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Javier Kipen

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May 19, 2021, 3:15:53 PM5/19/21

to mosaic

Hello! We are developing nanopores and we wanted to try the available data analysis interfaces, and also make python scripts to the specific plots we want to obtain. I tried to install mosaic but could not solve some problems during installation in Windows. I followed the steps (https://pages.nist.gov/mosaic//html/doc/InstallWindows.html#installwin) but installed via conda the requirements mentioned in the github .txt (I had to install gunicorn via pip). But then when I run " pip install mosaic-nist" it says:

pip install mosaic-nist

Collecting mosaic-nist

Using cached mosaic-nist-2.1.tar.gz (7.2 MB)

Requirement already satisfied: cython==0.28.5 in c:\users\javier\appdata\roaming\python\python37\site-packages (from mosaic-nist) (0.28.5)

Requirement already satisfied: pandas==0.25.3 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (0.25.3)

Requirement already satisfied: lmfit==0.9.14 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (0.9.14)

Requirement already satisfied: uncertainties==3.1.2 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (3.1.2)

Requirement already satisfied: PyWavelets==1.1.1 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (1.1.1)

Requirement already satisfied: nose==1.3.7 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (1.3.7)

Requirement already satisfied: pyinstaller==4.2 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (4.2)

Requirement already satisfied: numpy==1.17.4 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (1.17.4)

Requirement already satisfied: scipy==1.3.2 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (1.3.2)

Requirement already satisfied: docutils==0.15.2 in c:\users\javier\appdata\roaming\python\python37\site-packages (from mosaic-nist) (0.15.2)

Requirement already satisfied: flask==1.1.1 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (1.1.1)

Requirement already satisfied: coverage==4.5.4 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (4.5.4)

Requirement already satisfied: codecov==2.1.11 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (2.1.11)

Requirement already satisfied: gunicorn==20.0.4 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from mosaic-nist) (20.0.4)

Requirement already satisfied: requests>=2.7.9 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from codecov==2.1.11->mosaic-nist) (2.25.1)

Requirement already satisfied: click>=5.1 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from flask==1.1.1->mosaic-nist) (8.0.0)

Requirement already satisfied: Jinja2>=2.10.1 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from flask==1.1.1->mosaic-nist) (3.0.0)

Requirement already satisfied: itsdangerous>=0.24 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from flask==1.1.1->mosaic-nist) (2.0.0)

Requirement already satisfied: Werkzeug>=0.15 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from flask==1.1.1->mosaic-nist) (1.0.1)

Requirement already satisfied: setuptools>=3.0 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from gunicorn==20.0.4->mosaic-nist) (49.6.0.post20210108)

Requirement already satisfied: six>1.10 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from lmfit==0.9.14->mosaic-nist) (1.15.0)

Requirement already satisfied: asteval>=0.9.12 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from lmfit==0.9.14->mosaic-nist) (0.9.23)

Requirement already satisfied: pytz>=2017.2 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pandas==0.25.3->mosaic-nist) (2021.1)

Requirement already satisfied: python-dateutil>=2.6.1 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pandas==0.25.3->mosaic-nist) (2.8.1)

Requirement already satisfied: pyinstaller-hooks-contrib>=2020.6 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pyinstaller==4.2->mosaic-nist) (2020.11)

Requirement already satisfied: pywin32-ctypes>=0.2.0 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pyinstaller==4.2->mosaic-nist) (0.2.0)

Requirement already satisfied: pefile>=2017.8.1 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pyinstaller==4.2->mosaic-nist) (2019.4.18)

Requirement already satisfied: altgraph in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pyinstaller==4.2->mosaic-nist) (0.17)

Requirement already satisfied: importlib-metadata in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pyinstaller==4.2->mosaic-nist) (3.10.0)

Requirement already satisfied: colorama in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from click>=5.1->flask==1.1.1->mosaic-nist) (0.4.4)

Requirement already satisfied: MarkupSafe>=2.0.0rc2 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from Jinja2>=2.10.1->flask==1.1.1->mosaic-nist) (2.0.0)

Requirement already satisfied: future in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from pefile>=2017.8.1->pyinstaller==4.2->mosaic-nist) (0.18.2)

Requirement already satisfied: urllib3<1.27,>=1.21.1 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from requests>=2.7.9->codecov==2.1.11->mosaic-nist) (1.26.4)

Requirement already satisfied: chardet<5,>=3.0.2 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from requests>=2.7.9->codecov==2.1.11->mosaic-nist) (4.0.0)

Requirement already satisfied: certifi>=2017.4.17 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from requests>=2.7.9->codecov==2.1.11->mosaic-nist) (2020.12.5)

Requirement already satisfied: idna<3,>=2.5 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from requests>=2.7.9->codecov==2.1.11->mosaic-nist) (2.10)

Requirement already satisfied: zipp>=0.5 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from importlib-metadata->pyinstaller==4.2->mosaic-nist) (3.4.1)

Requirement already satisfied: typing-extensions>=3.6.4 in c:\users\javier\anaconda3\envs\mosaicenv\lib\site-packages (from importlib-metadata->pyinstaller==4.2->mosaic-nist) (3.7.4.3)

Building wheels for collected packages: mosaic-nist

Building wheel for mosaic-nist (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: 'C:\Users\Javier\anaconda3\envs\mosaicENV\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\Javier\\AppData\\Local\\Temp\\pip-install-425614k3\\mosaic-nist_e75b4d142b674d3ea10250591537b924\\setup.py'"'"'; __file__='"'"'C:\\Users\\Javier\\AppData\\Local\\Temp\\pip-install-425614k3\\mosaic-nist_e75b4d142b674d3ea10250591537b924\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\Javier\AppData\Local\Temp\pip-wheel-941o9kat'

cwd: C:\Users\Javier\AppData\Local\Temp\pip-install-425614k3\mosaic-nist_e75b4d142b674d3ea10250591537b924\

Complete output (142 lines):

Global settings not found. Using default values

running bdist_wheel

running build

running build_py

creating build

creating build\lib

creating build\lib\mosaic

copying mosaic\commonExceptions.py -> build\lib\mosaic

copying mosaic\errors.py -> build\lib\mosaic

copying mosaic\mosaicSetup.py -> build\lib\mosaic

copying mosaic\readGlobalSettings.py -> build\lib\mosaic

copying mosaic\settings.py -> build\lib\mosaic

copying mosaic\_version.py -> build\lib\mosaic

copying mosaic\__init__.py -> build\lib\mosaic

creating build\lib\mosaic\filters

copying mosaic\filters\besselLowpassFilter.py -> build\lib\mosaic\filters

copying mosaic\filters\convolutionFilter.py -> build\lib\mosaic\filters

copying mosaic\filters\metaIOFilter.py -> build\lib\mosaic\filters

copying mosaic\filters\waveletDenoiseFilter.py -> build\lib\mosaic\filters

copying mosaic\filters\__init__.py -> build\lib\mosaic\filters

creating build\lib\mosaic\mdio

copying mosaic\mdio\metaMDIO.py -> build\lib\mosaic\mdio

copying mosaic\mdio\sqlite3MDIO.py -> build\lib\mosaic\mdio

copying mosaic\mdio\__init__.py -> build\lib\mosaic\mdio

creating build\lib\mosaic\trajio

copying mosaic\trajio\abfTrajIO.py -> build\lib\mosaic\trajio

copying mosaic\trajio\binTrajIO.py -> build\lib\mosaic\trajio

copying mosaic\trajio\chimeraTrajIO.py -> build\lib\mosaic\trajio

copying mosaic\trajio\metaTrajIO.py -> build\lib\mosaic\trajio

copying mosaic\trajio\qdfTrajIO.py -> build\lib\mosaic\trajio

copying mosaic\trajio\tsvTrajIO.py -> build\lib\mosaic\trajio

copying mosaic\trajio\__init__.py -> build\lib\mosaic\trajio

creating build\lib\mosaic\process

copying mosaic\process\adept.py -> build\lib\mosaic\process

copying mosaic\process\adept2State.py -> build\lib\mosaic\process

copying mosaic\process\cusumPlus.py -> build\lib\mosaic\process

copying mosaic\process\metaEventProcessor.py -> build\lib\mosaic\process

copying mosaic\process\__init__.py -> build\lib\mosaic\process

creating build\lib\mosaic\partition

copying mosaic\partition\eventSegment.py -> build\lib\mosaic\partition

copying mosaic\partition\metaEventPartition.py -> build\lib\mosaic\partition

copying mosaic\partition\__init__.py -> build\lib\mosaic\partition

creating build\lib\mosaic\apps

copying mosaic\apps\ConvertTrajIO.py -> build\lib\mosaic\apps

copying mosaic\apps\SingleChannelAnalysis.py -> build\lib\mosaic\apps

copying mosaic\apps\__init__.py -> build\lib\mosaic\apps

creating build\lib\mosaic\tests

copying mosaic\tests\adept2State_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\adept_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\algorithmCommon.py -> build\lib\mosaic\tests

copying mosaic\tests\apps_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\cusum_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\eventPartitionCommon.py -> build\lib\mosaic\tests

copying mosaic\tests\eventPartitionParallel_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\eventPartition_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\import_Tests.py -> build\lib\mosaic\tests

copying mosaic\tests\mdio_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\testutil.py -> build\lib\mosaic\tests

copying mosaic\tests\trajio_Test.py -> build\lib\mosaic\tests

copying mosaic\tests\__init__.py -> build\lib\mosaic\tests

creating build\lib\mosaic\trajio\qdf

copying mosaic\trajio\qdf\qdf.py -> build\lib\mosaic\trajio\qdf

copying mosaic\trajio\qdf\__init__.py -> build\lib\mosaic\trajio\qdf

creating build\lib\mosaic\trajio\abf

copying mosaic\trajio\abf\abf.py -> build\lib\mosaic\trajio\abf

copying mosaic\trajio\abf\__init__.py -> build\lib\mosaic\trajio\abf

creating build\lib\mosaic\utilities

copying mosaic\utilities\analysis.py -> build\lib\mosaic\utilities

copying mosaic\utilities\fit_funcs.py -> build\lib\mosaic\utilities

copying mosaic\utilities\ga.py -> build\lib\mosaic\utilities

copying mosaic\utilities\ionic_current_stats.py -> build\lib\mosaic\utilities

copying mosaic\utilities\mosaicLogFormat.py -> build\lib\mosaic\utilities

copying mosaic\utilities\mosaicLogging.py -> build\lib\mosaic\utilities

copying mosaic\utilities\mosaicLogHandlers.py -> build\lib\mosaic\utilities

copying mosaic\utilities\mosaicTiming.py -> build\lib\mosaic\utilities

copying mosaic\utilities\resource_path.py -> build\lib\mosaic\utilities

copying mosaic\utilities\sqlQuery.py -> build\lib\mosaic\utilities

copying mosaic\utilities\util.py -> build\lib\mosaic\utilities

copying mosaic\utilities\__init__.py -> build\lib\mosaic\utilities

creating build\lib\mosaicweb

copying mosaicweb\run.py -> build\lib\mosaicweb

copying mosaicweb\runTests.py -> build\lib\mosaicweb

copying mosaicweb\views.py -> build\lib\mosaicweb

copying mosaicweb\__init__.py -> build\lib\mosaicweb

creating build\lib\mosaicweb\mosaicAnalysis

copying mosaicweb\mosaicAnalysis\analysisContour.py -> build\lib\mosaicweb\mosaicAnalysis

copying mosaicweb\mosaicAnalysis\analysisDBUtils.py -> build\lib\mosaicweb\mosaicAnalysis

copying mosaicweb\mosaicAnalysis\analysisHistogram.py -> build\lib\mosaicweb\mosaicAnalysis

copying mosaicweb\mosaicAnalysis\analysisStatistics.py -> build\lib\mosaicweb\mosaicAnalysis

copying mosaicweb\mosaicAnalysis\analysisTimeSeries.py -> build\lib\mosaicweb\mosaicAnalysis

copying mosaicweb\mosaicAnalysis\mosaicAnalysis.py -> build\lib\mosaicweb\mosaicAnalysis

copying mosaicweb\mosaicAnalysis\__init__.py -> build\lib\mosaicweb\mosaicAnalysis

creating build\lib\mosaicweb\plotlyUtils

copying mosaicweb\plotlyUtils\plotlyWrapper.py -> build\lib\mosaicweb\plotlyUtils

copying mosaicweb\plotlyUtils\__init__.py -> build\lib\mosaicweb\plotlyUtils

creating build\lib\mosaicweb\sessionManager

copying mosaicweb\sessionManager\sessionManager.py -> build\lib\mosaicweb\sessionManager

copying mosaicweb\sessionManager\__init__.py -> build\lib\mosaicweb\sessionManager

creating build\lib\mosaicweb\utils

copying mosaicweb\utils\utils.py -> build\lib\mosaicweb\utils

copying mosaicweb\utils\__init__.py -> build\lib\mosaicweb\utils

running build_scripts

creating build\scripts-3.7

copying bin\analysis.py -> build\scripts-3.7

copying addons\mathematica\MosaicAnalysis.m -> build\scripts-3.7

copying addons\mathematica\MosaicUtils.m -> build\scripts-3.7

copying addons\mathematica\Util.m -> build\scripts-3.7

copying addons\MATLAB\openandquery.m -> build\scripts-3.7

copying .scripts\install-addons-sh -> build\scripts-3.7

copying .scripts\pyinstaller-sh -> build\scripts-3.7

Traceback (most recent call last):

File "<string>", line 1, in <module>

File "C:\Users\Javier\AppData\Local\Temp\pip-install-425614k3\mosaic-nist_e75b4d142b674d3ea10250591537b924\setup.py", line 204, in <module>

platforms=['MacOS', 'Windows', 'Linux'],

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\site-packages\setuptools\__init__.py", line 163, in setup

return distutils.core.setup(**attrs)

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\core.py", line 148, in setup

dist.run_commands()

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\dist.py", line 966, in run_commands

self.run_command(cmd)

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\dist.py", line 985, in run_command

cmd_obj.run()

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\site-packages\wheel\bdist_wheel.py", line 299, in run

self.run_command('build')

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\cmd.py", line 313, in run_command

self.distribution.run_command(command)

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\dist.py", line 985, in run_command

cmd_obj.run()

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\command\build.py", line 135, in run

self.run_command(cmd_name)

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\cmd.py", line 313, in run_command

self.distribution.run_command(command)

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\dist.py", line 985, in run_command

cmd_obj.run()

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\command\build_scripts.py", line 50, in run

self.copy_scripts()

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\command\build_scripts.py", line 64, in copy_scripts

script = convert_path(script)

File "C:\Users\Javier\anaconda3\envs\mosaicENV\lib\distutils\util.py", line 112, in convert_path

raise ValueError("path '%s' cannot end with '/'" % pathname)

ValueError: path 'mosaicweb/' cannot end with '/'

----------------------------------------

ERROR: Failed building wheel for mosaic-nist

Running setup.py clean for mosaic-nist

Failed to build mosaic-nist

Installing collected packages: mosaic-nist

Running setup.py install for mosaic-nist ... error

ERROR: Command errored out with exit status 1:

command: 'C:\Users\Javier\anaconda3\envs\mosaicENV\python.exe' -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\Javier\\AppData\\Local\\Temp\\pip-install-425614k3\\mosaic-nist_e75b4d142b674d3ea10250591537b924\\setup.py'"'"'; __file__='"'"'C:\\Users\\Javier\\AppData\\Local\\Temp\\pip-install-425614k3\\mosaic-nist_e75b4d142b674d3ea10250591537b924\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\Javier\AppData\Local\Temp\pip-record-f7nwpg48\install-record.txt' --single-version-externally-managed --compile --install-headers 'C:\Users\Javier\anaconda3\envs\mosaicENV\Include\mosaic-nist'

cwd: C:\Users\Javier\AppData\Local\Temp\pip-install-425614k3\mosaic-nist_e75b4d142b674d3ea10250591537b924\

Complete output (144 lines):

Global settings not found. Using default values

running install