Problem with installation #27

anastasiiasatyr · 2019-07-26T10:14:03Z

Hello,
I have a problem with installation on the stage of building dependencies.

After I put a command:
pip install -r bulkvis/requirements.txt
it writes with huge error:

ERROR: Command errored out with exit status 1:
command: /home/threadripper/bulkvis-env/bin/python3 /home/threadripper/bulkvis-env/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-7n5ntt49/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools Cython 'numpy==1.9.3; python_version=='"'"'3.5'"'"'' 'numpy==1.12.1; python_version=='"'"'3.6'"'"'' 'numpy==1.13.1; python_version>='"'"'3.7'"'"''
cwd: None
Complete output (3954 lines):
Ignoring numpy: markers 'python_version == "3.5"' don't match your environment
Ignoring numpy: markers 'python_version == "3.6"' don't match your environment
Collecting wheel
Using cached https://files.pythonhosted.org/packages/bb/10/44230dd6bf3563b8f227dbf344c908d412ad2ff48066476672f3a72e174e/wheel-0.33.4-py2.py3-none-any.whl
Collecting setuptools
Using cached https://files.pythonhosted.org/packages/ec/51/f45cea425fd5cb0b0380f5b0f048ebc1da5b417e48d304838c02d6288a1e/setuptools-41.0.1-py2.py3-none-any.whl
Collecting Cython
Using cached https://files.pythonhosted.org/packages/14/43/8cfcae48235d2553c55f1f8bec21b8f5ae21b617d7d0e59023ab4b0ddfaf/Cython-0.29.12-cp37-cp37m-manylinux1_x86_64.whl
Collecting numpy==1.13.1
Using cached https://files.pythonhosted.org/packages/c0/3a/40967d9f5675fbb097ffec170f59c2ba19fc96373e73ad47c2cae9a30aed/numpy-1.13.1.zip
Installing collected packages: wheel, setuptools, Cython, numpy
Running setup.py install for numpy: started
Running setup.py install for numpy: still running...
Running setup.py install for numpy: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /home/threadripper/bulkvis-env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-zs1v_8d8/numpy/setup.py'"'"'; file='"'"'/tmp/pip-install-zs1v_8d8/numpy/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-y_k32ehd/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-7n5ntt49/overlay --compile --install-headers /home/threadripper/bulkvis-env/include/site/python3.7/numpy
cwd: /tmp/pip-install-zs1v_8d8/numpy/
Complete output (3934 lines):
Running from numpy source directory.

ERROR: Command errored out with exit status 1: /home/threadripper/bulkvis-env/bin/python3 /home/threadripper/bulkvis-env/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-7n5ntt49/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools Cython 'numpy==1.9.3; python_version=='"'"'3.5'"'"'' 'numpy==1.12.1; python_version=='"'"'3.6'"'"'' 'numpy==1.13.1; python_version>='"'"'3.7'"'"'' Check the logs for full command output.

alexomics · 2019-07-26T10:18:13Z

In your bulkvis environment, what is the output of pip list?

anastasiiasatyr · 2019-07-26T10:23:22Z

Package Version

pip 19.2.1
setuptools 40.8.0

alexomics · 2019-07-26T10:29:08Z

Are you able to install the dependencies individually?

eg:

pip install bokeh
pip install h5py
pip install Jinja2
pip install MarkupSafe
pip install numpy
pip install pandas
pip install Pillow
pip install python-dateutil
pip install pytz
pip install PyYAML
pip install selenium
pip install six
pip install tornado
pip install tqdm

One of these may cause an error, if so which?

anastasiiasatyr · 2019-07-26T10:35:07Z

I've actually installed all the packages by hand and all of them were successfully installed without any error.

Hereafter, I wanted to set configuration by:

python utils/set_config.py -b <> -i /path/to/bulkfile/directory -e /path/to/readfile/directory -m /path/to/mapfile/directory -c config.ini

but I don't know where to take this <>

My config.ini file has the following content:

[data]
dir = /home/threadripper/Anastas/ExperimentData/fast5_skip+pass
out = /home/threadripper/Anastas/ExperimentData/fast5_bulkvis
map = /home/threadripper/bulkvis/utils/gen_bmf.py
[plot_opts]
wdg_width = 300
plot_width = 1600
plot_height = 1000
y_min = 0
y_max = 2200
label_height = 800
upper_cut_off = 2200
lower_cut_off = -1000
; recommended that this is kept as 'canvas' opts: ['canvas', 'svg', 'webgl']
output_backend = canvas
[labels]
adapter = True
mux_uncertain = True
strand1 = False
user1 = True
event = False
user2 = False
multiple = False
unclassed = False
pore = True
strand = True
transition = True
unavailable = False
zero = False
saturated = False
unblocking = True
good_single = False
below = False
above = True
inrange = False
unclassified = False
unclassified_following_reset = False
pending_manual_reset = False
pending_mux_change = False

alexomics · 2019-07-26T10:45:13Z

The python script set_config.py has the help text:

$ python set_config.py -h
usage: set_config.py [-h] -b  -i  -e  -m  [-c]

Generate a configuration file required for bulkvis to run

General options:
  -h, --help          Show this help and exit

Input sources:
  -b , --bulkfile     A bulk-fast5 file to get labels from
  -i , --input-dir    The path to tbe folder containing bulk-files for
                      visualisation
  -e , --export-dir   The path to tbe folder where read-files will be written
                      by bulkvis
  -m , --map-dir      The path to tbe folder where map files, created by
                      gen_bmf.py, are stored

Output:
  -c , --config       Path to the config.ini file in your bulkvis installation

So the -b parameter is a bulk FAST5 file generated by MinKNOW.

Looking at your config it seems you are using read FAST5 files, which will not work.
The map field specifies where the output of the script utils/gen_bmf.py is stored and should not be the python script itself.

anastasiiasatyr · 2019-07-26T10:54:46Z

I still don't see what this should be:

-b , --bulkfile A bulk-fast5 file to get labels from

i , --input-dir The path to tbe folder containing bulk-files for visualisation (I understand it as my .fast5 files which i obtained from sequencer output)

--m , --map-dir The path to tbe folder where map files, created by
gen_bmf.py, are stored (which files are map files? whale_merge.py; whale_plot.py, whale_watch.py and so on?)

alexomics · 2019-07-26T11:08:18Z

The -b parameter is a single bulk FAST5 file that has been generated by MinKNOW. It is an aggregation of all the data processed by MinKNOW during a sequencing experiment. It is used by set_config.py to find the labels that MinKNOW assigned to reads during the run.

The -i parameter should point to the folder containing your bulk FAST5 file, this is required so that bulkvis knows where to search for your input data.

The -m parameter should point to the folder that contains .bmf files. These files are generated by gen_bmf.py, and are a merge of the sequencing_summary.txt files from basecalling and mapping.paf files (generated by minimap2) from mapping your FASTQ data. This folder should exist but can be empty.

anastasiiasatyr · 2019-07-30T05:14:15Z

I understood, thanks a lot!

Shahzadi-ETS · 2019-10-04T21:31:15Z

hi,
I am trying to install numpy on window python 3.4.4
but the error occurred, i even reinstall the whole python and assign the path to the administration system . Kindly anyone of you guides me or help me, how to install. If the error is,
error: Microsoft Visual C++ 10.0 is required. Get it with "Microsoft Windows S
DK 7.1": www.microsoft.com/download/details.aspx?id=8279

ERROR: Failed building wheel for numpy
Running setup.py clean for numpy
ERROR: Command errored out with exit status 1:
command: 'c:\python34\python.exe' -u -c 'import sys, setuptools, tokenize; sy
s.argv[0] = '"'"'C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1
\numpy\setup.py'"'"'; file='"'"'C:\Users\an95120\AppData\Local\Temp\p
ip-install-xuqde9e1\numpy\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', op
en)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec
(compile(code, file, '"'"'exec'"'"'))' clean --all
cwd: C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy
Complete output (10 lines):
Running from numpy source directory.

setup.py clean is not supported, use one of the following instead:

- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
                    files that aren't checked into the git repo)

Add --force to your command to use it anyway if you must (unsupported).

ERROR: Failed cleaning build dir for numpy
Failed to build numpy
Installing collected packages: numpy
Running setup.py install for numpy ... error
ERROR: Command errored out with exit status 1:
command: 'c:\python34\python.exe' -u -c 'import sys, setuptools, tokenize;
sys.argv[0] = '"'"'C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e
1\numpy\setup.py'"'"'; file='"'"'C:\Users\an95120\AppData\Local\Temp
\pip-install-xuqde9e1\numpy\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"',
open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();ex
ec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\an95120
AppData\Local\Temp\pip-record-41uj2idn\install-record.txt' --single-version-exte
rnally-managed --compile
cwd: C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy
Complete output (226 lines):
Running from numpy source directory.

Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:

  - `pip install .`       (from a git repo or downloaded source
                           release)
  - `pip install numpy`   (last NumPy release on PyPi)


blas_opt_info:
blas_mkl_info:
customize MSVCCompiler
  libraries mkl_rt not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\

\libs']
NOT AVAILABLE

blis_info:
customize MSVCCompiler
  libraries blis not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\\l

ibs']
NOT AVAILABLE

openblas_info:
customize MSVCCompiler
customize MSVCCompiler
  libraries openblas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python3

4\libs']
get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv
', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelVisualFCompiler
Could not locate executable ifort
Could not locate executable ifl
customize AbsoftFCompiler
Could not locate executable f90
customize CompaqVisualFCompiler
Could not locate executable DF
customize IntelItaniumVisualFCompiler
Could not locate executable efl
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize G95FCompiler
Could not locate executable g95
customize IntelEM64VisualFCompiler
customize IntelEM64TFCompiler
Could not locate executable efort
Could not locate executable efc
customize PGroupFlangCompiler
don't know how to compile Fortran code on platform 'nt'
NOT AVAILABLE

atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries tatlas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\

\libs']
NOT AVAILABLE

atlas_3_10_blas_info:
customize MSVCCompiler
  libraries satlas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\

\libs']
NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in ['c:\\python34\\lib', 'C:\\

', 'c:\python34\libs']
NOT AVAILABLE

atlas_blas_info:
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in ['c:\\python34\\lib', 'C:\\', '

c:\python34\libs']
NOT AVAILABLE

accelerate_info:
  NOT AVAILABLE

C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti

ls\system_info.py:639: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
blas_info:
customize MSVCCompiler
libraries blas not found in ['c:\python34\lib', 'C:\', 'c:\python34\l
ibs']
NOT AVAILABLE

C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti

ls\system_info.py:639: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
self.calc_info()
blas_src_info:
NOT AVAILABLE

C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti

ls\system_info.py:639: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
self.calc_info()
NOT AVAILABLE

'svnversion' is not recognized as an internal or external command,
operable program or batch file.
non-existing path in 'numpy\\distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
customize MSVCCompiler
  libraries mkl_rt not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\

\libs']
NOT AVAILABLE

openblas_lapack_info:
customize MSVCCompiler
customize MSVCCompiler
  libraries openblas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python3

4\libs']
NOT AVAILABLE

openblas_clapack_info:
customize MSVCCompiler
customize MSVCCompiler
  libraries openblas,lapack not found in ['c:\\python34\\lib', 'C:\\', 'c:\\

python34\libs']
NOT AVAILABLE

atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries tatlas,tatlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries tatlas,tatlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries tatlas,tatlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
  NOT AVAILABLE

atlas_3_10_info:
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries satlas,satlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries satlas,satlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries satlas,satlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_3_10_info'>
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_threads_info'>
  NOT AVAILABLE

atlas_info:
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_info'>
  NOT AVAILABLE

lapack_info:
customize MSVCCompiler
  libraries lapack not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\

\libs']
NOT AVAILABLE

C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti

ls\system_info.py:639: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE

C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti

ls\system_info.py:639: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE

c:\python34\lib\distutils\dist.py:260: UserWarning: Unknown distribution opt

ion: 'define_macros'
warnings.warn(msg)
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler
options
running build_src
build_src
building py_modules sources
building library "npymath" sources
error: Microsoft Visual C++ 10.0 is required. Get it with "Microsoft Windows
SDK 7.1": www.microsoft.com/download/details.aspx?id=8279
----------------------------------------
ERROR: Command errored out with exit status 1: 'c:\python34\python.exe' -u -c 'i
mport sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\an95120\AppData
\Local\Temp\pip-install-xuqde9e1\numpy\setup.py'"'"'; file='"'"'C:\User
s\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\setup.py'"'"';f=g
etattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n
'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' in
stall --record 'C:\Users\an95120\AppData\Local\Temp\pip-record-41uj2idn\install-
record.txt' --single-version-externally-managed --compile Check the logs for ful
l command output.

arjolpanci · 2020-01-14T17:12:14Z

hi,

I am trying to install numpy on window python 3.4.4
but the error occurred, i even reinstall the whole python and assign the path to the administration system . Kindly anyone of you guides me or help me, how to install. If the error is,
error: Microsoft Visual C++ 10.0 is required. Get it with "Microsoft Windows S
DK 7.1": www.microsoft.com/download/details.aspx?id=8279
ERROR: Failed building wheel for numpy
Running setup.py clean for numpy
ERROR: Command errored out with exit status 1:
command: 'c:\python34\python.exe' -u -c 'import sys, setuptools, tokenize; sy
s.argv[0] = '"'"'C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1
\numpy\setup.py'"'"'; file='"'"'C:\Users\an95120\AppData\Local\Temp\p
ip-install-xuqde9e1\numpy\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', op
en)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec
(compile(code, file, '"'"'exec'"'"'))' clean --all
cwd: C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy
Complete output (10 lines):
Running from numpy source directory.

setup.py clean is not supported, use one of the following instead:
- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
                    files that aren't checked into the git repo)
Add --force to your command to use it anyway if you must (unsupported).

ERROR: Failed cleaning build dir for numpy
Failed to build numpy
Installing collected packages: numpy
Running setup.py install for numpy ... error
ERROR: Command errored out with exit status 1:
command: 'c:\python34\python.exe' -u -c 'import sys, setuptools, tokenize;
sys.argv[0] = '"'"'C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e
1\numpy\setup.py'"'"'; file='"'"'C:\Users\an95120\AppData\Local\Temp
\pip-install-xuqde9e1\numpy\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"',
open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();ex
ec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\an95120
AppData\Local\Temp\pip-record-41uj2idn\install-record.txt' --single-version-exte
rnally-managed --compile
cwd: C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy
Complete output (226 lines):
Running from numpy source directory.
Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:

  - `pip install .`       (from a git repo or downloaded source
                           release)
  - `pip install numpy`   (last NumPy release on PyPi)


blas_opt_info:
blas_mkl_info:
customize MSVCCompiler
  libraries mkl_rt not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\
\libs']
NOT AVAILABLE
blis_info:
customize MSVCCompiler
  libraries blis not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\\l
ibs']
NOT AVAILABLE
openblas_info:
customize MSVCCompiler
customize MSVCCompiler
  libraries openblas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python3
4\libs']
get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv
', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelVisualFCompiler
Could not locate executable ifort
Could not locate executable ifl
customize AbsoftFCompiler
Could not locate executable f90
customize CompaqVisualFCompiler
Could not locate executable DF
customize IntelItaniumVisualFCompiler
Could not locate executable efl
customize Gnu95FCompiler
Could not locate executable gfortran
Could not locate executable f95
customize G95FCompiler
Could not locate executable g95
customize IntelEM64VisualFCompiler
customize IntelEM64TFCompiler
Could not locate executable efort
Could not locate executable efc
customize PGroupFlangCompiler
don't know how to compile Fortran code on platform 'nt'
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries tatlas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\
\libs']
NOT AVAILABLE
atlas_3_10_blas_info:
customize MSVCCompiler
  libraries satlas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\
\libs']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in ['c:\\python34\\lib', 'C:\\
', 'c:\python34\libs']
NOT AVAILABLE
atlas_blas_info:
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in ['c:\\python34\\lib', 'C:\\', '
c:\python34\libs']
NOT AVAILABLE
accelerate_info:
  NOT AVAILABLE

C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti
ls\system_info.py:639: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
blas_info:
customize MSVCCompiler
libraries blas not found in ['c:\python34\lib', 'C:', 'c:\python34\l
ibs']
NOT AVAILABLE
C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti
ls\system_info.py:639: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
self.calc_info()
blas_src_info:
NOT AVAILABLE
C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti
ls\system_info.py:639: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
self.calc_info()
NOT AVAILABLE
'svnversion' is not recognized as an internal or external command,
operable program or batch file.
non-existing path in 'numpy\\distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
customize MSVCCompiler
  libraries mkl_rt not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\
\libs']
NOT AVAILABLE
openblas_lapack_info:
customize MSVCCompiler
customize MSVCCompiler
  libraries openblas not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python3
4\libs']
NOT AVAILABLE
openblas_clapack_info:
customize MSVCCompiler
customize MSVCCompiler
  libraries openblas,lapack not found in ['c:\\python34\\lib', 'C:\\', 'c:\\
python34\libs']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries tatlas,tatlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries tatlas,tatlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries tatlas,tatlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
  NOT AVAILABLE

atlas_3_10_info:
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries satlas,satlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries satlas,satlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries satlas,satlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_3_10_info'>
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries ptf77blas,ptcblas,atlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_threads_info'>
  NOT AVAILABLE

atlas_info:
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in c:\python34\lib
customize MSVCCompiler
  libraries lapack_atlas not found in C:\
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in C:\
customize MSVCCompiler
  libraries lapack_atlas not found in c:\python34\libs
customize MSVCCompiler
  libraries f77blas,cblas,atlas not found in c:\python34\libs
<class 'numpy.distutils.system_info.atlas_info'>
  NOT AVAILABLE

lapack_info:
customize MSVCCompiler
  libraries lapack not found in ['c:\\python34\\lib', 'C:\\', 'c:\\python34\
\libs']
NOT AVAILABLE
C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti
ls\system_info.py:639: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE
C:\Users\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\numpy\distuti
ls\system_info.py:639: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE
c:\python34\lib\distutils\dist.py:260: UserWarning: Unknown distribution opt
ion: 'define_macros'
warnings.warn(msg)
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler
options
running build_src
build_src
building py_modules sources
building library "npymath" sources
error: Microsoft Visual C++ 10.0 is required. Get it with "Microsoft Windows
SDK 7.1": www.microsoft.com/download/details.aspx?id=8279

ERROR: Command errored out with exit status 1: 'c:\python34\python.exe' -u -c 'i
mport sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\an95120\AppData
\Local\Temp\pip-install-xuqde9e1\numpy\setup.py'"'"'; file='"'"'C:\User
s\an95120\AppData\Local\Temp\pip-install-xuqde9e1\numpy\setup.py'"'"';f=g
etattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n
'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' in
stall --record 'C:\Users\an95120\AppData\Local\Temp\pip-record-41uj2idn\install-
record.txt' --single-version-externally-managed --compile Check the logs for ful
l command output.

Hello, I am having the same issue. Did you manage to fix this?

alexomics self-assigned this Jul 26, 2019

anastasiiasatyr closed this as completed Jul 30, 2019

alexomics mentioned this issue Jan 15, 2020

Installation problems #31

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Problem with installation #27

Problem with installation #27

anastasiiasatyr commented Jul 26, 2019

alexomics commented Jul 26, 2019

anastasiiasatyr commented Jul 26, 2019

alexomics commented Jul 26, 2019 •

edited

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anastasiiasatyr commented Jul 26, 2019 •

edited

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alexomics commented Jul 26, 2019

anastasiiasatyr commented Jul 26, 2019

alexomics commented Jul 26, 2019

anastasiiasatyr commented Jul 30, 2019

Shahzadi-ETS commented Oct 4, 2019

arjolpanci commented Jan 14, 2020

hi,

Problem with installation #27

Problem with installation #27

Comments

anastasiiasatyr commented Jul 26, 2019

alexomics commented Jul 26, 2019

anastasiiasatyr commented Jul 26, 2019

alexomics commented Jul 26, 2019 • edited Loading

anastasiiasatyr commented Jul 26, 2019 • edited Loading

alexomics commented Jul 26, 2019

anastasiiasatyr commented Jul 26, 2019

alexomics commented Jul 26, 2019

anastasiiasatyr commented Jul 30, 2019

Shahzadi-ETS commented Oct 4, 2019

arjolpanci commented Jan 14, 2020

hi,

alexomics commented Jul 26, 2019 •

edited

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anastasiiasatyr commented Jul 26, 2019 •

edited

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