I first try to run the basic pip install command for it:
C:\Program Files (x86)\Python35-32>pip install lxml
Collecting lxml
Using cached lxml-3.6.4.tar.gz
Building wheels for collected packages: lxml
Running setup.py bdist_wheel for lxml ... error
Complete output from command "c:\program files (x86)\python35-32\python.exe" -u -c "import setuptools, tokenize;__file__='C:\\Users\\Djidiouf\\AppData\\Local\\Temp\\pip-build-ovqa6ncd\\lxml\\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\Djidiouf\AppData\Local\Temp\tmp9hzx5gztpip-wheel- --python-tag cp35:
Building lxml version 3.6.4.
Building without Cython.
ERROR: b"'xslt-config' is not recognized as an internal or external command,\r\noperable program or batch file.\r\n"
** make sure the development packages of libxml2 and libxslt are installed **
C:\Users\Djidiouf\AppData\Local\Temp\xmlXPathInitbqgvj3pt.c(1): fatal error C1083: Cannot open include file: 'libxml/xpath.h': No such file or directory
*********************************************************************************
Could not find function xmlCheckVersion in library libxml2. Is libxml2 installed?
*********************************************************************************
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\cl.exe' failed with exit status 2
----------------------------------------
Command ""c:\program files (x86)\python35-32\python.exe" -u -c "import setuptools, tokenize;__file__='C:\\Users\\Djidiouf\\AppData\\Local\\Temp\\pip-build-ovqa6ncd\\lxml\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\Djidiouf\AppData\Local\Temp\pip-kk7fdpzx-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\Djidiouf\AppData\Local\Temp\pip-build-ovqa6ncd\lxml\
I tried to install libxml2:
C:\Program Files (x86)\Python35-32>pip install libxml2
Collecting libxml2
Could not find a version that satisfies the requirement libxml2 (from versions: )
No matching distribution found for libxml2
And I also tried to install libxslt:
C:\Program Files (x86)\Python35-32>pip install libxslt
Collecting libxslt
Could not find a version that satisfies the requirement libxslt (from versions: )
No matching distribution found for libxslt
I also tried to build lxml from sources ( https://github.com/lxml/lxml ) but it needs the libxml2 dependencies as well.
I tried to install it with wheel as well after downloading the lxml file from http://www.lfd.uci.edu/~gohlke/pythonlibs/#lxml :
C:\Program Files (x86)\Python35-32>pip install C:\Users\Djidiouf\Downloads\lxml-3.6.4-cp35-cp35m-win_amd64.whl
lxml-3.6.4-cp35-cp35m-win_amd64.whl is not a supported wheel on this platform.
It seems that this wheel file doesn't support either Windows 10 or Python 3.5.
Any help will be appreciated.
lxml uses libxml2, libxslt (in background) but libxml2, libxslt are not Python modules - it's C/C++ libraries. So you can't install them using pip. You have to download and install them manually.
You can find precompiled lxml for Windows on Unofficial Windows Binaries for Python Extension Packages
cp35 in file name means version for Python 3.5.
win32 in file name means version for 32bit Python.
amd64 in file name means version for 64bit Python.
You probably use 32bit Python because I see 32 and (x86) in your path
C:\program files (x86)\python35-32\python.exe
You should find links to libxml2, libxslt on this page too. This libraries has .dll and .exe files and you can put them in any folder which is in PATH variable. Libraries mostly are installed in C:\Windows or in subfolder.
libxml2, libxslt may have also C/C++ header files *.h which you may need when you compile lxml. (on Linux this files are in separated packages
libxml2-dev, libxslt-dev)
BTW: You can use Anaconda distribution (instead of Python.org distribution). It installs the same Python but with some precompiled modules - ie. it installs lxml automatically. Anaconda can be the best solution for Windows users.
List of all modules: https://docs.continuum.io/anaconda/pkg-docs
Also, check your pip --version. I had v19.0 and Gohlke .whl binaries would not install. Upgrade to 19.2 or greater.
Related
I cannot install psycopg2 on my M1 Mac and I used pip3.
When I tried to install with pip3 install psycopg2 The output like that:
ERROR: Command errored out with exit status 1:
command: /opt/homebrew/opt/python#3.9/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-install-9wiqe2nr/psycopg2_147a5ae8fd5a47079480274f4225edbf/setup.py'"'"'; __file__='"'"'/private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-install-9wiqe2nr/psycopg2_147a5ae8fd5a47079480274f4225edbf/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-06hnnl2t
cwd: /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-install-9wiqe2nr/psycopg2_147a5ae8fd5a47079480274f4225edbf/
Complete output (23 lines):
running egg_info
creating /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-06hnnl2t/psycopg2.egg-info
writing /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-06hnnl2t/psycopg2.egg-info/PKG-INFO
writing dependency_links to /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-06hnnl2t/psycopg2.egg-info/dependency_links.txt
writing top-level names to /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-06hnnl2t/psycopg2.egg-info/top_level.txt
writing manifest file '/private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-06hnnl2t/psycopg2.egg-info/SOURCES.txt'
Error: pg_config executable not found.
pg_config is required to build psycopg2 from source. Please add the directory
containing pg_config to the $PATH or specify the full executable path with the
option:
python setup.py build_ext --pg-config /path/to/pg_config build ...
or with the pg_config option in 'setup.cfg'.
If you prefer to avoid building psycopg2 from source, please install the PyPI
'psycopg2-binary' package instead.
For further information please check the 'doc/src/install.rst' file (also at
<https://www.psycopg.org/docs/install.html>).
----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/fd/ae/98cb7a0cbb1d748ee547b058b14604bd0e9bf285a8e0cc5d148f8a8a952e/psycopg2-2.8.6.tar.gz#sha256=fb23f6c71107c37fd667cb4ea363ddeb936b348bbd6449278eb92c189699f543 (from https://pypi.org/simple/psycopg2/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Using cached psycopg2-2.8.5.tar.gz (380 kB)
ERROR: Command errored out with exit status 1:
command: /opt/homebrew/opt/python#3.9/bin/python3.9 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-install-9wiqe2nr/psycopg2_97efcf6747c249769acdc8430ba4238f/setup.py'"'"'; __file__='"'"'/private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-install-9wiqe2nr/psycopg2_97efcf6747c249769acdc8430ba4238f/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-ap2am61r
cwd: /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-install-9wiqe2nr/psycopg2_97efcf6747c249769acdc8430ba4238f/
Complete output (23 lines):
running egg_info
creating /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-ap2am61r/psycopg2.egg-info
writing /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-ap2am61r/psycopg2.egg-info/PKG-INFO
writing dependency_links to /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-ap2am61r/psycopg2.egg-info/dependency_links.txt
writing top-level names to /private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-ap2am61r/psycopg2.egg-info/top_level.txt
writing manifest file '/private/var/folders/m5/vhnyyjg16gd352x6wdhpjysh0000gn/T/pip-pip-egg-info-ap2am61r/psycopg2.egg-info/SOURCES.txt'
Error: pg_config executable not found.
pg_config is required to build psycopg2 from source. Please add the directory
containing pg_config to the $PATH or specify the full executable path with the
option:
python setup.py build_ext --pg-config /path/to/pg_config build ...
or with the pg_config option in 'setup.cfg'.
If you prefer to avoid building psycopg2 from source, please install the PyPI
'psycopg2-binary' package instead.
For further information please check the 'doc/src/install.rst' file (also at
<https://www.psycopg.org/docs/install.html>).
==============================================================================
Its beginning of the error, After that its tried to install each previous version of Psycopg
==============================================================================
Also, I tried to install with source code with :
git clone https://github.com/psycopg/psycopg2.git
cd psycopg2
python3 setup.py build
Its return as error like that:
running build
running build_py
running build_ext
Error: pg_config executable not found.
pg_config is required to build psycopg2 from source. Please add the directory
containing pg_config to the $PATH or specify the full executable path with the
option:
python setup.py build_ext --pg-config /path/to/pg_config build ...
or with the pg_config option in 'setup.cfg'.
If you prefer to avoid building psycopg2 from source, please install the PyPI
'psycopg2-binary' package instead.
For further information please check the 'doc/src/install.rst' file (also at
<https://www.psycopg.org/docs/install.html>).
Also
python3 setup.py build
return the same error as python3 setup.py build
How can I install it?
try this:
brew install libpq --build-from-source
brew install openssl
export LDFLAGS="-L/opt/homebrew/opt/openssl#1.1/lib -L/opt/homebrew/opt/libpq/lib"
export CPPFLAGS="-I/opt/homebrew/opt/openssl#1.1/include -I/opt/homebrew/opt/libpq/include"
pip3 install psycopg2
Before reverting to any of the older answers, I would recommend trying the following:
Install Postgres using brew install postgres, then pip3 install psycopg2.
Worked on Mac M1, Monterey, Python 3.9.
Thanks to Kori Vernon.
Thanks to active development, now there is a new release of psycopg2 as well as psycopg2-binary which is compatible with M1 devices.
Ver. 2.9.1 works smooth. Tried and tested
Reference - https://github.com/psycopg/psycopg2/issues/1200
Following this steps solved my problem:
❯ brew install postgresql#14
# If you open a new terminal tab you will see that pg_config is available
❯ export CPPFLAGS="-I/opt/homebrew/opt/openssl#1.1/include"
❯ export LDFLAGS="-L/opt/homebrew/opt/openssl#1.1/lib -L${HOME}/.pyenv/versions/3.10.7/lib" # use your current python version
❯ python -V
Python 3.10.7 # make sure it matches the same above configuration
❯ pip install psycopg2-binary==2.8.5
Installing numba and llvmlite Python on Windows 10 failure
I have tried to install Python numba on Windows 10 using
pip install numba
with partial success, but a failure installing llvmlite
Requirement already satisfied: numpy>=1.15 in c:\users\paul\appdata\local\programs\python\python39\lib\site-packages (from numba) (1.19.2+mkl)
Requirement already satisfied: setuptools in c:\users\paul\appdata\local\programs\python\python39\lib\site-packages (from numba) (49.2.1)
Building wheels for collected packages: numba, llvmlite
Building wheel for numba (setup.py) ... done
Created wheel for numba: filename=numba-0.51.2-cp39-cp39-win_amd64.whl size=2173229 sha256=249a12f2e1436ac244e2730f6e7ddb5bd53413460dcbdc4ed4e6aeebbf16d6ce
Stored in directory: c:\users\paul\appdata\local\pip\cache\wheels\0a\51\41\9f5a61bcd9d25271d7021e05cbabcd574fb3d534d07654b780
Building wheel for llvmlite (setup.py) ... error
ERROR: Command errored out with exit status 1:
CMake Error at CMakeLists.txt:9 (find_package):
Could not find a package configuration file provided by "LLVM" with any of
the following names:
LLVMConfig.cmake
llvm-config.cmake
Add the installation prefix of "LLVM" to CMAKE_PREFIX_PATH or set
"LLVM_DIR" to a directory containing one of the above files. If "LLVM"
provides a separate development package or SDK, be sure it has been installed.
-- Configuring incomplete, errors occurred!
Doesn't know where LLVM is installed?
So I used Windows Environment editor to add LLVM_DIR with value C:\Program Files\mingw-w64\winlibs-x86_64-posix-seh-gcc-9.3.0-llvm-10.0.0-mingw-w64-7.0.0-r4\mingw64\lib\cmake\llvm
in the hope that it will use one of the four Clang versions that I have installed at C:\LLVM\clang-1100, C:\LLVM\clang-1000 ...
latest binary is C:\LLVM\clang-1100\LLVM\bin
I also have VS 1017 and 1019 installed, and all compilers are working OK from other IDEs and builds.
and downloaded the most recent wheel
llvmlite-0.34.0-cp39-cp39-win_amd64.whl
and added LLVM_DIR to system PATH
C:\Program Files\mingw-w64\winlibs-x86_64-posix-seh-gcc-9.3.0-llvm-10.0.0-mingw-w64-7.0.0-r4\mingw64\lib\cmake\llvm
This allows it to more nearly work, but fails using MSVC
Microsoft (R) Build Engine version 15.9.21+g9802d43bc3 for .NET Framework
Copyright (C) Microsoft Corporation. All rights reserved.
C:\Program Files (x86)\Microsoft Visual Studio\2017\Professional\Common7\IDE\VC\VCTargets\Microsoft.CppBuild.targets(399,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [C:\Users\Paul\AppData\Local\Temp\pip-install-xvvf77_z\llvmlite\ffi\build\ZERO_CHECK.vcxproj]
C:\Program Files (x86)\Microsoft Visual Studio\2017\Professional\Common7\IDE\VC\VCTargets\Microsoft.CppBuild.targets(399,5): warning MSB8029: The Intermediate directory or Output directory cannot reside under the Temporary directory as it could lead to issues with incremental build. [C:\Users\Paul\AppData\Local\Temp\pip-install-xvvf77_z\llvmlite\ffi\build\llvmlite.vcxproj]
LINK : fatal error LNK1181: cannot open input file 'D:\winlibs64_stage\custombuilt\lib\libffi.dll.a' [C:\Users\Paul\AppData\Local\Temp\pip-install-xvvf77_z\llvmlite\ffi\build\llvmlite.vcxproj]
Trying generator 'Visual Studio 15 2017 Win64'
Traceback (most recent call last):
File "C:\Users\Paul\AppData\Local\Temp\pip-install-xvvf77_z\llvmlite\ffi\build.py", line 191, in <module>
main()
File "C:\Users\Paul\AppData\Local\Temp\pip-install-xvvf77_z\llvmlite\ffi\build.py", line 179, in main
main_win32()
File "C:\Users\Paul\AppData\Local\Temp\pip-install-xvvf77_z\llvmlite\ffi\build.py", line 94, in main_win32
subprocess.check_call(['cmake', '--build', build_dir, '--config', config])
File "c:\users\paul\appdata\local\programs\python\python39\lib\subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '--build', 'C:\\Users\\Paul\\AppData\\Local\\Temp\\pip-install-xvvf77_z\\llvmlite\\ffi\\build', '--config', 'Release']' returned non-zero exit status 1.
error: command 'c:\\users\\paul\\appdata\\local\\programs\\python\\python39\\python.exe' failed with exit code 1
----------------------------------------
ERROR: Command errored out with exit status 1: 'c:\users\paul\appdata\local\programs\python\python39\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\Paul\\AppData\\Local\\Temp\\pip-install-xvvf77_z\\llvmlite\\setup.py'"'"'; __file__='"'"'C:\\Users\\Paul\\AppData\\Local\\Temp\\pip-install-xvvf77_z\\llvmlite\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\Paul\AppData\Local\Temp\pip-record-l4absc_g\install-record.txt' --single-version-externally-managed --compile --install-headers 'c:\users\paul\appdata\local\programs\python\python39\Include\llvmlite' Check the logs for full command output.
This suggests that the output folder location is not specified, or that VS incremental build option is not set to 'not used'.
Or that I should use an LLVM version, but I don't know how to specify which one, and not use VS2017.
Suggestions how to get out of this rabbit hole most welcome ;-)
Thanks
Paul
I wanted to install librosa but I get stack with this error, but I managed to solve it with this:
first I download the last version of llvmlite Here
than I run the following command:
pip install llvmlite-0.35.0-cp39-cp39-win_amd64.whl
next for all packages need by librosa I install them as follow:
pip install --no-deps packageName
or just for more sample do as follow :
pip install librosa --ignore-installed llvmlite
I am trying to install deeptools on an Anaconda2 prompt for Python 3.7 and 2.7 by following this tutorial.
First, I got an environment error which I solved by running the following:
$ conda create --name dianaenv python=2.7
$ conda activate dianaenv
$ conda config --add channels bioconda
$ conda install -c bioconda deeptools
But now I get the error below when running the last conda install:
The error: 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. This can take several minutes. Press CTRL-C to abort.- failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Package vs2008_runtime conflicts for: python=2.7 -> vs2008_runtime Package sqlite conflicts for: python=2.7 -> sqlite[version='>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.27.2,<4.0a0|>=3.30.1,<4.0a0'] Package pysam conflicts for: deeptools -> pysam[version='>=0.14.0'] Package vc conflicts for: python=2.7 -> vc[version='9.*|>=9,<10.0a0'] Package deeptoolsintervals conflicts for: deeptools -> deeptoolsintervals[version='>=0.1.8'] Package matplotlib conflicts for: deeptools -> matplotlib[version='>=2.1.1|>=3.0.0'] Package pybigwig conflicts for: deeptools -> pybigwig[version='>=0.2.3'] Package ca-certificates conflicts for: python=2.7 -> ca-certificates Package scipy conflicts for: deeptools -> scipy[version='>=0.17.0'] Package py2bit conflicts for: deeptools -> py2bit[version='>=0.2.0'] Package plotly conflicts for: deeptools -> plotly[version='>=1.9.0|>=2.0.0'] Package pip conflicts for: python=2.7 -> pip Package numpy conflicts for: deeptools -> numpy[version='>=1.9.0'] Package pandas conflicts for: deeptools -> pandas
I also tried to install the requirements individually and installing numpy, scipy and matplotlib. Which all worked fine. But when I try to install py2bit, pybigwig or pysam, I also get the following errors:
$ pip install py2bit
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Collecting py2bit Using cached https://files.pythonhosted.org/packages/53/bb/547a927bed736ead3dc909e1e552d57c9034bb9493eff80544c0cf6e4828/py2bit-0.3.0.tar.gz Building wheels for collected packages: py2bit Building wheel for py2bit setup.py) ... error ERROR: Command errored out with exit status 1: command: 'C:\Users\User\Anaconda2\envs\dianaenv\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\setup.py'"'"'; file='"'"'c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\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\user\appdata\local\temp\pip-wheel-vrkfci' --python-tag cp27 cwd: c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\ Complete output (21 lines): C:\Users\User\Anaconda2\envs\dianaenv\lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'classifier' warnings.warn(msg) running bdist_wheel running build running build_py creating build creating build\lib.win-amd64-2.7 creating build\lib.win-amd64-2.7\py2bitTest copying py2bitTest\test.py -> build\lib.win-amd64-2.7\py2bitTest copying py2bitTest__init__.py -> build\lib.win-amd64-2.7\py2bitTest running egg_info writing py2bit.egg-info\PKG-INFO writing top-level names to py2bit.egg-info\top_level.txt writing dependency_links to py2bit.egg-info\dependency_links.txt reading manifest file 'py2bit.egg-info\SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'py2bit.egg-info\SOURCES.txt' copying py2bitTest\foo.2bit -> build\lib.win-amd64-2.7\py2bitTest running build_ext building 'py2bit' extension error: Microsoft Visual C++ 9.0 is required. Get it from http://aka.ms/vcpython27
ERROR: Failed building wheel for py2bit Running setup.py clean for py2bit Failed to build py2bit Installing collected packages: py2bit Running setup.py install for py2bit ... error ERROR: Command errored out with exit status 1: command: 'C:\Users\User\Anaconda2\envs\dianaenv\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\setup.py'"'"'; file='"'"'c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'c:\users\user\appdata\local\temp\pip-record-xmdylh\install-record.txt' --single-version-externally-managed --compile cwd: c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\ Complete output (21 lines): C:\Users\User\Anaconda2\envs\dianaenv\lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'classifier' warnings.warn(msg) running install running build running build_py creating build creating build\lib.win-amd64-2.7 creating build\lib.win-amd64-2.7\py2bitTest copying py2bitTest\test.py -> build\lib.win-amd64-2.7\py2bitTest copying py2bitTest__init__.py -> build\lib.win-amd64-2.7\py2bitTest running egg_info writing py2bit.egg-info\PKG-INFO writing top-level names to py2bit.egg-info\top_level.txt writing dependency_links to py2bit.egg-info\dependency_links.txt reading manifest file 'py2bit.egg-info\SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'py2bit.egg-info\SOURCES.txt' copying py2bitTest\foo.2bit -> build\lib.win-amd64-2.7\py2bitTest running build_ext building 'py2bit' extension error: Microsoft Visual C++ 9.0 is required. Get it from http://aka.ms/vcpython27 ---------------------------------------- ERROR: Command errored out with exit status 1: 'C:\Users\User\Anaconda2\envs\dianaenv\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\setup.py'"'"'; file='"'"'c:\users\user\appdata\local\temp\pip-install-6nxreu\py2bit\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'c:\users\user\appdata\local\temp\pip-record-xmdylh\install-record.txt' --single-version-externally-managed --compile Check the logs for full command output.
Also, if I try to use pip install I get the following matplotlib error:
$ pip install --user deeptools
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support Collecting deeptools Using cached https://files.pythonhosted.org/packages/82/8e/d9d4b66b2ce1bd48f1db43357c8eb019ae3e8bb1bb7a9e82667db981e1df/deepTools-3.3.1.tar.gz Collecting numpy>=1.9.0 Downloading https://files.pythonhosted.org/packages/48/83/203c397ecec78bdd618a0fb04a47482cfa2ae5ea2c6d428ed94258fe8671/numpy-1.16.5-cp27-cp27m-win_amd64.whl (11.9MB) |UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU| 11.9MB 2.5MB/s Collecting scipy>=0.17.0 Downloading https://files.pythonhosted.org/packages/49/73/22e125f335986fdc3b03c09cdf8ffe0d9d5471eec301aeb2e33db78b3e7f/scipy-1.2.2-cp27-cp27m-win_amd64.whl (30.5MB) |UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU| 30.5MB 187kB/s ERROR: Could not find a version that satisfies the requirement matplotlib>=3.0.0 (from deeptools) (from versions: 0.86, 0.86.1, 0.86.2, 0.91.0, 0.91.1, 1.0.1, 1.1.0, 1.1.1, 1.2.0, 1.2.1, 1.3.0, 1.3.1, 1.4.0, 1.4.1rc1, 1.4.1, 1.4.2, 1.4.3, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 2.0.0b1, 2.0.0b2, 2.0.0b3, 2.0.0b4, 2.0.0rc1, 2.0.0rc2, 2.0.0, 2.0.1, 2.0.2, 2.1.0rc1, 2.1.0, 2.1.1, 2.1.2, 2.2.0rc1, 2.2.0, 2.2.2, 2.2.3, 2.2.4) ERROR: No matching distribution found for matplotlib>=3.0.0 (from deeptools)
I tried uninstalling and reinstalling anaconda and other packages, but it does not work.
Q: How do I resolve a UnsatisfiableError when installing deeptools?
Judging by the vs2008_runtime, this is a Windows system, however, Bioconda only supports Unix and Linux. Moreover, deeptools requires deeptools-intervals which also only supports Unix and Linux.
I don't work with Windows, but I've heard good things about Windows Subsystem for Linux (WSL). That way, you could install a Linux version of Conda (as in this article). Though for scientific work I'd strongly encourage installing Miniconda instead of Anaconda.
In trying to install a python package via pip I get the error:
Failed building wheel for atari-py
Running setup.py clean for atari-py
Failed to build atari-py
Installing collected packages: atari-py, PyOpenGL
Running setup.py install for atari-py ... error
Complete output from command C:\Users\xxxxxx\AppData\Local\Continuum\Anaconda2\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\xxxxxx\\appdata\\local\\temp\\pip-build-qhuh1q\\atari-py\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record c:\users\xxxxxx\appdata\local\temp\pip-z8wnzs-record\install-record.txt --single-version-externally-managed --compile:
running install
running build
Unable to execute 'make build -C atari_py/ale_interface -j 3'. HINT: are you sure `make` is installed?
error: [Error 2] The system cannot find the file specified
In my system when I type make:
C:\Users\xxxxxx>make
'make' is not recognized as an internal or external command,
operable program or batch file.
So, clearly make is missing. But I installed make using conda:
C:\Users\xxxxxx>conda install mingw
Fetching package metadata .........
Solving package specifications: ..........
# All requested packages already installed.
# packages in environment at C:\Users\xxxxxx\AppData\Local\Continuum\Anaconda2:
#
mingw 4.7
So I have mingw 4.7 already installed.
How could I remove the error and get the package?
Many thanks for the help.
make is not in your PATH.
Do echo %PATH% and check if the path to your msys utilities is in there. Otherwise you can edit this variable by following the instructions here: Adding directory to PATH Environment Variable in Windows
For a while now i have been trying to figure out how to install lxml but have had no such luck. As a last ditch of hope. I've come here for some solutions or clarification. So far I've already tried nearly all the ways told before in other answer threads but have had no luck.
Firstly I've tried the following:
pip install lxml
pip3 install lxml
python -m pip install lxml
Which threw an error...
ERROR: b"'xslt-config' is not recognized as an internal or external command,\r\noperable program or batch file.\r\n"
** make sure the development packages of libxml2 and libxslt are installed **
C:\Users\Me\AppData\Local\Temp\xmlXPathInit1owazwq3.c(1): fatal error C1083: Cannot open include file: 'libxml/xpath.h': No such file or directory
*********************************************************************************
Could not find function xmlCheckVersion in library libxml2. Is libxml2 installed?
*********************************************************************************
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\cl.exe' failed with exit status 2
----------------------------------------
Failed building wheel for lxml
I then went on and tried to install wheel...
python -m pip install wheel
C:\Users\Me>python -m pip install wheel
Requirement already satisfied (use --upgrade to upgrade): wheel in c:\python35\lib\site-packages
Which seems to have worked.
However when i tried to install lxml again...
Could not find function xmlCheckVersion in library libxml2. Is libxml2 installed?
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\cl.exe' failed with exit status 2
Command "c:\python35\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Me\\AppData\\Local\\Temp\\pip-build-klrlh4_w\\lxml\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\Me\AppData\Local\Temp\pip-k3saekal-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\Me\AppData\Local\Temp\pip-build-klrlh4_w\lxml\
i then tried downloading the .whl files..
python -m pip install lxml-3.6.0-cp35-cp35m-win_amd64.whl
^Downloaded nearly all of these .whl files
only to come to the same conclusion each and every
lxml-3.6.0-cp35-cp35m-win_amd64.whl is not a supported wheel on this platform.
Sadly none of these have been able to install lxml...
Is lxml able to run on python3.5.1?
Any help at all will be helpful :)
Check what version you need to download with...
import sys
is_64bits = sys.maxsize > 2**32
print(is_64bits )
Then download the right version of lxml.. http://www.lfd.uci.edu/~gohlke/pythonlibs/#lxml
All credit goes to #Manjabes - https://stackoverflow.com/users/396571/manjabes
Thanks for the help <3