I'm trying to install Spacy on my computer but when I run
pip.exe install spacy
I obtain this error:
Requirement already satisfied (use --upgrade to upgrade): spacy in c:\python27
Collecting numpy (from spacy)
Using cached numpy-1.9.2.tar.gz
Running from numpy source directory.
Collecting murmurhash (from spacy)
Using cached murmurhash-0.24.tar.gz
warning: manifest_maker: MANIFEST.in, line 5: 'recursive-include' expects <dir> <pattern1> <pattern2> ...
warning: manifest_maker: MANIFEST.in, line 6: unknown action '*.py'
warning: manifest_maker: MANIFEST.in, line 7: unknown action '*.rst'
Collecting cymem>=1.11 (from spacy)
Using cached cymem-1.11.tar.gz
Collecting preshed (from spacy)
Using cached preshed-0.37.tar.gz
zip_safe flag not set; analyzing archive contents...
headers_workaround.__init__: module references __file__
Installed c:\users\hp-por~1\appdata\local\temp\pip-build-y5elnp\preshed\.eggs\headers_workaround-0.17-py2.7.egg
Collecting thinc (from spacy)
Using cached thinc-1.75.tar.gz
zip_safe flag not set; analyzing archive contents...
headers_workaround.__init__: module references __file__
Installed c:\users\hp-por~1\appdata\local\temp\pip-build-y5elnp\thinc\.eggs\headers_workaround-0.17-py2.7.egg
Requirement already satisfied (use --upgrade to upgrade): unidecode in c:\python27\lib\site-packages (from spacy)
Requirement already satisfied (use --upgrade to upgrade): wget in c:\python27\lib\site-packages (from spacy)
Requirement already satisfied (use --upgrade to upgrade): plac in c:\python27\lib\site-packages (from spacy)
Requirement already satisfied (use --upgrade to upgrade): six in c:\python27\lib\site-packages (from spacy)
Installing collected packages: thinc, preshed, cymem, murmurhash, numpy
Running setup.py install for thinc
building 'thinc.learner' extension
C:\Users\HP-PORTABLE\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -I. -IC:\Python27\include -IC:\Python27\include -IC:\Python27\PC /Tpthinc/learner.cpp /Fobuild\temp.win32-2.7\Release\thinc/learner.obj -O3
cl : Command line warning D9002 : ignoring unknown option '-O3'
learner.cpp
thinc/learner.cpp(238) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory
error: command 'C:\\Users\\HP-PORTABLE\\AppData\\Local\\Programs\\Common\\Microsoft\\Visual C++ for Python\\9.0\\VC\\Bin\\cl.exe' failed with exit status 2
Complete output from command C:\Python27\python.exe -c "import setuptools, tokenize;__file__='c:\\users\\hp-por~1\\appdata\\local\\temp\\pip-build-y5elnp\\thinc\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\hp-por~1\appdata\local\temp\pip-qxxztl-record\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build\lib.win32-2.7
creating build\lib.win32-2.7\thinc
copying thinc\context_fields.py -> build\lib.win32-2.7\thinc
copying thinc\util.py -> build\lib.win32-2.7\thinc
copying thinc\__init__.py -> build\lib.win32-2.7\thinc
copying thinc\cache.pyx -> build\lib.win32-2.7\thinc
copying thinc\cy_svm.pyx -> build\lib.win32-2.7\thinc
copying thinc\features.pyx -> build\lib.win32-2.7\thinc
copying thinc\learner.pyx -> build\lib.win32-2.7\thinc
copying thinc\search.pyx -> build\lib.win32-2.7\thinc
copying thinc\thinc.pyx -> build\lib.win32-2.7\thinc
copying thinc\weights.pyx -> build\lib.win32-2.7\thinc
copying thinc\cache.pxd -> build\lib.win32-2.7\thinc
copying thinc\cy_svm.pxd -> build\lib.win32-2.7\thinc
copying thinc\features.pxd -> build\lib.win32-2.7\thinc
copying thinc\learner.pxd -> build\lib.win32-2.7\thinc
copying thinc\search.pxd -> build\lib.win32-2.7\thinc
copying thinc\thinc.pxd -> build\lib.win32-2.7\thinc
copying thinc\typedefs.pxd -> build\lib.win32-2.7\thinc
copying thinc\weights.pxd -> build\lib.win32-2.7\thinc
copying thinc\__init__.pxd -> build\lib.win32-2.7\thinc
copying thinc\compile_time_constants.pxi -> build\lib.win32-2.7\thinc
running build_ext
building 'thinc.learner' extension
creating build\temp.win32-2.7
creating build\temp.win32-2.7\Release
creating build\temp.win32-2.7\Release\thinc
C:\Users\HP-PORTABLE\AppData\Local\Programs\Common\Microsoft\Visual C++ for Python\9.0\VC\Bin\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -I. -IC:\Python27\include -IC:\Python27\include -IC:\Python27\PC /Tpthinc/learner.cpp /Fobuild\temp.win32-2.7\Release\thinc/learner.obj -O3
cl : Command line warning D9002 : ignoring unknown option '-O3'
learner.cpp
thinc/learner.cpp(238) : fatal error C1083: Cannot open include file: 'stdint.h': No such file or directory
error: command 'C:\\Users\\HP-PORTABLE\\AppData\\Local\\Programs\\Common\\Microsoft\\Visual C++ for Python\\9.0\\VC\\Bin\\cl.exe' failed with exit status 2
----------------------------------------
Command "C:\Python27\python.exe -c "import setuptools, tokenize;__file__='c:\\users\\hp-por~1\\appdata\\local\\temp\\pip-build-y5elnp\\thinc\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\hp-por~1\appdata\local\temp\pip-qxxztl-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\hp-por~1\appdata\local\temp\pip-build-y5elnp\thinc
I've upgraded setuptools, but nothing changes.
I'm running a Windows 7 64b.
I've installed Visual C++ compiler Package for python 2.7.
I'm trying to install on 2 different PC with the same error.
In Windows, I have had a lot of problems installing packages via pip. One solution I found (and I still use it) it's using 'virtualenv' in order to create virtual enviroments for my projects. Pip seems to work better in venvs rather than C: routes.
You can install virtualenv via pip pip install virtualenv or check the installation guide.
After instalation, simply create a virtualenv in your project route (or wherever you want) and activate it. Open a cmd terminal and use:
> virtualenv name_of_the_enviroment
> name_of_the_enviroment/Scripts/activate
> pip install spacy
I hardly recommend to put your python routes in your Enviroment Variables, so you can use "pip", "python" etc in the cmd terminal.
Now, when you use "pip install some_package", it will be installed in the virtualenv instead. deactivate will deactivate the virtualenv.
Note: Please note that you must activate a virtualenv whenever you want to use packages or start the project with installed packages.
It could possibly be a conflict with other python packages installed in your virtual environment (venv). That was the case I had. I tried a pip install into a venv that had these packages already installed:
appnope==0.1.0
beautifulsoup4==4.5.1
bs4==0.0.1
chardet==2.3.0
cloudpickle==0.2.1
cssselect==1.0.0
cymem==1.31.2
decorator==4.0.10
entrypoints==0.2.2
headers-workaround==0.18
ipykernel==4.5.2
ipython==5.1.0
ipython-genutils==0.1.0
ipywidgets==5.2.2
Jinja2==2.8
jsonschema==2.5.1
jupyter==1.0.0
jupyter-client==4.4.0
jupyter-console==5.0.0
jupyter-core==4.2.1
lxml==3.6.4
MarkupSafe==0.23
mistune==0.7.3
murmurhash==0.26.4
nbconvert==4.2.0
nbformat==4.2.0
notebook==4.2.3
numpy==1.11.2
pandas==0.19.1
pathlib==1.0.1
pdfminer.six==20160614
pdfminer3k==1.3.1
pdfquery==0.4.3
pexpect==4.2.1
pickleshare==0.7.4
plac==0.9.6
ply==3.9
preshed==0.46.4
prompt-toolkit==1.0.9
ptyprocess==0.5.1
py==1.4.31
Pygments==2.1.3
pyquery==1.2.17
pytest==3.0.3
python-dateutil==2.6.0
pytz==2016.7
pyzmq==16.0.2
qtconsole==4.2.1
requests==2.11.1
roman==2.0.0
semver==2.7.2
simplegeneric==0.8.1
six==1.10.0
slate==0.3
sputnik==0.9.3
terminado==0.6
thinc==5.0.8
tornado==4.4.2
traitlets==4.3.1
ujson==1.35
wcwidth==0.1.7
widgetsnbextension==1.2.6
and it kept failing, even with upgrading setuptools.
Try creating a totally new environment conda create -n spacy python=3, proceeding with the installation of the default packages (openssl, pip, wheel, etc) and (after activating the new venv source activate spacy) then run pip install -U spacy. It installed into the virtual environment with no problems. From there install the other packages you need.
Related
I was trying to pip and conda install pygraphviz. I believe grahviz is installed since
(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ conda install -y graphviz
Collecting package metadata (current_repodata.json): done
Solving environment: done
# All requested packages already installed.
but when I try installing pygraphviz with pip I get the following:
(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ pip install pygraphviz
Collecting pygraphviz
Using cached pygraphviz-1.7.zip (118 kB)
Building wheels for collected packages: pygraphviz
Building wheel for pygraphviz (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"'; __file__='"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-b61bb2uf
cwd: /tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/
Complete output (55 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/testing.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/agraph.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz
creating build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
running egg_info
writing pygraphviz.egg-info/PKG-INFO
writing dependency_links to pygraphviz.egg-info/dependency_links.txt
writing top-level names to pygraphviz.egg-info/top_level.txt
reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.png' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.svn' found anywhere in distribution
no previously-included directories found matching 'doc/build'
writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
copying pygraphviz/graphviz.i -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.linux-x86_64-3.8/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/pygraphviz
gcc -pthread -B /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-3.8/pygraphviz/graphviz_wrap.o
In file included from /usr/include/graphviz/gvc.h:17:0,
from pygraphviz/graphviz_wrap.c:2712:
/usr/include/graphviz/types.h:49:20: fatal error: cgraph.h: No such file or directory
#include <cgraph.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for pygraphviz
Running setup.py clean for pygraphviz
Failed to build pygraphviz
Installing collected packages: pygraphviz
Running setup.py install for pygraphviz ... error
ERROR: Command errored out with exit status 1:
command: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"'; __file__='"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/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-mu112lx1/install-record.txt --single-version-externally-managed --compile --install-headers /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8/pygraphviz
cwd: /tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/
Complete output (55 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/pygraphviz
copying pygraphviz/scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/testing.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/agraph.py -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz
creating build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.linux-x86_64-3.8/pygraphviz/tests
running egg_info
writing pygraphviz.egg-info/PKG-INFO
writing dependency_links to pygraphviz.egg-info/dependency_links.txt
writing top-level names to pygraphviz.egg-info/top_level.txt
reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.png' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.svn' found anywhere in distribution
no previously-included directories found matching 'doc/build'
writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
copying pygraphviz/graphviz.i -> build/lib.linux-x86_64-3.8/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.linux-x86_64-3.8/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/pygraphviz
gcc -pthread -B /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-3.8/pygraphviz/graphviz_wrap.o
In file included from /usr/include/graphviz/gvc.h:17:0,
from pygraphviz/graphviz_wrap.c:2712:
/usr/include/graphviz/types.h:49:20: fatal error: cgraph.h: No such file or directory
#include <cgraph.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/setup.py'"'"'; __file__='"'"'/tmp/pip-install-rc_2rzek/pygraphviz_904720f7fa8b49f4a7006870a0d5e479/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-mu112lx1/install-record.txt --single-version-externally-managed --compile --install-headers /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2/include/python3.8/pygraphviz Check the logs for full command output.
with conda:
(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ conda install -y -c anaconda pygraphviz
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages. failed
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- pygraphviz -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
what are the sources of my errors? [note I am on a linux machine, not mac os, my mac phygraphviz works fine]
I saw the following related questions:
Pip install pygraphviz fails: Failed building wheel for pygraphviz
Couldn't install pygraphviz
https://github.com/pygraphviz/pygraphviz/issues/347
https://github.com/pygraphviz/pygraphviz/issues/358
but they didn't help because I cannot run apt-get
(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ apt-get install python-dev graphviz libgraphviz-dev pkg-config
-bash: apt-get: command not found
Edit:
note I also did try to install grapviz with pip but that didn't solve my problems:
(metalearningpy1.7.1c10.2) miranda9~/ML4Coq $ pip install graphviz
Collecting graphviz
Downloading graphviz-0.16-py2.py3-none-any.whl (19 kB)
Installing collected packages: graphviz
Successfully installed graphviz-0.16
Edit 2:
I found out that graphviz is there but why can't it find it?
(metalearningpy1.7.1c10.2) miranda9~ $ rpm -qa |grep graphviz
graphviz-gd-2.30.1-21.el7.x86_64
graphviz-2.30.1-21.el7.x86_64
graphviz-devel-2.30.1-21.el7.x86_64
Edit 3:
I'd also like this to work with pip install -e . e.g. see installation of ultimate utils (https://github.com/brando90/ultimate-utils):
Due to a depedency on pygraphviz you will likely need to install graphviz first. Next, install graphviz. On mac, brew install graphviz. On Ubuntu, sudo apt install graphviz. After graphviz is install, install uutils in edibable mode and all it's depedencies with pip:
pip install -e ~/ultimate-utils/ultimate-utils-proj-src
as a gitissue: https://github.com/brando90/ultimate-utils/issues/6
Well, it seems that using conda-forge worked!
(metalearningpy1.7.1c10.2) miranda9~ $ conda install -y -c conda-forge pygraphviz
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/miranda9/miniconda3/envs/metalearningpy1.7.1c10.2
added / updated specs:
- pygraphviz
The following packages will be downloaded:
package | build
---------------------------|-----------------
libgcc-ng-9.3.0 | h2828fa1_19 7.8 MB conda-forge
libgomp-9.3.0 | h2828fa1_19 376 KB conda-forge
pygraphviz-1.7 | py38h0d738da_0 125 KB conda-forge
------------------------------------------------------------
Total: 8.3 MB
The following NEW packages will be INSTALLED:
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
libgomp conda-forge/linux-64::libgomp-9.3.0-h2828fa1_19
pygraphviz conda-forge/linux-64::pygraphviz-1.7-py38h0d738da_0
The following packages will be UPDATED:
certifi pkgs/main::certifi-2020.12.5-py38h06a~ --> conda-forge::certifi-2020.12.5-py38h578d9bd_1
libgcc-ng pkgs/main::libgcc-ng-9.1.0-hdf63c60_0 --> conda-forge::libgcc-ng-9.3.0-h2828fa1_19
The following packages will be SUPERSEDED by a higher-priority channel:
_libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge
ca-certificates pkgs/main::ca-certificates-2021.4.13-~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0
openssl pkgs/main::openssl-1.1.1k-h27cfd23_0 --> conda-forge::openssl-1.1.1k-h7f98852_0
Downloading and Extracting Packages
libgcc-ng-9.3.0 | 7.8 MB | ##################################################################################################################################################################################################################################################################################################################################################################################### | 100%
pygraphviz-1.7 | 125 KB | ##################################################################################################################################################################################################################################################################################################################################################################################### | 100%
libgomp-9.3.0 | 376 KB | ##################################################################################################################################################################################################################################################################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Note:
However, notice that pygraphviz doesn't recommend using conda to install their pkg for some reason
We recommend avoiding Anaconda and conda-forge to install Graphviz and PyGraphviz.
however since pip keeps failing for me - despite graphviz being installed in the cluster - see the output of rpm:
[rundblom#vision-12 ~]$ rpm -qa |grep graphviz
graphviz-devel-2.30.1-21.el7.x86_64
graphviz-2.30.1-21.el7.x86_64
graphviz-gd-2.30.1-21.el7.x86_64
so idk what is wrong with using pip. I would have preferred to load a module in the usual HPC way but that isn't an option for me right now...
I was able to compile it on CentOS with graphviz-devel installed. Originally I got the same error as above, the missing cgraph.h, but by providing a header lookup path to the compiler I could make it build:
CPPFLAGS="-I/usr/include/graphviz" pip install pygraphviz
When I tried to use the package though I had symbol lookup errors. So in the end I gave up and went with conda.
I tried installing turbodbc and it gives me the following error and not sure what's wrong here.
My python version is 3.7
My command line output from Windows 10 Pro.
C:\Users\marunachalam\Downloads>pip install turbodbc
Collecting turbodbc
Using cached turbodbc-3.3.0.tar.gz (78 kB)
Requirement already satisfied: pybind11>=2.2.0 in c:\users\marunachalam\appdata\local\programs\python\python37-32\lib\site-packages (from turbodbc) (2.4.3)
Requirement already satisfied: six in c:\users\marunachalam\appdata\local\programs\python\python37-32\lib\site-packages (from turbodbc) (1.13.0)
Building wheels for collected packages: turbodbc
Building wheel for turbodbc (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: 'c:\users\marunachalam\appdata\local\programs\python\python37-32\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\MARUNA~1\\AppData\\Local\\Temp\\pip-install-akbat0nu\\turbodbc\\setup.py'"'"'; __file__='"'"'C:\\Users\\MARUNA~1\\AppData\\Local\\Temp\\pip-install-akbat0nu\\turbodbc\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\MARUNA~1\AppData\Local\Temp\pip-wheel-qdxgecq5'
cwd: C:\Users\MARUNA~1\AppData\Local\Temp\pip-install-akbat0nu\turbodbc\
Complete output (27 lines):
warning: BOOST_ROOT enviroment variable not set
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win32-3.7
creating build\lib.win32-3.7\turbodbc
copying turbodbc\api_constants.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\connect.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\connection.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\constructors.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\cursor.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\data_types.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\exceptions.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\options.py -> build\lib.win32-3.7\turbodbc
copying turbodbc\__init__.py -> build\lib.win32-3.7\turbodbc
running egg_info
writing turbodbc.egg-info\PKG-INFO
writing dependency_links to turbodbc.egg-info\dependency_links.txt
writing requirements to turbodbc.egg-info\requires.txt
writing top-level names to turbodbc.egg-info\top_level.txt
reading manifest file 'turbodbc.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'turbodbc.egg-info\SOURCES.txt'
running build_ext
building 'turbodbc_intern' extension
error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": https://visualstudio.microsoft.com/downloads/
----------------------------------------
ERROR: Failed building wheel for turbodbc
Running setup.py clean for turbodbc
Failed to build turbodbc
Disclaimer : Turbodc installation has problems with python version 3.8+. You will be able to install Turbodc on python 3.8+, but you'll face another error while using it (https://github.com/blue-yonder/turbodbc/issues/258). So if you want to use Turbodbc, better to stick to python version 3.7 and below. Now lets get Turbodbc installed on your machine
This is going to be a long one. Stay with me -
As the error states, firstly you need 'Microsoft Visual C++ Build Tools'. You'll get it on this page: https://visualstudio.microsoft.com/downloads/. Scroll down to 'Build Tools for Visual Studio'. Download it.
Run the installer. Select 'C++ build tools' to install. Make sure to choose 'Windows 10 (or whatever version you prefer) SDK' as well to prevent this error later - https://github.com/openssl/openssl/issues/586
After installing build tools if you try to install Turbodbc (pip install turbodbc), you'll see another error - python fatal error C1083: Cannot open include file: 'boost/locale.hpp'. Which is to say the battle is half won. To resolve this error follow the steps listed here - https://github.com/blue-yonder/turbodbc/issues/236. For your ease, I'll copy them below -
Download boost from https://www.boost.org/ (click on the "Current Release" version link, in my case "Version 1.72.0", then download the Windows zip file).
Unzip the zipfile somewhere on your PC.
In a command prompt, navigate to the boost top-level directory.
Run .\bootstrap.bat (this generates the b2 executable)
Run .\b2 (this generates the stage directory and contents, takes a few minutes to run)
Set the BOOST_ROOT env variable with something like
set BOOST_ROOT=C:\your\path\to\boost\boost_1_72_0\boost_1_72_0
Run pip install turbodbc
That's all. Turbodbc should now be installed in your machine.
Try follow
Sat, Jan 2 at 9:16 PM
https://www.boost.org/doc/libs/1_71_0/more/getting_started/windows.html. got working on windows 10 using Python39, download/install MS Visual Studio 2019 Community, unzip boost, set BOOST_ROOT env variable, rerun pip install turbodbc
I'm using python 2.7 on a windows box.I'm able to install flask using pip install, as you can see below:
However, after I created a virtualenv, I got below error when trying to do the same thing.
scripts:
$pip install virtualenv
$cd /d d:
$mkdir test
$cd test
$virtualenv flaskEnv
$cd flaskEnv/Scritps/
$activate
$cd ../../
$pip install flask
log file as below:
Collecting flask
Using cached Flask-0.11.1-py2.py3-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): click>=2.0 in c:\projects\flask-react\flsk\lib\site-packages (from flask)
Requirement already satisfied (use --upgrade to upgrade): Werkzeug>=0.7 in c:\projects\flask-react\flsk\lib\site-packages (from flask)
Collecting Jinja2>=2.4 (from flask)
Using cached Jinja2-2.8-py2.py3-none-any.whl
Collecting itsdangerous>=0.21 (from flask)
Collecting MarkupSafe (from Jinja2>=2.4->flask)
Using cached MarkupSafe-0.23.tar.gz
Building wheels for collected packages: MarkupSafe
Running setup.py bdist_wheel for MarkupSafe: started
Running setup.py bdist_wheel for MarkupSafe: finished with status 'error'
Complete output from command c:\projects\flask-react\flsk\scripts\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\admini~1\\appdata\\local\\temp\\pip-build-3ep417\\MarkupSafe\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d c:\users\admini~1\appdata\local\temp\tmp8mkr70pip-wheel- --python-tag cp27:
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win32-2.7
creating build\lib.win32-2.7\markupsafe
copying markupsafe\tests.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\_compat.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\_constants.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\_native.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\__init__.py -> build\lib.win32-2.7\markupsafe
running egg_info
writing MarkupSafe.egg-info\PKG-INFO
writing top-level names to MarkupSafe.egg-info\top_level.txt
writing dependency_links to MarkupSafe.egg-info\dependency_links.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'MarkupSafe.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'MarkupSafe.egg-info\SOURCES.txt'
copying markupsafe\_speedups.c -> build\lib.win32-2.7\markupsafe
running build_ext
building 'markupsafe._speedups' extension
error: [Error 2] The system cannot find the file specified
----------------------------------------
Running setup.py clean for MarkupSafe
Failed to build MarkupSafe
Installing collected packages: MarkupSafe, Jinja2, itsdangerous, flask
Running setup.py install for MarkupSafe: started
Running setup.py install for MarkupSafe: finished with status 'error'
Complete output from command c:\projects\flask-react\flsk\scripts\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\admini~1\\appdata\\local\\temp\\pip-build-3ep417\\MarkupSafe\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\admini~1\appdata\local\temp\pip-8v3_ep-record\install-record.txt --single-version-externally-managed --compile --install-headers c:\projects\flask-react\flsk\include\site\python2.7\MarkupSafe:
running install
running build
running build_py
creating build
creating build\lib.win32-2.7
creating build\lib.win32-2.7\markupsafe
copying markupsafe\tests.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\_compat.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\_constants.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\_native.py -> build\lib.win32-2.7\markupsafe
copying markupsafe\__init__.py -> build\lib.win32-2.7\markupsafe
running egg_info
writing MarkupSafe.egg-info\PKG-INFO
writing top-level names to MarkupSafe.egg-info\top_level.txt
writing dependency_links to MarkupSafe.egg-info\dependency_links.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'MarkupSafe.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'MarkupSafe.egg-info\SOURCES.txt'
copying markupsafe\_speedups.c -> build\lib.win32-2.7\markupsafe
running build_ext
building 'markupsafe._speedups' extension
error: [Error 2] The system cannot find the file specified
Does the error message mean something to anyone?
thanks
This issue seems to be related with the setuptools version installed in your virtualenv. Downgrading to an older version fixed it for me.
From your virtualenv:
pip install setuptools==21.2.1
pip install flask
I had this problem yesterday. I resolved it by downloading the MarkupSafe wheel and installing with pip. The problem was way over my head. Something about compiler flags in order to suppress an error when generating the Speedups file, I think.
1) Download the wheel from the link above.
2) On Windows, open a command window in the same directory as the wheel.
3) run "pip Install "
The setup.py of MarkupSafe is broken for Win7 on my system where there is no C compiler. (I keep a separate VM for VC++ work) I did this to get it working:
pip download MarkupSafe
mkdir temp
open MarkupSafe-0.23.tar.gz with 7-zip, extract all to temp
cd temp
edit setup.py line 119 to read: if 0: #not (is_pypy or is_jython):
python setup.py install
I did not try to debug setup.py to work correctly. I just wanted to try out Flask since it's supposed to be lightweight and easy to learn, and the official docs say it installs on Windows. Maybe I should go back to Perl...
Unlike the other poster, a global pip install of MarkupSafe didn't work for me either.
These links have other views/insights on the problem:
https://github.com/pallets/markupsafe/issues/26
https://github.com/babun/babun/issues/315
ok. I figure it out. I don't think there is anything wrong in the way I install flask, as I already mentioned in my question, I am able to install it globally (without running within a virtualenv).
the MarkupSafe package has an extension which is implement using c, and I don't have windows sdk installed on my local machine, so when ve_build_ext runs,
**** it always fail **
the difference is if not (is_pypy or is_jython) , it gives a warning, which is what i got when installing it globally; it crashes, though, when running under a virtualenv. So I'm pretty sure that hasattr(sys, 'pypy_version_info') return true when running under a virtualenv.
Does anybody have an idea what "hasattr(sys, 'pypy_version_info')" mean??
# fail safe compilation shamelessly stolen from the simplejson
# setup.py file. Original author: Bob Ippolito
is_jython = 'java' in sys.platform
is_pypy = hasattr(sys, 'pypy_version_info')
def run_setup(with_binary):
ext = Extension('markupsafe._speedups', ['markupsafe/_speedups.c'])
ext_modules = [ext] if with_binary else []
def try_building_extension():
try:
run_setup(True)
except BuildFailed:
LINE = '=' * 74
BUILD_EXT_WARNING = 'WARNING: The C extension could not be ' \
'compiled, speedups are not enabled.'
echo(LINE)
echo(BUILD_EXT_WARNING)
echo('Failure information, if any, is above.')
echo('Retrying the build without the C extension now.')
echo()
run_setup(False)
echo(LINE)
echo(BUILD_EXT_WARNING)
echo('Plain-Python installation succeeded.')
echo(LINE)
if not (is_pypy or is_jython):
try_building_extension()
else:
run_setup(False)
I had this issue today and was able to resolve it by manually installing MarkupSafe from a wheel file, per Lincoln's suggestion above. You can download the appropriate file here. There were several available. I don't know what the difference between all of them is, but the only one that would even install on Windows 10 was the one called MarkupSafe-0.23-cp27-none-win32.whl. After downloading it, I copied it into the directory I created using virtualenv (not sure if that's necessary but that's what I did) and installed it with pip:
C:\flask-test\venv>pip install MarkupSafe-0.23-cp27-none-win32.whl
from that directory. After that I went back to the main directory and installed Flask
C:\flask-test\venv>cd ..
C:\flask-test>pip install Flask
and it worked fine.
I'm having trouble while installing PyGraphviz.
I'm using Anaconda in Mac OS X.
Error messages indicates some reasons, but I already checked out it is installed in anaconda directory.
Sundongui-MacBook-Pro:site-packages sundong$ pwd
/Users/sundong/anaconda/lib/python2.7/site-packages
Sundongui-MacBook-Pro:site-packages sundong$ pip install graphviz --upgrade
Requirement already up-to-date: graphviz in /Users/sundong/anaconda/lib/python2.7/site-packages
According to the error messages, How can I change the the include_dirs and library_dirs variables in setup.py??
Here is the error message that I meet
Sundongui-MacBook-Pro:anaconda sundong$ pip install pygraphviz
Collecting pygraphviz
Using cached pygraphviz-1.3.1.tar.gz
Building wheels for collected packages: pygraphviz
Running setup.py bdist_wheel for pygraphviz
Complete output from command /Users/sundong/anaconda/bin/python -c "import setuptools;__file__='/private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/tmpwR_08Dpip-wheel-:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.5-x86_64-2.7
creating build/lib.macosx-10.5-x86_64-2.7/pygraphviz
copying pygraphviz/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz
copying pygraphviz/agraph.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz
copying pygraphviz/release.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz
copying pygraphviz/version.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz
creating build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_attributes.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz/tests
running egg_info
writing pygraphviz.egg-info/PKG-INFO
writing top-level names to pygraphviz.egg-info/top_level.txt
writing dependency_links to pygraphviz.egg-info/dependency_links.txt
warning: manifest_maker: standard file '-c' not found
reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.svn' found anywhere in distribution
no previously-included directories found matching 'doc/build'
writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
copying pygraphviz/graphviz.i -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.macosx-10.5-x86_64-2.7/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.macosx-10.5-x86_64-2.7
creating build/temp.macosx-10.5-x86_64-2.7/pygraphviz
gcc -fno-strict-aliasing -I/Users/sundong/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/sundong/anaconda/include/python2.7 -c pygraphviz/graphviz_wrap.c -o build/temp.macosx-10.5-x86_64-2.7/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:2954:10: fatal error: 'graphviz/cgraph.h' file not found
#include "graphviz/cgraph.h"
^
1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Failed building wheel for pygraphviz
Failed to build pygraphviz
Installing collected packages: pygraphviz
Running setup.py install for pygraphviz
Complete output from command /Users/sundong/anaconda/bin/python -c "import setuptools, tokenize;__file__='/private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-qgosXm-record/install-record.txt --single-version-externally-managed --compile:
running install
Trying pkg-config
Failed to find pkg-config
Trying dotneato-config
Failed to find dotneato-config
Failed to find dotneato-config
Your Graphviz installation could not be found.
1) You don't have Graphviz installed:
Install Graphviz (http://graphviz.org)
2) Your Graphviz package might incomplete.
Install the binary development subpackage (e.g. libgraphviz-dev or similar.)
3) You are using Windows
There are no PyGraphviz binary packages for Windows but you might be
able to build it from this source. See
http://networkx.lanl.gov/pygraphviz/reference/faq.html
If you think your installation is correct you will need to manually
change the include_dirs and library_dirs variables in setup.py to
point to the correct locations of your graphviz installation.
The current setting of library_dirs and include_dirs is:
library_dirs=None
include_dirs=None
error: Error locating graphviz.
----------------------------------------
Command "/Users/sundong/anaconda/bin/python -c "import setuptools, tokenize;__file__='/private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-qgosXm-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/p6/rjy4tf353bzfy7gsl5jn_yvc0000gn/T/pip-build-bLb4AR/pygraphviz
brew install graphviz
then:
pip install --install-option="--include-path=/usr/local/include/" --install-option="--library-path=/usr/local/lib/" pygraphviz
Both path in bold should NOT contain "graphviz".
https://github.com/pygraphviz/pygraphviz/issues/100#issuecomment-237560404
Worked for me on OSX 10.14.1
Assuming that you've already installed graphviz software:
As described in this blog post use the following parameters whilst trying to run pip install pygraphviz
--install-option="--include-path=/usr/local/include/graphviz/" \
--install-option="--library-path=/usr/local/lib/graphviz"
So the final command would look like pip install pygraphviz --install-option="--include-path=/usr/local/include/graphviz/" --install-option="--library-path=/usr/local/lib/graphviz".
What this does is this explicitly specified where the libraries of the original program (graphviz) exist for the python extension to use. Unfortunately, this doesn't seem to get automatically recognized.
Worked on MacOS Sierra with Python 3.6
try the following (make sure to have anaconda-client installed and updated):
conda install --channel https://conda.anaconda.org/garylschultz pygraphviz
Graphviz can be installed via homebrew: brew install graphviz.
Then do:
cd /usr/local/Cellar/graphviz/VERSION/include/graphviz
mkdir graphviz
cp cgraph.h graphviz/
And finally:
pip install graphviz
Tested on Sierra and woks fine.
How do I install cairocffi through pip?
cairocffi is a CFFI-based drop-in replacement for Pycairo https://github.com/SimonSapin/cairocffi.
I'm trying to install it on Ubuntu 14.04:
alvas#ubi:~$ cat /etc/*-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=14.04
DISTRIB_CODENAME=trusty
DISTRIB_DESCRIPTION="Ubuntu 14.04.2 LTS"
NAME="Ubuntu"
VERSION="14.04.2 LTS, Trusty Tahr"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 14.04.2 LTS"
VERSION_ID="14.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
I've tried installing with the standard pip command but I get this:
$ sudo pip install cairocffi
The directory '/home/alvas/.cache/pip/log' or its parent directory is not owned by the current user and the debug log has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/home/alvas/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/home/alvas/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting cairocffi
Downloading cairocffi-0.6.tar.gz (75kB)
100% |████████████████████████████████| 77kB 34kB/s
Collecting cffi>=0.6 (from cairocffi)
Downloading cffi-0.9.2.tar.gz (209kB)
100% |████████████████████████████████| 212kB 97kB/s
Requirement already satisfied (use --upgrade to upgrade): pycparser in /usr/local/lib/python3.4/dist-packages (from cffi>=0.6->cairocffi)
Installing collected packages: cffi, cairocffi
Running setup.py install for cffi
Complete output from command /usr/bin/python3 -c "import setuptools, tokenize;__file__='/tmp/pip-build-d3kjzf__/cffi/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ll323a3c-record/install-record.txt --single-version-externally-managed --compile:
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.4
creating build/lib.linux-x86_64-3.4/cffi
copying cffi/commontypes.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/lock.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/api.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/verifier.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/__init__.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/cparser.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/backend_ctypes.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/vengine_gen.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/gc_weakref.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/ffiplatform.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/model.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/vengine_cpy.py -> build/lib.linux-x86_64-3.4/cffi
running build_ext
building '_cffi_backend' extension
creating build/temp.linux-x86_64-3.4
creating build/temp.linux-x86_64-3.4/c
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DUSE__THREAD -I/usr/include/ffi -I/usr/include/libffi -I/usr/include/python3.4m -c c/_cffi_backend.c -o build/temp.linux-x86_64-3.4/c/_cffi_backend.o
c/_cffi_backend.c:13:17: fatal error: ffi.h: No such file or directory
#include <ffi.h>
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Command "/usr/bin/python3 -c "import setuptools, tokenize;__file__='/tmp/pip-build-d3kjzf__/cffi/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ll323a3c-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-d3kjzf__/cffi
I've manually checked the permission and I realized that there's no write access permission. Why is that so? And why isn't sudo working to overwrite the permission?
$ ls -la .cache/pip/log/
total 60
drwxrwxr-x 2 alvas alvas 4096 Feb 3 10:51 .
drwx------ 4 alvas alvas 4096 Apr 12 23:16 ..
-rw-rw-r-- 1 alvas alvas 49961 Apr 12 23:18 debug.log
When I tried sudo -H pip install cairoffi, I got:
sudo -H pip install cairocffi
Collecting cairocffi
Using cached cairocffi-0.6.tar.gz
Collecting cffi>=0.6 (from cairocffi)
Downloading cffi-0.9.2.tar.gz (209kB)
100% |████████████████████████████████| 212kB 29kB/s
Requirement already satisfied (use --upgrade to upgrade): pycparser in /usr/local/lib/python3.4/dist-packages (from cffi>=0.6->cairocffi)
Installing collected packages: cffi, cairocffi
Running setup.py install for cffi
Complete output from command /usr/bin/python3 -c "import setuptools, tokenize;__file__='/tmp/pip-build-2sv6pbsp/cffi/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-xk4kkjrj-record/install-record.txt --single-version-externally-managed --compile:
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.4
creating build/lib.linux-x86_64-3.4/cffi
copying cffi/commontypes.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/lock.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/api.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/verifier.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/__init__.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/cparser.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/backend_ctypes.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/vengine_gen.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/gc_weakref.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/ffiplatform.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/model.py -> build/lib.linux-x86_64-3.4/cffi
copying cffi/vengine_cpy.py -> build/lib.linux-x86_64-3.4/cffi
running build_ext
building '_cffi_backend' extension
creating build/temp.linux-x86_64-3.4
creating build/temp.linux-x86_64-3.4/c
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -DUSE__THREAD -I/usr/include/ffi -I/usr/include/libffi -I/usr/include/python3.4m -c c/_cffi_backend.c -o build/temp.linux-x86_64-3.4/c/_cffi_backend.o
c/_cffi_backend.c:13:17: fatal error: ffi.h: No such file or directory
#include <ffi.h>
^
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
----------------------------------------
Command "/usr/bin/python3 -c "import setuptools, tokenize;__file__='/tmp/pip-build-2sv6pbsp/cffi/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-xk4kkjrj-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-2sv6pbsp/cffi
As #MattDMo suggested, i've tried apt-get install libffi but it still didn't work out:
alvas#ubi:~$ sudo apt-get install libffi libffi-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package libffi
But there isn't any libffi on the package manager, so i've tried libffi-dev:
alvas#ubi:~$ sudo apt-get install libffi-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following NEW packages will be installed:
libffi-dev
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 99.8 kB of archives.
After this operation, 323 kB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu/ trusty/main libffi-dev amd64 3.1~rc1+r3.0.13-12 [99.8 kB]
Fetched 99.8 kB in 1s (76.3 kB/s)
Selecting previously unselected package libffi-dev:amd64.
(Reading database ... 492855 files and directories currently installed.)
Preparing to unpack .../libffi-dev_3.1~rc1+r3.0.13-12_amd64.deb ...
Unpacking libffi-dev:amd64 (3.1~rc1+r3.0.13-12) ...
Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
Processing triggers for doc-base (0.10.5) ...
Processing 1 added doc-base file...
Processing triggers for install-info (5.2.0.dfsg.1-2) ...
Setting up libffi-dev:amd64 (3.1~rc1+r3.0.13-12) ...
It installs libffi-dev successfully but cairoffi is still not installing:
alvas#ubi:~$ sudo -H pip install cairoffi
Collecting cairoffi
Could not find a version that satisfies the requirement cairoffi (from versions: )
No matching distribution found for cairoffi
alvas#ubi:~$ sudo -H pip3 install cairoffi
Collecting cairoffi
Could not find a version that satisfies the requirement cairoffi (from versions: )
No matching distribution found for cairoffi
It's right in the error message:
No package 'libffi' found
You'll need to install libffi and libffi-dev through your distro's package manager (yum, apt-get, whatever) before the pip installation will work. Their names may very slightly from platform to platform.
Couldn't get it to work, even with libffi6 libffi-dev installed. Finally got it working with:
pip3 install -U pip
pip3 install -U setuptools
pip3 install --no-cache-dir cairocffi
--no-cache-dir was the trick, thanks to: https://github.com/Kozea/cairocffi/issues/125#issuecomment-476295293
For me, on Windows 10 using python 3.5.3rc1, pip install cairocffi was failing. Doing pip install cffi was sufficient to let it succeed.