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error: INCLUDE environment variable is empty
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error: INCLUDE environment variable is empty
#1
Hi,
I am new to Python.
I used python2.7 to install biom-format package. The scripts and results are shown below. It is very grateful if you have any idea and suggestion.Thank you very much.

start
------------------
C:\Python27\Scripts>pip install C:\Users\xunwe\Downloads\biom-format-2.1.4.tar.gz
Processing c:\users\xunwe\downloads\biom-format-2.1.4.tar.gz
Requirement already satisfied: numpy>=1.3.0 in c:\python27\lib\site-packages (from biom-format==2.1.4)
Requirement already satisfied: pyqi==0.3.2 in c:\python27\lib\site-packages (from biom-format==2.1.4)
Requirement already satisfied: scipy>=0.13.0 in c:\python27\lib\site-packages (from biom-format==2.1.4)
Installing collected packages: biom-format
Running setup.py install for biom-format ... error
Complete output from command c:\python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\xunwe\\appdata\\local\\temp\\pip-avam5i-build\\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\xunwe\appdata\local\temp\pip-uxmtbf-record\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build\lib.win-amd64-2.7
creating build\lib.win-amd64-2.7\biom
copying biom\err.py -> build\lib.win-amd64-2.7\biom
copying biom\exception.py -> build\lib.win-amd64-2.7\biom
copying biom\parse.py -> build\lib.win-amd64-2.7\biom
copying biom\table.py -> build\lib.win-amd64-2.7\biom
copying biom\util.py -> build\lib.win-amd64-2.7\biom
copying biom\__init__.py -> build\lib.win-amd64-2.7\biom
creating build\lib.win-amd64-2.7\biom\commands
copying biom/commands\installation_informer.py -> build\lib.win-amd64-2.7\biom/commands
copying biom/commands\metadata_adder.py -> build\lib.win-amd64-2.7\biom/commands
copying biom/commands\table_converter.py -> build\lib.win-amd64-2.7\biom/commands
copying biom/commands\table_normalizer.py -> build\lib.win-amd64-2.7\biom/commands
copying biom/commands\table_subsetter.py -> build\lib.win-amd64-2.7\biom/commands
copying biom/commands\table_summarizer.py -> build\lib.win-amd64-2.7\biom/commands
copying biom/commands\table_validator.py -> build\lib.win-amd64-2.7\biom/commands
copying biom/commands\__init__.py -> build\lib.win-amd64-2.7\biom/commands
creating build\lib.win-amd64-2.7\biom\interfaces
copying biom/interfaces\__init__.py -> build\lib.win-amd64-2.7\biom/interfaces
creating build\lib.win-amd64-2.7\biom\interfaces\optparse
copying biom/interfaces/optparse\input_handler.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse
copying biom/interfaces/optparse\output_handler.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse
copying biom/interfaces/optparse\__init__.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse
creating build\lib.win-amd64-2.7\biom\interfaces\optparse\config
copying biom/interfaces/optparse/config\add_metadata.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
copying biom/interfaces/optparse/config\convert.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
copying biom/interfaces/optparse/config\normalize_table.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
copying biom/interfaces/optparse/config\show_install_info.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
copying biom/interfaces/optparse/config\subset_table.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
copying biom/interfaces/optparse/config\summarize_table.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
copying biom/interfaces/optparse/config\validate_table.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
copying biom/interfaces/optparse/config\__init__.py -> build\lib.win-amd64-2.7\biom/interfaces/optparse/config
creating build\lib.win-amd64-2.7\biom\interfaces\html
copying biom/interfaces/html\input_handler.py -> build\lib.win-amd64-2.7\biom/interfaces/html
copying biom/interfaces/html\output_handler.py -> build\lib.win-amd64-2.7\biom/interfaces/html
copying biom/interfaces/html\__init__.py -> build\lib.win-amd64-2.7\biom/interfaces/html
creating build\lib.win-amd64-2.7\biom\interfaces\html\config
copying biom/interfaces/html/config\add_metadata.py -> build\lib.win-amd64-2.7\biom/interfaces/html/config
copying biom/interfaces/html/config\convert.py -> build\lib.win-amd64-2.7\biom/interfaces/html/config
copying biom/interfaces/html/config\normalize_table.py -> build\lib.win-amd64-2.7\biom/interfaces/html/config
copying biom/interfaces/html/config\show_install_info.py -> build\lib.win-amd64-2.7\biom/interfaces/html/config
copying biom/interfaces/html/config\summarize_table.py -> build\lib.win-amd64-2.7\biom/interfaces/html/config
copying biom/interfaces/html/config\validate_table.py -> build\lib.win-amd64-2.7\biom/interfaces/html/config
copying biom/interfaces/html/config\__init__.py -> build\lib.win-amd64-2.7\biom/interfaces/html/config
running build_ext
building 'biom._filter' extension
error: INCLUDE environment variable is empty

----------------------------------------
Command "c:\python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\xunwe\\appdata\\local\\temp\\pip-avam5i-build\\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\xunwe\appdata\local\temp\pip-uxmtbf-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\xunwe\appdata\local\temp\pip-avam5i-build\

---------------------
end

Thank you!
Reply
#2
use pip install biom-format or if you want to download the package and install it from your pc, download the wheel file biom_format-2.1.6-cp27-cp27m-macosx_10_7_x86_64.whl (from pypi https://pypi.python.org/pypi/biom-format/2.1.6) and pip install biom_format-2.1.6-cp27-cp27m-macosx_10_7_x86_64.whl
by the way there are instructions on installation on http://biom-format.org/
Reply
#3
Hi Buran,
The whl file you mentioned seems only supports mac? But I am using win10.
pip install biom-format seems not working also.

C:\Python27\Scripts>pip install biom-format
Collecting biom-format
Using cached biom-format-2.1.6.tar.gz
Requirement already satisfied: click in c:\python27\lib\site-packages (from biom-format)
Requirement already satisfied: numpy>=1.3.0 in c:\python27\lib\site-packages (from biom-format)
Requirement already satisfied: future>=0.16.0 in c:\python27\lib\site-packages (from biom-format)
Requirement already satisfied: scipy>=0.13.0 in c:\python27\lib\site-packages (from biom-format)
Requirement already satisfied: pandas>=0.19.2 in c:\python27\lib\site-packages (from biom-format)
Requirement already satisfied: six>=1.10.0 in c:\python27\lib\site-packages (from biom-format)
Requirement already satisfied: pyqi in c:\python27\lib\site-packages (from biom-format)
Requirement already satisfied: pytz>=2011k in c:\python27\lib\site-packages (from pandas>=0.19.2->biom-format)
Requirement already satisfied: python-dateutil in c:\python27\lib\site-packages (from pandas>=0.19.2->biom-format)
Installing collected packages: biom-format
Running setup.py install for biom-format ... error
Complete output from command c:\python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\xunwe\\appdata\\local\\temp\\pip-build-q3r1ja\\biom-format\\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\xunwe\appdata\local\temp\pip-mdpxui-record\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build\lib.win-amd64-2.7
creating build\lib.win-amd64-2.7\biom
copying biom\err.py -> build\lib.win-amd64-2.7\biom
copying biom\exception.py -> build\lib.win-amd64-2.7\biom
copying biom\parse.py -> build\lib.win-amd64-2.7\biom
copying biom\table.py -> build\lib.win-amd64-2.7\biom
copying biom\util.py -> build\lib.win-amd64-2.7\biom
copying biom\__init__.py -> build\lib.win-amd64-2.7\biom
creating build\lib.win-amd64-2.7\tests
copying tests\test_err.py -> build\lib.win-amd64-2.7\tests
copying tests\test_parse.py -> build\lib.win-amd64-2.7\tests
copying tests\test_table.py -> build\lib.win-amd64-2.7\tests
copying tests\test_util.py -> build\lib.win-amd64-2.7\tests
copying tests\__init__.py -> build\lib.win-amd64-2.7\tests
creating build\lib.win-amd64-2.7\biom\cli
copying biom\cli\installation_informer.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\metadata_adder.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_converter.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_head.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_ids.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_normalizer.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_subsetter.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_summarizer.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_validator.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\uc_processor.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\util.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\__init__.py -> build\lib.win-amd64-2.7\biom\cli
creating build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_add_metadata.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_show_install_info.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_subset_table.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_summarize_table.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_table_converter.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_table_normalizer.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_uc_processor.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_validate_table.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\__init__.py -> build\lib.win-amd64-2.7\tests\test_cli
creating build\lib.win-amd64-2.7\tests\test_data
copying tests\test_data\__init__.py -> build\lib.win-amd64-2.7\tests\test_data
running egg_info
writing requirements to biom_format.egg-info\requires.txt
writing biom_format.egg-info\PKG-INFO
writing top-level names to biom_format.egg-info\top_level.txt
writing dependency_links to biom_format.egg-info\dependency_links.txt
writing entry points to biom_format.egg-info\entry_points.txt
warning: manifest_maker: standard file '-c' not found

reading manifest file 'biom_format.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no directories found matching 'support_files'
no previously-included directories found matching 'docs\_build'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '.*.swp' found anywhere in distribution
writing manifest file 'biom_format.egg-info\SOURCES.txt'
copying biom\_filter.c -> build\lib.win-amd64-2.7\biom
copying biom\_filter.pyx -> build\lib.win-amd64-2.7\biom
copying biom\_subsample.c -> build\lib.win-amd64-2.7\biom
copying biom\_subsample.pyx -> build\lib.win-amd64-2.7\biom
copying biom\_transform.c -> build\lib.win-amd64-2.7\biom
copying biom\_transform.pyx -> build\lib.win-amd64-2.7\biom
creating build\lib.win-amd64-2.7\biom\assets
copying biom\assets\exercise_api.py -> build\lib.win-amd64-2.7\biom\assets
copying biom\assets\exercise_cli.sh -> build\lib.win-amd64-2.7\biom\assets
running build_ext
building 'biom._filter' extension
error: INCLUDE environment variable is empty

----------------------------------------
Command "c:\python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\xunwe\\appdata\\local\\temp\\pip-build-q3r1ja\\biom-format\\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\xunwe\appdata\local\temp\pip-mdpxui-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\xunwe\appdata\local\temp\pip-build-q3r1ja\biom-format\

C:\Python27\Scripts>
C:\Python27\Scripts>pip install C:\Users\xunwe\Downloads\biom_format-2.1.6-cp27-cp27m-macosx_10_7_x86_64.whl
biom_format-2.1.6-cp27-cp27m-macosx_10_7_x86_64.whl is not a supported wheel on this platform.

C:\Python27\Scripts>pip install C:\Users\xunwe\Downloads\biom-format-2.1.6.tar.gz
Processing c:\users\xunwe\downloads\biom-format-2.1.6.tar.gz
Requirement already satisfied: click in c:\python27\lib\site-packages (from biom-format==2.1.6)
Requirement already satisfied: numpy>=1.3.0 in c:\python27\lib\site-packages (from biom-format==2.1.6)
Requirement already satisfied: future>=0.16.0 in c:\python27\lib\site-packages (from biom-format==2.1.6)
Requirement already satisfied: scipy>=0.13.0 in c:\python27\lib\site-packages (from biom-format==2.1.6)
Requirement already satisfied: pandas>=0.19.2 in c:\python27\lib\site-packages (from biom-format==2.1.6)
Requirement already satisfied: six>=1.10.0 in c:\python27\lib\site-packages (from biom-format==2.1.6)
Requirement already satisfied: pyqi in c:\python27\lib\site-packages (from biom-format==2.1.6)
Requirement already satisfied: pytz>=2011k in c:\python27\lib\site-packages (from pandas>=0.19.2->biom-format==2.1.6)
Requirement already satisfied: python-dateutil in c:\python27\lib\site-packages (from pandas>=0.19.2->biom-format==2.1.6)
Installing collected packages: biom-format
Running setup.py install for biom-format ... error
Complete output from command c:\python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\xunwe\\appdata\\local\\temp\\pip-5fhulo-build\\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\xunwe\appdata\local\temp\pip-qd1293-record\install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build\lib.win-amd64-2.7
creating build\lib.win-amd64-2.7\biom
copying biom\err.py -> build\lib.win-amd64-2.7\biom
copying biom\exception.py -> build\lib.win-amd64-2.7\biom
copying biom\parse.py -> build\lib.win-amd64-2.7\biom
copying biom\table.py -> build\lib.win-amd64-2.7\biom
copying biom\util.py -> build\lib.win-amd64-2.7\biom
copying biom\__init__.py -> build\lib.win-amd64-2.7\biom
creating build\lib.win-amd64-2.7\tests
copying tests\test_err.py -> build\lib.win-amd64-2.7\tests
copying tests\test_parse.py -> build\lib.win-amd64-2.7\tests
copying tests\test_table.py -> build\lib.win-amd64-2.7\tests
copying tests\test_util.py -> build\lib.win-amd64-2.7\tests
copying tests\__init__.py -> build\lib.win-amd64-2.7\tests
creating build\lib.win-amd64-2.7\biom\cli
copying biom\cli\installation_informer.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\metadata_adder.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_converter.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_head.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_ids.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_normalizer.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_subsetter.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_summarizer.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\table_validator.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\uc_processor.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\util.py -> build\lib.win-amd64-2.7\biom\cli
copying biom\cli\__init__.py -> build\lib.win-amd64-2.7\biom\cli
creating build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_add_metadata.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_show_install_info.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_subset_table.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_summarize_table.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_table_converter.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_table_normalizer.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_uc_processor.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\test_validate_table.py -> build\lib.win-amd64-2.7\tests\test_cli
copying tests\test_cli\__init__.py -> build\lib.win-amd64-2.7\tests\test_cli
creating build\lib.win-amd64-2.7\tests\test_data
copying tests\test_data\__init__.py -> build\lib.win-amd64-2.7\tests\test_data
running egg_info
writing requirements to biom_format.egg-info\requires.txt
writing biom_format.egg-info\PKG-INFO
writing top-level names to biom_format.egg-info\top_level.txt
writing dependency_links to biom_format.egg-info\dependency_links.txt
writing entry points to biom_format.egg-info\entry_points.txt
warning: manifest_maker: standard file '-c' not found

reading manifest file 'biom_format.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no directories found matching 'support_files'
no previously-included directories found matching 'docs\_build'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '.*.swp' found anywhere in distribution
writing manifest file 'biom_format.egg-info\SOURCES.txt'
copying biom\_filter.c -> build\lib.win-amd64-2.7\biom
copying biom\_filter.pyx -> build\lib.win-amd64-2.7\biom
copying biom\_subsample.c -> build\lib.win-amd64-2.7\biom
copying biom\_subsample.pyx -> build\lib.win-amd64-2.7\biom
copying biom\_transform.c -> build\lib.win-amd64-2.7\biom
copying biom\_transform.pyx -> build\lib.win-amd64-2.7\biom
creating build\lib.win-amd64-2.7\biom\assets
copying biom\assets\exercise_api.py -> build\lib.win-amd64-2.7\biom\assets
copying biom\assets\exercise_cli.sh -> build\lib.win-amd64-2.7\biom\assets
running build_ext
building 'biom._filter' extension
error: INCLUDE environment variable is empty

----------------------------------------
Command "c:\python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\xunwe\\appdata\\local\\temp\\pip-5fhulo-build\\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\xunwe\appdata\local\temp\pip-qd1293-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\xunwe\appdata\local\temp\pip-5fhulo-build\
Reply
#4
(Mar-21-2018, 02:49 AM)xwchen Wrote: The whl file you mentioned seems only supports mac?
sorry, you are right. I appologize for overlookig that.
It looks that package is not tested on windows and support is unclear. Check the discussion here: https://github.com/biocore/biom-format/issues/736
Reply
#5
Thank you for the information.
Reply


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