ^~~~~~~~
                         curexc_type
    _line_profiler.c:7891:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
         *value = tstate->exc_value;
                          ^~~~~~~~~
                          curexc_value
    _line_profiler.c:7892:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         *tb = tstate->exc_traceback;
                       ^~~~~~~~~~~~~
                       curexc_traceback
    _line_profiler.c: In function ‘__Pyx__ExceptionReset’:
    _line_profiler.c:7899:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tmp_type = tstate->exc_type;
                            ^~~~~~~~
                            curexc_type
    _line_profiler.c:7900:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tmp_value = tstate->exc_value;
                             ^~~~~~~~~
                             curexc_value
    _line_profiler.c:7901:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tmp_tb = tstate->exc_traceback;
                          ^~~~~~~~~~~~~
                          curexc_traceback
    _line_profiler.c:7902:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tstate->exc_type = type;
                 ^~~~~~~~
                 curexc_type
    _line_profiler.c:7903:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tstate->exc_value = value;
                 ^~~~~~~~~
                 curexc_value
    _line_profiler.c:7904:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tstate->exc_traceback = tb;
                 ^~~~~~~~~~~~~
                 curexc_traceback
    _line_profiler.c: In function ‘__Pyx__GetException’:
    _line_profiler.c:7959:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tmp_type = tstate->exc_type;
                            ^~~~~~~~
                            curexc_type
    _line_profiler.c:7960:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tmp_value = tstate->exc_value;
                             ^~~~~~~~~
                             curexc_value
    _line_profiler.c:7961:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tmp_tb = tstate->exc_traceback;
                          ^~~~~~~~~~~~~
                          curexc_traceback
    _line_profiler.c:7962:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘curexc_type’?
         tstate->exc_type = local_type;
                 ^~~~~~~~
                 curexc_type
    _line_profiler.c:7963:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’; did you mean ‘curexc_value’?
         tstate->exc_value = local_value;
                 ^~~~~~~~~
                 curexc_value
    _line_profiler.c:7964:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’; did you mean ‘curexc_traceback’?
         tstate->exc_traceback = local_tb;
                 ^~~~~~~~~~~~~
                 curexc_traceback
    error: command 'gcc' failed with exit status 1
    
    ----------------------------------------
Command "/usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ob2zmt46/line-profiler/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-p1lprqxu/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-install-ob2zmt46/line-profiler/

The text was updated successfully, but these errors were encountered:

ghost · 2018-09-05T23:28:59Z

This is seems to be an issue with the precompiled *.c files being used instead of running cython over *.pyx. Here is a workaround:

git clone https://github.com/rkern/line_profiler.git
find line_profiler -name '*.pyx' -exec cython {} \;
cd line_profiler && pip install . --user

YuMan-Tam · 2018-09-12T00:24:44Z

I encountered exactly the same problem. The solution works perfectly. Thank you!

matrixise · 2018-09-20T08:29:30Z

+1 for the fix, could you fix this issue. thank you

Finistere · 2018-11-01T15:06:21Z

Pandas and others had the same issue pandas-dev/pandas#21785. Could you please make a new release with the latest Cython ?

doanguyen · 2018-12-11T18:01:18Z

The issue has been here for months but no patch yet, is someone going to put it on pypi?

kfrncs · 2019-01-08T19:29:23Z

Also had this issue, also fixed by @tazzaoui 's comment. Thanks.

balodja · 2019-02-13T11:31:50Z

Same issue here. Thanks for the workaround.

leolchat · 2019-04-23T16:33:20Z

+1

and manually to build it since a bug from rkern/line_profiler#132

Upstream problem is documented in rkern/line_profiler#132, but upstream seems unresponsive. This here tries to implement the fix suggested in the upstream issue by manually running Cython before pip installing. closes conda-forge#20

erezaei · 2019-06-14T23:14:33Z

What if I don't have it?

Because of rkern/line_profiler#132

boeddeker · 2019-12-10T15:40:45Z

For me, a direct install from github was also working:
pip install git+https://github.com/rkern/line_profiler
When Cython is installed, this should work, otherwise, the following may cause problems:

line_profiler/setup.py

Lines 12 to 25 in 3cdc2fa

    
           try: 
        
               from Cython.Distutils import build_ext 
        
               cmdclass = dict(build_ext=build_ext) 
        
               line_profiler_source = '_line_profiler.pyx' 
        
           except ImportError: 
        
               cmdclass = {} 
        
               line_profiler_source = '_line_profiler.c' 
        
               if not os.path.exists(line_profiler_source): 
        
                   raise distutils.errors.DistutilsError("""\ 
        
           You need Cython to build the line_profiler from a git checkout, or 
        
           alternatively use a release tarball from PyPI to build it without Cython.""") 
        
               else: 
        
                   warn("Could not import Cython. " 
        
                        "Using the available pre-generated C file.")

chuaxr · 2019-12-26T07:23:25Z

I was using Ubuntu installed on windows and also needed to install gcc (via sudo apt install gcc) before the pip install git+.

matjojo mentioned this issue Sep 18, 2018

'pip install' fails but different from #132 and #127 #133

Open

AdrianSosic mentioned this issue Jan 29, 2019

undefined symbol: gsl_rng_uniform_int slinderman/pypolyagamma#29

Closed

caethan added the being considered Actively being investigated by maintainers for merging label Feb 8, 2019

Cuizi7 mentioned this issue Feb 16, 2019

Py3.7 pip install error ricequant/rqalpha#410

Closed

andreas-h mentioned this issue Mar 12, 2019

Support Python 3.7 conda-forge/line_profiler-feedstock#20

Closed

This was referenced Mar 20, 2019

DOC: Interim installation note until PyPI release is fixed #145

Merged

MNT: Always compile Cython at build time #149

Open

yssource added a commit to yssource/rqalpha that referenced this issue May 27, 2019

Pipenv supported, disable line-profiler in requirements.txt

71f6cc1

and manually to build it since a bug from rkern/line_profiler#132

andreas-h mentioned this issue May 31, 2019

WIP: support Python 3.7 conda-forge/line_profiler-feedstock#21

Closed

5 tasks

bmoscon mentioned this issue Jul 12, 2019

Python3 WIP garethdmm/gryphon#61

Open

arokem added a commit to neurohackademy/nh-jupyterhub-dockerfile that referenced this issue Jul 23, 2019

Line profiler has to be installed separately

ae9bd3b

Because of rkern/line_profiler#132

asmodehn mentioned this issue Jul 24, 2019

Modernize Python 2 code to prepare for Python 3 garethdmm/gryphon#60

Closed

jllanfranchi mentioned this issue Sep 9, 2019

Python 3.7: pip install fails due to line_profiler icecube/pisa#541

Closed

adamjstewart mentioned this issue Oct 7, 2019

update py-line-profiler to work with current python spack/spack#13059

Closed

zouyj0921 mentioned this issue Oct 24, 2019

Failed to build line-profiler #168

Open

sbraz mentioned this issue Jan 16, 2020

dev-python/line_profiler: version bump 3.0.2 gentoo/gentoo#14344

Closed

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`pip install` fails with Python 3.7 #132

`pip install` fails with Python 3.7 #132

ghost commented Sep 5, 2018 •

edited by ghost

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ghost commented Sep 5, 2018

YuMan-Tam commented Sep 12, 2018

matrixise commented Sep 20, 2018

Finistere commented Nov 1, 2018

doanguyen commented Dec 11, 2018

kfrncs commented Jan 8, 2019

balodja commented Feb 13, 2019

leolchat commented Apr 23, 2019

erezaei commented Jun 14, 2019

boeddeker commented Dec 10, 2019

chuaxr commented Dec 26, 2019

pip install fails with Python 3.7 #132

pip install fails with Python 3.7 #132

Comments

ghost commented Sep 5, 2018 • edited by ghost Loading

ghost commented Sep 5, 2018

YuMan-Tam commented Sep 12, 2018

matrixise commented Sep 20, 2018

Finistere commented Nov 1, 2018

doanguyen commented Dec 11, 2018

kfrncs commented Jan 8, 2019

balodja commented Feb 13, 2019

leolchat commented Apr 23, 2019

erezaei commented Jun 14, 2019

boeddeker commented Dec 10, 2019

chuaxr commented Dec 26, 2019

`pip install` fails with Python 3.7 #132

`pip install` fails with Python 3.7 #132

ghost commented Sep 5, 2018 •

edited by ghost

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