fix Dockerfile with PALMSpy

Added a builder stage for compiling and installing the PALMSpy package.

Thanks @emolinaro!
I am now able to do palmspy --help and I think I now need to update my R code to send palmspy --gps-path ....... to the system rather than /opt/conda/envs/palmspy/bin/conda run -n palmspy palmspy --gps-path ......
So, I will have to update my R code before I can fully test this. I will be able to do tomorrow afternoon or Thursday morning. Either way, sounds like it is nearly there.

No luck yet, when I build the image I repeatedly see the following error/warning in red:
/root/.bashrc: line 1: activate: No such file or directory
Any idea what the problem might be?
Please find full console output below:

Console output:

vincent@vincent-VirtualBox:~/projects/HabitusGUI/Docker$ docker build -t habitus-app .
Sending build context to Docker daemon  5.632kB
Step 1/26 : FROM continuumio/miniconda3:4.10.3 as builder
4.10.3: Pulling from continuumio/miniconda3
33847f680f63: Pull complete
ff810a0db00f: Pull complete
2cb7a358a8ff: Pull complete
Digest: sha256:a137c7da98c8680467490e15ac3c54e25db77495be1737076b053a6790ad6082
Status: Downloaded newer image for continuumio/miniconda3:4.10.3
 ---> 83812c01cb60
Step 2/26 : LABEL software="HabitusGUI"       author="Vincent van Hees<EMAIL_ADDRESS>Emiliano Molinaro<EMAIL_ADDRESS>     version="0.1.2"       license="MIT, Apache-2.0, LGPL-2.0"       description="HabitusGUI is a Shiny app that aids the researcher to work with                    PALMSpy, GGIR, and activityCount.                   This dockerfile installs both the app and all it's depenencies."
 ---> Running in 82bc4a7ca433
Removing intermediate container 82bc4a7ca433
 ---> f80a74dcd337
Step 3/26 : MAINTAINER Vincent van Hees<EMAIL_ADDRESS> ---> Running in cdcba3557486
Removing intermediate container cdcba3557486
 ---> ebb8bb1d2859
Step 4/26 : ARG VERSION=${VERSION:-1.9.6}
 ---> Running in b2f8eeb1ccd9
Removing intermediate container b2f8eeb1ccd9
 ---> 31503fe6d382
Step 5/26 : SHELL ["/bin/bash",  "--login", "-c"]
 ---> Running in 75a9f0986d6a
Removing intermediate container 75a9f0986d6a
 ---> da5949980e2b
Step 6/26 : RUN apt-get update  && apt-get install -y git build-essential --no-install-recommends  && apt-get clean  && rm -rf /var/lib/apt/lists/*
 ---> Running in 5fd3b94969bc
Get:1 http://security.debian.org/debian-security buster/updates InRelease [65.4 kB]
Get:2 http://deb.debian.org/debian buster InRelease [122 kB]
Get:3 http://deb.debian.org/debian buster-updates InRelease [51.9 kB]
Get:4 http://security.debian.org/debian-security buster/updates/main amd64 Packages [309 kB]
Get:5 http://deb.debian.org/debian buster/main amd64 Packages [7906 kB]
Get:6 http://deb.debian.org/debian buster-updates/main amd64 Packages [15.2 kB]
Fetched 8470 kB in 2s (4525 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
git is already the newest version (1:2.20.1-2+deb10u3).
The following additional packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 dpkg-dev g++
  g++-8 gcc gcc-8 libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev
  libcc1-0 libdpkg-perl libgcc-8-dev libgomp1 libisl19 libitm1 liblsan0
  libmpc3 libmpfr6 libmpx2 libquadmath0 libstdc++-8-dev libtsan0 libubsan1
  linux-libc-dev make patch xz-utils
Suggested packages:
  binutils-doc cpp-doc gcc-8-locales debian-keyring g++-multilib
  g++-8-multilib gcc-8-doc libstdc++6-8-dbg gcc-multilib manpages-dev autoconf
  automake libtool flex bison gdb gcc-doc gcc-8-multilib libgcc1-dbg
  libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
  libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg glibc-doc gnupg
  | gnupg2 bzr libstdc++-8-doc make-doc ed diffutils-doc
Recommended packages:
  fakeroot gnupg | gnupg2 libalgorithm-merge-perl manpages manpages-dev
  libfile-fcntllock-perl liblocale-gettext-perl
The following NEW packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu build-essential cpp cpp-8
  dpkg-dev g++ g++-8 gcc gcc-8 libasan5 libatomic1 libbinutils libc-dev-bin
  libc6-dev libcc1-0 libdpkg-perl libgcc-8-dev libgomp1 libisl19 libitm1
  liblsan0 libmpc3 libmpfr6 libmpx2 libquadmath0 libstdc++-8-dev libtsan0
  libubsan1 linux-libc-dev make patch xz-utils
0 upgraded, 34 newly installed, 0 to remove and 9 not upgraded.
Need to get 47.3 MB of archives.
After this operation, 181 MB of additional disk space will be used.

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Removing intermediate container 5fd3b94969bc
 ---> 0baee4e906f1
Step 7/26 : WORKDIR /tmp
 ---> Running in 159a3835c5da
Removing intermediate container 159a3835c5da
 ---> 6e5c556e923a
Step 8/26 : RUN git clone https://github.com/emolinaro/PALMSpy.git
 ---> Running in 190f004fedd8
Cloning into 'PALMSpy'...
Removing intermediate container 190f004fedd8
 ---><PHONE_NUMBER>a7
Step 9/26 : WORKDIR PALMSpy
 ---> Running in 8770a681fa67
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 ---> a030fa0b1c33
Step 10/26 : ENV PATH /opt/conda/envs/palmspy/bin:$PATH
 ---> Running in 79e8b33b9839
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 ---> 9c229db83b26
Step 11/26 : ENV CONDA_PREFIX="/opt/conda/envs/palmspy"
 ---> Running in 7e7aafd76ade
Removing intermediate container 7e7aafd76ade
 ---> 6474dd319620
Step 12/26 : RUN conda create -n palmspy python=3.7 openjdk=8.0 make=4.2.1 -y  && conda activate palmspy  && echo "source activate palmspy" > ~/.bashrc  && make  && make install  && make check  && make clean
 ---> Running in 42a026d300a5
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/envs/palmspy

  added / updated specs:
    - make=4.2.1
    - openjdk=8.0
    - python=3.7

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |             main           3 KB
    _openmp_mutex-4.5          |            1_gnu          22 KB
    ca-certificates-2021.10.26 |       h06a4308_2         115 KB
    certifi-2021.10.8          |   py37h06a4308_0         151 KB
    ld_impl_linux-64-2.35.1    |       h7274673_9         586 KB
    libffi-3.3                 |       he6710b0_2          50 KB
    libgcc-ng-9.3.0            |      h5101ec6_17         4.8 MB
    libgomp-9.3.0              |      h5101ec6_17         311 KB
    libstdcxx-ng-9.3.0         |      hd4cf53a_17         3.1 MB
    make-4.2.1                 |       h1bed415_1         415 KB
    ncurses-6.3                |       h7f8727e_2         782 KB
    openjdk-8.0.152            |       h7b6447c_3        57.4 MB
    openssl-1.1.1l             |       h7f8727e_0         2.5 MB
    pip-21.2.2                 |   py37h06a4308_0         1.8 MB
    python-3.7.11              |       h12debd9_0        45.3 MB
    readline-8.1               |       h27cfd23_0         362 KB
    setuptools-58.0.4          |   py37h06a4308_0         775 KB
    sqlite-3.36.0              |       hc218d9a_0         990 KB
    tk-8.6.11                  |       h1ccaba5_0         3.0 MB
    wheel-0.37.0               |     pyhd3eb1b0_1          33 KB
    xz-5.2.5                   |       h7b6447c_0         341 KB
    zlib-1.2.11                |       h7b6447c_3         103 KB
    ------------------------------------------------------------
                                           Total:       122.9 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.10.26-h06a4308_2
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  make               pkgs/main/linux-64::make-4.2.1-h1bed415_1
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openjdk            pkgs/main/linux-64::openjdk-8.0.152-h7b6447c_3
  openssl            pkgs/main/linux-64::openssl-1.1.1l-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.2-py37h06a4308_0
  python             pkgs/main/linux-64::python-3.7.11-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-58.0.4-py37h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  wheel              pkgs/main/noarch::wheel-0.37.0-pyhd3eb1b0_1
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Downloading and Extracting Packages
openssl-1.1.1l       | 2.5 MB    | ########## | 100%
libgcc-ng-9.3.0      | 4.8 MB    | ########## | 100%
python-3.7.11        | 45.3 MB   | ########## | 100%
certifi-2021.10.8    | 151 KB    | ########## | 100%
make-4.2.1           | 415 KB    | ########## | 100%
tk-8.6.11            | 3.0 MB    | ########## | 100%
ld_impl_linux-64-2.3 | 586 KB    | ########## | 100%
pip-21.2.2           | 1.8 MB    | ########## | 100%
openjdk-8.0.152      | 57.4 MB   | ########## | 100%
libffi-3.3           | 50 KB     | ########## | 100%
zlib-1.2.11          | 103 KB    | ########## | 100%
ncurses-6.3          | 782 KB    | ########## | 100%
libgomp-9.3.0        | 311 KB    | ########## | 100%
_openmp_mutex-4.5    | 22 KB     | ########## | 100%
sqlite-3.36.0        | 990 KB    | ########## | 100%
xz-5.2.5             | 341 KB    | ########## | 100%
setuptools-58.0.4    | 775 KB    | ########## | 100%
readline-8.1         | 362 KB    | ########## | 100%
_libgcc_mutex-0.1    | 3 KB      | ########## | 100%
ca-certificates-2021 | 115 KB    | ########## | 100%
libstdcxx-ng-9.3.0   | 3.1 MB    | ########## | 100%
wheel-0.37.0         | 33 KB     | ########## | 100%
Preparing transaction: ...working... done
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Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate palmspy
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Install dependencies...

/opt/conda/envs/palmspy/bin/pip install -r requirements.txt
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Collecting prometheus-client==0.6.0
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Collecting timezonefinder==5.2.0
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Requirement already satisfied: setuptools>=18.5 in /opt/conda/envs/palmspy/lib/python3.7/site-packages (from ipython==7.4.0->-r requirements.txt (line 11)) (58.0.4)
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Collecting importlib-metadata>=0.12
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Collecting typing-extensions>=3.6.4
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Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.6-py3-none-any.whl (97 kB)
Building wheels for collected packages: backcall, pandocfilters, prometheus-client, pyrsistent, pyspark, regex, tornado, tzwhere
  Building wheel for backcall (setup.py): started
  Building wheel for backcall (setup.py): finished with status 'done'
  Created wheel for backcall: filename=backcall-0.1.0-py3-none-any.whl size=10413 sha256=ea5383462ed8e8316d3d72cbc8f92f6a84cd21a11e4ae913900d722c8a6f4656
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  Stored in directory: /root/.cache/pip/wheels/6e/d8/31/c7c67f483036e5841d084f1138abdc078ba7c390544aa0ef28
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  Building wheel for pyspark (setup.py): started
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  Created wheel for pyspark: filename=pyspark-2.4.2-py2.py3-none-any.whl size=194264323 sha256=9d4e0ae55762a01fde49145eba60791d89ddf99f353ac5e4af04e92c4de9496f
  Stored in directory: /root/.cache/pip/wheels/6d/87/6c/8f2c5da1ec8f9328b2b505138798da07d7658220919005ec47
  Building wheel for regex (setup.py): started
  Building wheel for regex (setup.py): finished with status 'done'
  Created wheel for regex: filename=regex-2019.3.9-cp37-cp37m-linux_x86_64.whl size=671097 sha256=09ed6cc46b6ea6f38825a5df5037151c5fb9043c4a694bb4c1089bcbad11c55f
  Stored in directory: /root/.cache/pip/wheels/3c/2b/cb/bd56052497a3f96d924d8bc5afa2c4157cd39997b3508c70ca
  Building wheel for tornado (setup.py): started
  Building wheel for tornado (setup.py): finished with status 'done'
  Created wheel for tornado: filename=tornado-6.0.2-cp37-cp37m-linux_x86_64.whl size=424289 sha256=422ce52d8f1e2b42586f4cfc9cab2b4ccb2526f91a551d29403eeda39859a224
  Stored in directory: /root/.cache/pip/wheels/10/ec/4d/1aca4b143f2a19439632329f1d5b6b9f62ee9508ddf30f9d2c
  Building wheel for tzwhere (setup.py): started
  Building wheel for tzwhere (setup.py): finished with status 'done'
  Created wheel for tzwhere: filename=tzwhere-3.0.3-py3-none-any.whl size=23742600 sha256=7b32657c7273f56cc61b4d44500fb6f9679c788d47bd40e8e24deb9703fdcd7e
  Stored in directory: /root/.cache/pip/wheels/a4/27/39/8c57d78844da3630f08a30bfe9da5eac9a290e0a7edcb98218
Successfully built backcall pandocfilters prometheus-client pyrsistent pyspark regex tornado tzwhere
Installing collected packages: six, ipython-genutils, decorator, wcwidth, traitlets, pyrsistent, pyparsing, ptyprocess, parso, attrs, webencodings, tornado, pyzmq, python-dateutil, Pygments, prompt-toolkit, pickleshare, pexpect, packaging, MarkupSafe, jupyter-core, jsonschema, jedi, backcall, testpath, pandocfilters, nbformat, mistune, jupyter-client, Jinja2, ipython, entrypoints, defusedxml, bleach, terminado, Send2Trash, prometheus-client, nbconvert, ipykernel, zipp, typing-extensions, notebook, widgetsnbextension, importlib-metadata, zope.interface, toml, Shapely, regex, qtconsole, pytz, py4j, py, pluggy, numpy, jupyter-console, ipywidgets, iniconfig, wheel, virtualenv, tzwhere, timezonefinder, pytest, pyspark, pandas, jupyter, DateTime, datefinder, certifi, appnope
  Attempting uninstall: wheel
    Found existing installation: wheel 0.37.0
    Uninstalling wheel-0.37.0:
      Successfully uninstalled wheel-0.37.0
  Attempting uninstall: certifi
    Found existing installation: certifi 2021.10.8
    Uninstalling certifi-2021.10.8:
      Successfully uninstalled certifi-2021.10.8
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Successfully installed DateTime-4.3 Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 Send2Trash-1.5.0 Shapely-1.6.4.post2 appnope-0.1.0 attrs-19.1.0 backcall-0.1.0 bleach-4.1.0 certifi-2019.3.9 datefinder-0.7.0 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-4.8.2 iniconfig-1.1.1 ipykernel-5.1.0 ipython-7.4.0 ipython-genutils-0.2.0 ipywidgets-7.4.2 jedi-0.13.3 jsonschema-3.0.1 jupyter-1.0.0 jupyter-client-5.2.4 jupyter-console-6.0.0 jupyter-core-4.4.0 mistune-0.8.4 nbconvert-5.4.1 nbformat-4.4.0 notebook-5.7.8 numpy-1.16.2 packaging-21.3 pandas-0.24.2 pandocfilters-1.4.2 parso-0.4.0 pexpect-4.7.0 pickleshare-0.7.5 pluggy-0.13.1 prometheus-client-0.6.0 prompt-toolkit-2.0.9 ptyprocess-0.6.0 py-1.11.0 py4j-0.10.7 pyparsing-3.0.6 pyrsistent-0.14.11 pyspark-2.4.2 pytest-6.1.2 python-dateutil-2.8.0 pytz-2019.1 pyzmq-18.0.1 qtconsole-4.4.3 regex-2019.3.9 six-1.12.0 terminado-0.8.2 testpath-0.4.2 timezonefinder-5.2.0 toml-0.10.2 tornado-6.0.2 traitlets-4.3.2 typing-extensions-4.0.1 tzwhere-3.0.3 virtualenv-16.0.0 wcwidth-0.1.7 webencodings-0.5.1 wheel-0.33.6 widgetsnbextension-3.4.2 zipp-3.6.0 zope.interface-4.6.0

Build the package...

/opt/conda/envs/palmspy/bin/python3 setup.py sdist bdist_wheel
running sdist
running egg_info
creating palmspy.egg-info
writing palmspy.egg-info/PKG-INFO
writing dependency_links to palmspy.egg-info/dependency_links.txt
writing top-level names to palmspy.egg-info/top_level.txt
writing manifest file 'palmspy.egg-info/SOURCES.txt'
reading manifest file 'palmspy.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'palmspy.egg-info/SOURCES.txt'
running check
creating palmspy-1.9.6
creating palmspy-1.9.6/palmspy.egg-info
creating palmspy-1.9.6/src
copying files to palmspy-1.9.6...
copying LICENSE -> palmspy-1.9.6
copying README.md -> palmspy-1.9.6
copying palmspy -> palmspy-1.9.6
copying palmspy.py -> palmspy-1.9.6
copying setup.py -> palmspy-1.9.6
copying palmspy.egg-info/PKG-INFO -> palmspy-1.9.6/palmspy.egg-info
copying palmspy.egg-info/SOURCES.txt -> palmspy-1.9.6/palmspy.egg-info
copying palmspy.egg-info/dependency_links.txt -> palmspy-1.9.6/palmspy.egg-info
copying palmspy.egg-info/top_level.txt -> palmspy-1.9.6/palmspy.egg-info
copying src/AccProcessing.py -> palmspy-1.9.6/src
copying src/GPSProcessing.py -> palmspy-1.9.6/src
copying src/__init__.py -> palmspy-1.9.6/src
copying src/help_menu.py -> palmspy-1.9.6/src
copying src/tools.py -> palmspy-1.9.6/src
Writing palmspy-1.9.6/setup.cfg
creating dist
Creating tar archive
removing 'palmspy-1.9.6' (and everything under it)
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/src
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copying src/AccProcessing.py -> build/lib/src
copying src/tools.py -> build/lib/src
running build_scripts
creating build/scripts-3.7
copying and adjusting palmspy.py -> build/scripts-3.7
copying and adjusting palmspy -> build/scripts-3.7
changing mode of build/scripts-3.7/palmspy.py from 644 to 755
changing mode of build/scripts-3.7/palmspy from 644 to 755
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64
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copying build/lib/src/__init__.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/GPSProcessing.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/help_menu.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/AccProcessing.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/tools.py -> build/bdist.linux-x86_64/wheel/src
running install_egg_info
Copying palmspy.egg-info to build/bdist.linux-x86_64/wheel/palmspy-1.9.6-py3.7.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data
creating build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts
copying build/scripts-3.7/palmspy -> build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts
copying build/scripts-3.7/palmspy.py -> build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts
changing mode of build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts/palmspy to 755
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adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
creating build/bdist.linux-x86_64/wheel/palmspy-1.9.6.dist-info/WHEEL
creating 'dist/palmspy-1.9.6-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'palmspy-1.9.6.data/scripts/palmspy'
adding 'palmspy-1.9.6.data/scripts/palmspy.py'
adding 'src/AccProcessing.py'
adding 'src/GPSProcessing.py'
adding 'src/__init__.py'
adding 'src/help_menu.py'
adding 'src/tools.py'
adding 'palmspy-1.9.6.dist-info/LICENSE'
adding 'palmspy-1.9.6.dist-info/METADATA'
adding 'palmspy-1.9.6.dist-info/WHEEL'
adding 'palmspy-1.9.6.dist-info/top_level.txt'
adding 'palmspy-1.9.6.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel

Install the package...

/opt/conda/envs/palmspy/bin/pip install ./dist/palmspy-*-py3-none-any.whl --force-reinstall
Processing ./dist/palmspy-1.9.6-py3-none-any.whl
Installing collected packages: palmspy
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
Successfully installed palmspy-1.9.6

Sanity check...

/opt/conda/envs/palmspy/bin/palmspy --help
usage: palmspy --gps-path GPS_PATH --acc-path ACC_PATH [GPS options] [accelerometer options] [Spark options]

PALMSpy is an implementation of the Personal Activity and Location Measurement
System (PALMS), written in Python and integrated with Apache Spark for
cluster-computing. The program detects personal activity patterns of
individual participants wearing a GPS data logger and a physical activity
monitor.

optional arguments:
  -h, --help            show this help message and exit
  --config-file FILE    load JSON file with configuration settings
  --version, -v         show program's version number and exit

required arguments:
  --gps-path GPS_PATH   directory of GPS raw data
  --acc-path ACC_PATH   directory of accelerometer raw data

GPS options:
  --interval INT        duration of interval between results in seconds
                        (default: 30)
  --insert-missing      gaps in GPS fixes are replaced by the last valid fix
                        (default: False)
  --insert-until        inserts until a max time (set by --insert-max-seconds)
                        is reached; by default, inserts will be added until
                        loss of signal time is reached (default: False)
  --insert-max-seconds INT
                        max number of seconds to replace missing fixes with
                        last valid fix (valid if --insert-until is enabled)
                        (default: 600)
  --los-max-duration INT
                        max number of seconds allowed to pass before loss of
                        signal is declared (default: 600)
  --filter-invalid-values
                        remove invalid fixes (default: False)
  --max-speed INT       fix is invalid if speed is greater than this value (in
                        km/hr) (default: 130)
  --max-ele-change INT  fix is invalid if elevation change is greater than
                        this value (in meters) (default: 1000)
  --min-change-3-fixes INT
                        fix is invalid if change in distance between fix 1 and
                        3 is less than this value (in meters) (default: 10)
  --detect-trip         calculate the fix trip type: STATIONARY (0), START
                        POINT (1), MID POINT (2), PAUSE POINT (3), and END
                        POINT (4) (default: False)
  --min-distance INT    minimum distance (in meters) that must be travelled
                        over one minute to indicate the start of a trip.
                        Default value corresponds to a typical walking speed
                        of 2 km/hr (default: 34)
  --min-trip-length INT
                        trips less than this distance (in meters) are not
                        considered trips (default: 100)
  --min-trip-duration INT
                        trips less than this duration (in seconds) are not
                        considered trips (default: 180)
  --min-pause-duration INT
                        when the duration at a location exceeds this value (in
                        seconds), the point is marked as PAUSE POINT (default:
                        180)
  --max-pause-duration INT
                        when the duration of a pause exceeds this value (in
                        seconds), the point is marked as an END POINT
                        (default: 300)
  --detect-trip-mode    calculate the mode of transportation based on the
                        speed: STATIONARY (0), PEDESTRIAN (1), BICYCLE (2),
                        and VEHICLE (3) (default: False)
  --vehicle-cutoff INT  speeds greater than this value (in km/hr) will be
                        marked as VEHICLE (default: 25)
  --bicycle-cutoff INT  speeds greater than this value (in km/hr) will be
                        marked as BICYCLE (default: 10)
  --walk-cutoff INT     speeds greater than this value (in km/hr) will be
                        marked as PEDESTRIAN (default: 1)
  --percentile-to-sample INT
                        speed comparisons are made at this percentile
                        (default: 90)
  --min-segment-length INT
                        minimum length (in meters) of segments used to
                        classify mode of transportation (default: 30)

accelerometer options:
  --include-acc         append raw accelerometer data to the final output
                        (default: False)
  --include-vect        calculate the activity intensity from the
                        accelerometer vector magnitude (default: False)
  --mark-non-wearing    mark non-wearing time (set actvity count and activity
                        intensity equal to -2) (default: False)
  --minutes-zeros-row INT
                        minimum non-wearing time (in minutes), corresponding
                        to consecutive zeros in the activity count (default:
                        30)
  --detect-activity-bouts
                        detect activity bouts (default: False)
  --activity-bout-duration INT
                        minimum activity bout duration (in minutes) (default:
                        5)
  --activity-bout-up INT
                        activity bout upper limit (default: 9999)
  --activity-bout-low INT
                        activity bout lower limit (default: 1953)
  --activity-bout-tol INT
                        activity bout tolerance (default: 2)
  --detect-sedentary-bouts
                        detect sedentary bouts (default: False)
  --sedentary-bout-duration INT
                        sedentary bout duration (in minutes) (default: 30)
  --sedentary-bout-up INT
                        sedentary bout upper limit (default: 100)
  --sedentary-bout-tol INT
                        sedentary bout tolerance (default: 1)
  --very-hard-cut INT   very hard activity cutoff value (default: 9498)
  --hard-cut INT        hard activity cutoff value (default: 5725)
  --moderate-cut INT    moderate activity cutoff value (default: 1953)
  --light-cut INT       light activity cutoff value (default: 100)

merge options:
  --merge-acc-to-gps    merge accelerometer data to GPS data and export them
                        in one single file; by default, the processed
                        accelerometer and GPS data will be saved in two
                        different files (default: False)
  --merge-gps-to-acc    merge GPS data to accelerometer data and export them
                        in one single file; by default, the processed
                        accelerometer and GPS data will be saved in two
                        different files (default: False)

Spark options:
  --num-cores INT       total number of cores used in the calculation
                        (default: 8)
  --driver-mem STR      amount of memory to use for the driver process, i.e.
                        where SparkContext is initialized, in the same format
                        as JVM memory strings with a size unit suffix ("k",
                        "m", "g" or "t") (default: 16g)
  --executor-mem STR    amount of memory to use per executor process, in the
                        same format as JVM memory strings with a size unit
                        suffix ("k", "m", "g" or "t") (default: 16g)
  --mem-fraction FLOAT  expresses the size of the execution and storage memory
                        as a fraction of the (JVM heap space - 300MB). The
                        rest of the space (40%) is reserved for user data
                        structures, internal metadata in Spark, and
                        safeguarding against OOM errors in the case of sparse
                        and unusually large records (default: 0.6)
  --default-partitions INT
                        Default number of partitions returned by
                        transformations like join, reduceByKey, and
                        parallelize (default: 20)
  --shuffle-partitions INT
                        configures the number of partitions to use when
                        shuffling data for joins or aggregations (default: 20)
  --mem-offHeap-enabled
                        if true, off-heap memory will be used for certain
                        operations. If off-heap memory use is enabled, then
                        --mem-offHeap-size must be positive (default: True)
  --mem-offHeap-size STR
                        the absolute amount of memory in bytes which can be
                        used for off-heap allocation. This must be set to a
                        positive value when --mem-offHeap-enabled is true
                        (default: 16g)
  --clean-checkpoints   controls whether to clean checkpoint files if the
                        reference is out of scope (default: True)
  --codegen-wholeStage  enable whole-stage code generation (experimental)
                        (default: False)
  --codegen-fallback    when true, whole-stage codegen could be temporary
                        disabled for the part of query that fails to compile
                        generated code (default: True)
  --broadcast-timeout INT
                        timeout in seconds for the broadcast wait time in
                        broadcast joins (default: 1200)
  --networkTimeout STR  default timeout for all network interactions (default:
                        800s)

Cleanup...

Sending build context to Docker daemon  5.632kB
Step 1/26 : FROM continuumio/miniconda3:4.10.3 as builder
 ---> 83812c01cb60
Step 2/26 : LABEL software="HabitusGUI"       author="Vincent van Hees<EMAIL_ADDRESS>Emiliano Molinaro<EMAIL_ADDRESS>     version="0.1.2"       license="MIT, Apache-2.0, LGPL-2.0"       description="HabitusGUI is a Shiny app that aids the researcher to work with                    PALMSpy, GGIR, and activityCount.                   This dockerfile installs both the app and all it's depenencies."
 ---> Running in 50031e98779f
Removing intermediate container 50031e98779f
 ---> bb3380372489
Step 3/26 : MAINTAINER Vincent van Hees<EMAIL_ADDRESS> ---> Running in 238bdbdbda9f
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 ---> 388e84dfc005
Step 4/26 : ARG VERSION=${VERSION:-1.9.6}
 ---> Running in aaca87876221
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 ---> 5ba9f2dc936c
Step 5/26 : SHELL ["/bin/bash",  "--login", "-c"]
 ---> Running in 7b29a6cad03f
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 ---> 40e504bd988d
Step 6/26 : RUN apt-get update  && apt-get install -y git build-essential --no-install-recommends  && apt-get clean  && rm -rf /var/lib/apt/lists/*
 ---> Running in 3fbc6fd37261
Get:1 http://security.debian.org/debian-security buster/updates InRelease [65.4 kB]
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Reading package lists...
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Building dependency tree...
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git is already the newest version (1:2.20.1-2+deb10u3).
The following additional packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 dpkg-dev g++
  g++-8 gcc gcc-8 libasan5 libatomic1 libbinutils libc-dev-bin libc6-dev
  libcc1-0 libdpkg-perl libgcc-8-dev libgomp1 libisl19 libitm1 liblsan0
  libmpc3 libmpfr6 libmpx2 libquadmath0 libstdc++-8-dev libtsan0 libubsan1
  linux-libc-dev make patch xz-utils
Suggested packages:
  binutils-doc cpp-doc gcc-8-locales debian-keyring g++-multilib
  g++-8-multilib gcc-8-doc libstdc++6-8-dbg gcc-multilib manpages-dev autoconf
  automake libtool flex bison gdb gcc-doc gcc-8-multilib libgcc1-dbg
  libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
  libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg glibc-doc gnupg
  | gnupg2 bzr libstdc++-8-doc make-doc ed diffutils-doc
Recommended packages:
  fakeroot gnupg | gnupg2 libalgorithm-merge-perl manpages manpages-dev
  libfile-fcntllock-perl liblocale-gettext-perl
The following NEW packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu build-essential cpp cpp-8
  dpkg-dev g++ g++-8 gcc gcc-8 libasan5 libatomic1 libbinutils libc-dev-bin
  libc6-dev libcc1-0 libdpkg-perl libgcc-8-dev libgomp1 libisl19 libitm1
  liblsan0 libmpc3 libmpfr6 libmpx2 libquadmath0 libstdc++-8-dev libtsan0
  libubsan1 linux-libc-dev make patch xz-utils
0 upgraded, 34 newly installed, 0 to remove and 9 not upgraded.
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Removing intermediate container 3fbc6fd37261
 ---> b2533d8a8063
Step 7/26 : WORKDIR /tmp
 ---> Running in ba5fc50d20c6
Removing intermediate container ba5fc50d20c6
 ---> 914949a5e97f
Step 8/26 : RUN git clone https://github.com/emolinaro/PALMSpy.git
 ---> Running in b5c0348777e8
Cloning into 'PALMSpy'...
Removing intermediate container b5c0348777e8
 ---> bb69d31fd145
Step 9/26 : WORKDIR PALMSpy
 ---> Running in 9c003f5a0451
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 ---> f71187027afd
Step 10/26 : ENV PATH /opt/conda/envs/palmspy/bin:$PATH
 ---> Running in edf19c13c1ae
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 ---> 8e9eef070560
Step 11/26 : ENV CONDA_PREFIX="/opt/conda/envs/palmspy"
 ---> Running in 6fefd87c3e24
Removing intermediate container 6fefd87c3e24
 ---> e450c9142d68
Step 12/26 : RUN conda create -n palmspy python=3.7 openjdk=8.0 make=4.2.1 -y  && conda activate palmspy  && echo "source activate palmspy" > ~/.bashrc  && make  && make install  && make check  && make clean
 ---> Running in 8c563122746c
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda/envs/palmspy

  added / updated specs:
    - make=4.2.1
    - openjdk=8.0
    - python=3.7

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |             main           3 KB
    _openmp_mutex-4.5          |            1_gnu          22 KB
    ca-certificates-2021.10.26 |       h06a4308_2         115 KB
    certifi-2021.10.8          |   py37h06a4308_0         151 KB
    ld_impl_linux-64-2.35.1    |       h7274673_9         586 KB
    libffi-3.3                 |       he6710b0_2          50 KB
    libgcc-ng-9.3.0            |      h5101ec6_17         4.8 MB
    libgomp-9.3.0              |      h5101ec6_17         311 KB
    libstdcxx-ng-9.3.0         |      hd4cf53a_17         3.1 MB
    make-4.2.1                 |       h1bed415_1         415 KB
    ncurses-6.3                |       h7f8727e_2         782 KB
    openjdk-8.0.152            |       h7b6447c_3        57.4 MB
    openssl-1.1.1l             |       h7f8727e_0         2.5 MB
    pip-21.2.2                 |   py37h06a4308_0         1.8 MB
    python-3.7.11              |       h12debd9_0        45.3 MB
    readline-8.1               |       h27cfd23_0         362 KB
    setuptools-58.0.4          |   py37h06a4308_0         775 KB
    sqlite-3.36.0              |       hc218d9a_0         990 KB
    tk-8.6.11                  |       h1ccaba5_0         3.0 MB
    wheel-0.37.0               |     pyhd3eb1b0_1          33 KB
    xz-5.2.5                   |       h7b6447c_0         341 KB
    zlib-1.2.11                |       h7b6447c_3         103 KB
    ------------------------------------------------------------
                                           Total:       122.9 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    pkgs/main/linux-64::ca-certificates-2021.10.26-h06a4308_2
  certifi            pkgs/main/linux-64::certifi-2021.10.8-py37h06a4308_0
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
  libffi             pkgs/main/linux-64::libffi-3.3-he6710b0_2
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
  libgomp            pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
  make               pkgs/main/linux-64::make-4.2.1-h1bed415_1
  ncurses            pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
  openjdk            pkgs/main/linux-64::openjdk-8.0.152-h7b6447c_3
  openssl            pkgs/main/linux-64::openssl-1.1.1l-h7f8727e_0
  pip                pkgs/main/linux-64::pip-21.2.2-py37h06a4308_0
  python             pkgs/main/linux-64::python-3.7.11-h12debd9_0
  readline           pkgs/main/linux-64::readline-8.1-h27cfd23_0
  setuptools         pkgs/main/linux-64::setuptools-58.0.4-py37h06a4308_0
  sqlite             pkgs/main/linux-64::sqlite-3.36.0-hc218d9a_0
  tk                 pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
  wheel              pkgs/main/noarch::wheel-0.37.0-pyhd3eb1b0_1
  xz                 pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Downloading and Extracting Packages
_openmp_mutex-4.5    | 22 KB     | ########## | 100%
libstdcxx-ng-9.3.0   | 3.1 MB    | ########## | 100%
python-3.7.11        | 45.3 MB   | ########## | 100%
setuptools-58.0.4    | 775 KB    | ########## | 100%
xz-5.2.5             | 341 KB    | ########## | 100%
_libgcc_mutex-0.1    | 3 KB      | ########## | 100%
tk-8.6.11            | 3.0 MB    | ########## | 100%
make-4.2.1           | 415 KB    | ########## | 100%
ca-certificates-2021 | 115 KB    | ########## | 100%
zlib-1.2.11          | 103 KB    | ########## | 100%
readline-8.1         | 362 KB    | ########## | 100%
wheel-0.37.0         | 33 KB     | ########## | 100%
ld_impl_linux-64-2.3 | 586 KB    | ########## | 100%
openssl-1.1.1l       | 2.5 MB    | ########## | 100%
libgcc-ng-9.3.0      | 4.8 MB    | ########## | 100%
pip-21.2.2           | 1.8 MB    | ########## | 100%
libgomp-9.3.0        | 311 KB    | ########## | 100%
libffi-3.3           | 50 KB     | ########## | 100%
ncurses-6.3          | 782 KB    | ########## | 100%
certifi-2021.10.8    | 151 KB    | ########## | 100%
sqlite-3.36.0        | 990 KB    | ########## | 100%
openjdk-8.0.152      | 57.4 MB   | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
#
# To activate this environment, use
#
#     $ conda activate palmspy
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Install dependencies...

/opt/conda/envs/palmspy/bin/pip install -r requirements.txt
Collecting appnope==0.1.0
  Downloading appnope-0.1.0-py2.py3-none-any.whl (4.0 kB)
Collecting attrs==19.1.0
  Downloading attrs-19.1.0-py2.py3-none-any.whl (35 kB)
Collecting backcall==0.1.0
  Downloading backcall-0.1.0.zip (11 kB)
Collecting certifi==2019.3.9
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Collecting defusedxml==0.6.0
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Collecting jedi==0.13.3
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Collecting MarkupSafe==1.1.1
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Collecting mistune==0.8.4
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Collecting nbconvert==5.4.1
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Collecting nbformat==4.4.0
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Collecting notebook==5.7.8
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Collecting numpy==1.16.2
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Collecting pandas==0.24.2
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Collecting pandocfilters==1.4.2
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Collecting parso==0.4.0
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Collecting pexpect==4.7.0
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Collecting pickleshare==0.7.5
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Collecting prometheus-client==0.6.0
  Downloading prometheus_client-0.6.0.tar.gz (36 kB)
Collecting prompt-toolkit==2.0.9
  Downloading prompt_toolkit-2.0.9-py3-none-any.whl (337 kB)
Collecting ptyprocess==0.6.0
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Collecting py4j==0.10.7
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Collecting Pygments==2.3.1
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Collecting pyrsistent==0.14.11
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Collecting pyspark==2.4.2
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Collecting pytest==6.1.2
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Collecting python-dateutil==2.8.0
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Collecting pytz==2019.1
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Collecting pyzmq==18.0.1
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Collecting qtconsole==4.4.3
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Collecting regex==2019.3.9
  Downloading regex-2019.03.09.tar.gz (643 kB)
Collecting Send2Trash==1.5.0
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Collecting Shapely==1.6.4.post2
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Collecting six==1.12.0
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Collecting terminado==0.8.2
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Collecting testpath==0.4.2
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Collecting tornado==6.0.2
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Collecting traitlets==4.3.2
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Collecting tzwhere==3.0.3
  Downloading tzwhere-3.0.3.tar.gz (23.7 MB)
Collecting virtualenv==16.0.0
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Collecting wcwidth==0.1.7
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Collecting webencodings==0.5.1
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Collecting wheel==0.33.6
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Collecting widgetsnbextension==3.4.2
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Collecting zope.interface==4.6.0
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Collecting timezonefinder==5.2.0
  Downloading timezonefinder-5.2.0-py36.py37.py38-none-any.whl (43.0 MB)
Requirement already satisfied: setuptools>=18.5 in /opt/conda/envs/palmspy/lib/python3.7/site-packages (from ipython==7.4.0->-r requirements.txt (line 11)) (58.0.4)
Collecting bleach
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Collecting packaging
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Collecting py>=1.8.2
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Collecting iniconfig
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Collecting pluggy<1.0,>=0.12
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Collecting importlib-metadata>=0.12
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Collecting zipp>=0.5
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Collecting typing-extensions>=3.6.4
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Collecting pyparsing!=3.0.5,>=2.0.2
  Downloading pyparsing-3.0.6-py3-none-any.whl (97 kB)
Building wheels for collected packages: backcall, pandocfilters, prometheus-client, pyrsistent, pyspark, regex, tornado, tzwhere
  Building wheel for backcall (setup.py): started
  Building wheel for backcall (setup.py): finished with status 'done'
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  Building wheel for prometheus-client (setup.py): finished with status 'done'
  Created wheel for prometheus-client: filename=prometheus_client-0.6.0-py3-none-any.whl size=39585 sha256=c85c885e18ae544924c8c92258990fde3fa6ab57a700f5a7a2ed15d992c5b341
  Stored in directory: /root/.cache/pip/wheels/6e/d8/31/c7c67f483036e5841d084f1138abdc078ba7c390544aa0ef28
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  Building wheel for pyrsistent (setup.py): finished with status 'done'
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  Stored in directory: /root/.cache/pip/wheels/20/78/0a/4d5c19e3868f7dd8df2fa8c2933f01ba28948a3f0b10faccf4
  Building wheel for pyspark (setup.py): started
  Building wheel for pyspark (setup.py): finished with status 'done'
  Created wheel for pyspark: filename=pyspark-2.4.2-py2.py3-none-any.whl size=194264323 sha256=064c6848787d5d8db6e6685a46a5572b1aa9ac71024269262d225278f63da08f
  Stored in directory: /root/.cache/pip/wheels/6d/87/6c/8f2c5da1ec8f9328b2b505138798da07d7658220919005ec47
  Building wheel for regex (setup.py): started
  Building wheel for regex (setup.py): finished with status 'done'
  Created wheel for regex: filename=regex-2019.3.9-cp37-cp37m-linux_x86_64.whl size=671080 sha256=8d271038247a727e1eedfd43d6f64f50b2d928b31e40d4658d5455e219fd0306
  Stored in directory: /root/.cache/pip/wheels/3c/2b/cb/bd56052497a3f96d924d8bc5afa2c4157cd39997b3508c70ca
  Building wheel for tornado (setup.py): started
  Building wheel for tornado (setup.py): finished with status 'done'
  Created wheel for tornado: filename=tornado-6.0.2-cp37-cp37m-linux_x86_64.whl size=424282 sha256=aa9f4b4b440ea695900984dde72a2c52adbc594fa1ad536b261280861c7460b6
  Stored in directory: /root/.cache/pip/wheels/10/ec/4d/1aca4b143f2a19439632329f1d5b6b9f62ee9508ddf30f9d2c
  Building wheel for tzwhere (setup.py): started
  Building wheel for tzwhere (setup.py): finished with status 'done'
  Created wheel for tzwhere: filename=tzwhere-3.0.3-py3-none-any.whl size=23742600 sha256=aec14559bc4a247c2842cf1d75b89d09fb4cb61ab0b4e416948f6ebf2534c272
  Stored in directory: /root/.cache/pip/wheels/a4/27/39/8c57d78844da3630f08a30bfe9da5eac9a290e0a7edcb98218
Successfully built backcall pandocfilters prometheus-client pyrsistent pyspark regex tornado tzwhere
Installing collected packages: six, ipython-genutils, decorator, wcwidth, traitlets, pyrsistent, pyparsing, ptyprocess, parso, attrs, webencodings, tornado, pyzmq, python-dateutil, Pygments, prompt-toolkit, pickleshare, pexpect, packaging, MarkupSafe, jupyter-core, jsonschema, jedi, backcall, testpath, pandocfilters, nbformat, mistune, jupyter-client, Jinja2, ipython, entrypoints, defusedxml, bleach, terminado, Send2Trash, prometheus-client, nbconvert, ipykernel, zipp, typing-extensions, notebook, widgetsnbextension, importlib-metadata, zope.interface, toml, Shapely, regex, qtconsole, pytz, py4j, py, pluggy, numpy, jupyter-console, ipywidgets, iniconfig, wheel, virtualenv, tzwhere, timezonefinder, pytest, pyspark, pandas, jupyter, DateTime, datefinder, certifi, appnope
  Attempting uninstall: wheel
    Found existing installation: wheel 0.37.0
    Uninstalling wheel-0.37.0:
      Successfully uninstalled wheel-0.37.0
  Attempting uninstall: certifi
    Found existing installation: certifi 2021.10.8
    Uninstalling certifi-2021.10.8:
      Successfully uninstalled certifi-2021.10.8
Successfully installed DateTime-4.3 Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 Send2Trash-1.5.0 Shapely-1.6.4.post2 appnope-0.1.0 attrs-19.1.0 backcall-0.1.0 bleach-4.1.0 certifi-2019.3.9 datefinder-0.7.0 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 importlib-metadata-4.8.2 iniconfig-1.1.1 ipykernel-5.1.0 ipython-7.4.0 ipython-genutils-0.2.0 ipywidgets-7.4.2 jedi-0.13.3 jsonschema-3.0.1 jupyter-1.0.0 jupyter-client-5.2.4 jupyter-console-6.0.0 jupyter-core-4.4.0 mistune-0.8.4 nbconvert-5.4.1 nbformat-4.4.0 notebook-5.7.8 numpy-1.16.2 packaging-21.3 pandas-0.24.2 pandocfilters-1.4.2 parso-0.4.0 pexpect-4.7.0 pickleshare-0.7.5 pluggy-0.13.1 prometheus-client-0.6.0 prompt-toolkit-2.0.9 ptyprocess-0.6.0 py-1.11.0 py4j-0.10.7 pyparsing-3.0.6 pyrsistent-0.14.11 pyspark-2.4.2 pytest-6.1.2 python-dateutil-2.8.0 pytz-2019.1 pyzmq-18.0.1 qtconsole-4.4.3 regex-2019.3.9 six-1.12.0 terminado-0.8.2 testpath-0.4.2 timezonefinder-5.2.0 toml-0.10.2 tornado-6.0.2 traitlets-4.3.2 typing-extensions-4.0.1 tzwhere-3.0.3 virtualenv-16.0.0 wcwidth-0.1.7 webencodings-0.5.1 wheel-0.33.6 widgetsnbextension-3.4.2 zipp-3.6.0 zope.interface-4.6.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

Build the package...

/opt/conda/envs/palmspy/bin/python3 setup.py sdist bdist_wheel
running sdist
running egg_info
creating palmspy.egg-info
writing palmspy.egg-info/PKG-INFO
writing dependency_links to palmspy.egg-info/dependency_links.txt
writing top-level names to palmspy.egg-info/top_level.txt
writing manifest file 'palmspy.egg-info/SOURCES.txt'
reading manifest file 'palmspy.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'palmspy.egg-info/SOURCES.txt'
running check
creating palmspy-1.9.6
creating palmspy-1.9.6/palmspy.egg-info
creating palmspy-1.9.6/src
copying files to palmspy-1.9.6...
copying LICENSE -> palmspy-1.9.6
copying README.md -> palmspy-1.9.6
copying palmspy -> palmspy-1.9.6
copying palmspy.py -> palmspy-1.9.6
copying setup.py -> palmspy-1.9.6
copying palmspy.egg-info/PKG-INFO -> palmspy-1.9.6/palmspy.egg-info
copying palmspy.egg-info/SOURCES.txt -> palmspy-1.9.6/palmspy.egg-info
copying palmspy.egg-info/dependency_links.txt -> palmspy-1.9.6/palmspy.egg-info
copying palmspy.egg-info/top_level.txt -> palmspy-1.9.6/palmspy.egg-info
copying src/AccProcessing.py -> palmspy-1.9.6/src
copying src/GPSProcessing.py -> palmspy-1.9.6/src
copying src/__init__.py -> palmspy-1.9.6/src
copying src/help_menu.py -> palmspy-1.9.6/src
copying src/tools.py -> palmspy-1.9.6/src
Writing palmspy-1.9.6/setup.cfg
creating dist
Creating tar archive
removing 'palmspy-1.9.6' (and everything under it)
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/src
copying src/__init__.py -> build/lib/src
copying src/help_menu.py -> build/lib/src
copying src/GPSProcessing.py -> build/lib/src
copying src/AccProcessing.py -> build/lib/src
copying src/tools.py -> build/lib/src
running build_scripts
creating build/scripts-3.7
copying and adjusting palmspy.py -> build/scripts-3.7
copying and adjusting palmspy -> build/scripts-3.7
changing mode of build/scripts-3.7/palmspy.py from 644 to 755
changing mode of build/scripts-3.7/palmspy from 644 to 755
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/src
copying build/lib/src/__init__.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/GPSProcessing.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/help_menu.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/AccProcessing.py -> build/bdist.linux-x86_64/wheel/src
copying build/lib/src/tools.py -> build/bdist.linux-x86_64/wheel/src
running install_egg_info
Copying palmspy.egg-info to build/bdist.linux-x86_64/wheel/palmspy-1.9.6-py3.7.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data
creating build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts
copying build/scripts-3.7/palmspy -> build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts
copying build/scripts-3.7/palmspy.py -> build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts
changing mode of build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts/palmspy to 755
changing mode of build/bdist.linux-x86_64/wheel/palmspy-1.9.6.data/scripts/palmspy.py to 755
adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
creating build/bdist.linux-x86_64/wheel/palmspy-1.9.6.dist-info/WHEEL
creating 'dist/palmspy-1.9.6-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'palmspy-1.9.6.data/scripts/palmspy'
adding 'palmspy-1.9.6.data/scripts/palmspy.py'
adding 'src/AccProcessing.py'
adding 'src/GPSProcessing.py'
adding 'src/__init__.py'
adding 'src/help_menu.py'
adding 'src/tools.py'
adding 'palmspy-1.9.6.dist-info/LICENSE'
adding 'palmspy-1.9.6.dist-info/METADATA'
adding 'palmspy-1.9.6.dist-info/WHEEL'
adding 'palmspy-1.9.6.dist-info/top_level.txt'
adding 'palmspy-1.9.6.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel

Install the package...

/opt/conda/envs/palmspy/bin/pip install ./dist/palmspy-*-py3-none-any.whl --force-reinstall
Processing ./dist/palmspy-1.9.6-py3-none-any.whl
Installing collected packages: palmspy
Successfully installed palmspy-1.9.6
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv

Sanity check...

/opt/conda/envs/palmspy/bin/palmspy --help
usage: palmspy --gps-path GPS_PATH --acc-path ACC_PATH [GPS options] [accelerometer options] [Spark options]

PALMSpy is an implementation of the Personal Activity and Location Measurement
System (PALMS), written in Python and integrated with Apache Spark for
cluster-computing. The program detects personal activity patterns of
individual participants wearing a GPS data logger and a physical activity
monitor.

optional arguments:
  -h, --help            show this help message and exit
  --config-file FILE    load JSON file with configuration settings
  --version, -v         show program's version number and exit

required arguments:
  --gps-path GPS_PATH   directory of GPS raw data
  --acc-path ACC_PATH   directory of accelerometer raw data

GPS options:
  --interval INT        duration of interval between results in seconds
                        (default: 30)
  --insert-missing      gaps in GPS fixes are replaced by the last valid fix
                        (default: False)
  --insert-until        inserts until a max time (set by --insert-max-seconds)
                        is reached; by default, inserts will be added until
                        loss of signal time is reached (default: False)
  --insert-max-seconds INT
                        max number of seconds to replace missing fixes with
                        last valid fix (valid if --insert-until is enabled)
                        (default: 600)
  --los-max-duration INT
                        max number of seconds allowed to pass before loss of
                        signal is declared (default: 600)
  --filter-invalid-values
                        remove invalid fixes (default: False)
  --max-speed INT       fix is invalid if speed is greater than this value (in
                        km/hr) (default: 130)
  --max-ele-change INT  fix is invalid if elevation change is greater than
                        this value (in meters) (default: 1000)
  --min-change-3-fixes INT
                        fix is invalid if change in distance between fix 1 and
                        3 is less than this value (in meters) (default: 10)
  --detect-trip         calculate the fix trip type: STATIONARY (0), START
                        POINT (1), MID POINT (2), PAUSE POINT (3), and END
                        POINT (4) (default: False)
  --min-distance INT    minimum distance (in meters) that must be travelled
                        over one minute to indicate the start of a trip.
                        Default value corresponds to a typical walking speed
                        of 2 km/hr (default: 34)
  --min-trip-length INT
                        trips less than this distance (in meters) are not
                        considered trips (default: 100)
  --min-trip-duration INT
                        trips less than this duration (in seconds) are not
                        considered trips (default: 180)
  --min-pause-duration INT
                        when the duration at a location exceeds this value (in
                        seconds), the point is marked as PAUSE POINT (default:
                        180)
  --max-pause-duration INT
                        when the duration of a pause exceeds this value (in
                        seconds), the point is marked as an END POINT
                        (default: 300)
  --detect-trip-mode    calculate the mode of transportation based on the
                        speed: STATIONARY (0), PEDESTRIAN (1), BICYCLE (2),
                        and VEHICLE (3) (default: False)
  --vehicle-cutoff INT  speeds greater than this value (in km/hr) will be
                        marked as VEHICLE (default: 25)
  --bicycle-cutoff INT  speeds greater than this value (in km/hr) will be
                        marked as BICYCLE (default: 10)
  --walk-cutoff INT     speeds greater than this value (in km/hr) will be
                        marked as PEDESTRIAN (default: 1)
  --percentile-to-sample INT
                        speed comparisons are made at this percentile
                        (default: 90)
  --min-segment-length INT
                        minimum length (in meters) of segments used to
                        classify mode of transportation (default: 30)

accelerometer options:
  --include-acc         append raw accelerometer data to the final output
                        (default: False)
  --include-vect        calculate the activity intensity from the
                        accelerometer vector magnitude (default: False)
  --mark-non-wearing    mark non-wearing time (set actvity count and activity
                        intensity equal to -2) (default: False)
  --minutes-zeros-row INT
                        minimum non-wearing time (in minutes), corresponding
                        to consecutive zeros in the activity count (default:
                        30)
  --detect-activity-bouts
                        detect activity bouts (default: False)
  --activity-bout-duration INT
                        minimum activity bout duration (in minutes) (default:
                        5)
  --activity-bout-up INT
                        activity bout upper limit (default: 9999)
  --activity-bout-low INT
                        activity bout lower limit (default: 1953)
  --activity-bout-tol INT
                        activity bout tolerance (default: 2)
  --detect-sedentary-bouts
                        detect sedentary bouts (default: False)
  --sedentary-bout-duration INT
                        sedentary bout duration (in minutes) (default: 30)
  --sedentary-bout-up INT
                        sedentary bout upper limit (default: 100)
  --sedentary-bout-tol INT
                        sedentary bout tolerance (default: 1)
  --very-hard-cut INT   very hard activity cutoff value (default: 9498)
  --hard-cut INT        hard activity cutoff value (default: 5725)
  --moderate-cut INT    moderate activity cutoff value (default: 1953)
  --light-cut INT       light activity cutoff value (default: 100)

merge options:
  --merge-acc-to-gps    merge accelerometer data to GPS data and export them
                        in one single file; by default, the processed
                        accelerometer and GPS data will be saved in two
                        different files (default: False)
  --merge-gps-to-acc    merge GPS data to accelerometer data and export them
                        in one single file; by default, the processed
                        accelerometer and GPS data will be saved in two
                        different files (default: False)

Spark options:
  --num-cores INT       total number of cores used in the calculation
                        (default: 8)
  --driver-mem STR      amount of memory to use for the driver process, i.e.
                        where SparkContext is initialized, in the same format
                        as JVM memory strings with a size unit suffix ("k",
                        "m", "g" or "t") (default: 16g)
  --executor-mem STR    amount of memory to use per executor process, in the
                        same format as JVM memory strings with a size unit
                        suffix ("k", "m", "g" or "t") (default: 16g)
  --mem-fraction FLOAT  expresses the size of the execution and storage memory
                        as a fraction of the (JVM heap space - 300MB). The
                        rest of the space (40%) is reserved for user data
                        structures, internal metadata in Spark, and
                        safeguarding against OOM errors in the case of sparse
                        and unusually large records (default: 0.6)
  --default-partitions INT
                        Default number of partitions returned by
                        transformations like join, reduceByKey, and
                        parallelize (default: 20)
  --shuffle-partitions INT
                        configures the number of partitions to use when
                        shuffling data for joins or aggregations (default: 20)
  --mem-offHeap-enabled
                        if true, off-heap memory will be used for certain
                        operations. If off-heap memory use is enabled, then
                        --mem-offHeap-size must be positive (default: True)
  --mem-offHeap-size STR
                        the absolute amount of memory in bytes which can be
                        used for off-heap allocation. This must be set to a
                        positive value when --mem-offHeap-enabled is true
                        (default: 16g)
  --clean-checkpoints   controls whether to clean checkpoint files if the
                        reference is out of scope (default: True)
  --codegen-wholeStage  enable whole-stage code generation (experimental)
                        (default: False)
  --codegen-fallback    when true, whole-stage codegen could be temporary
                        disabled for the part of query that fails to compile
                        generated code (default: True)
  --broadcast-timeout INT
                        timeout in seconds for the broadcast wait time in
                        broadcast joins (default: 1200)
  --networkTimeout STR  default timeout for all network interactions (default:
                        800s)

Cleanup...

Removing intermediate container 8c563122746c
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Step 13/26 : WORKDIR /
 ---> Running in ce8403c05230
Removing intermediate container ce8403c05230
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Step 14/26 : FROM rocker/shiny
latest: Pulling from rocker/shiny
7b1a6ab2e44d: Pull complete
173642fec733: Pull complete
26795e478bd8: Pull complete
4e5c5480552d: Pull complete
0ff32ba8c09e: Pull complete
2958c7029362: Pull complete
Digest: sha256:270cdc63dcc7acb985fe5fe7aa00361d006339270abdda0a4ea45c821af311cd
Status: Downloaded newer image for rocker/shiny:latest
 ---> e855b61628d2
Step 15/26 : SHELL ["/bin/bash",  "--login", "-c"]
 ---> Running in a7071f4b4db0
Removing intermediate container a7071f4b4db0
 ---> 3d32eea51e9d
Step 16/26 : COPY --from=builder /opt/conda /opt/conda
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Step 17/26 : ENV PATH /opt/conda/envs/palmspy/bin:$PATH
 ---> Running in fda35730ffdb
Removing intermediate container fda35730ffdb
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Step 18/26 : ENV CONDA_PREFIX="/opt/conda/envs/palmspy"
 ---> Running in 0d19080f6935
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Step 19/26 : RUN echo "source activate palmspy" > ~/.bashrc
 ---> Running in e345bb359141
Removing intermediate container e345bb359141
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Step 20/26 : RUN apt-get update && apt-get install -y     libcurl4-gnutls-dev     libssl-dev
 ---> Running in 515da4fd96ed
/root/.bashrc: line 1: activate: No such file or directory
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Fetched 20.1 MB in 8s (2,503 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libcurl3-gnutls
Suggested packages:
  libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
  librtmp-dev libssh2-1-dev libssl-doc
The following packages will be REMOVED:
  libcurl4-openssl-dev
The following NEW packages will be installed:
  libcurl3-gnutls libcurl4-gnutls-dev libssl-dev
0 upgraded, 3 newly installed, 1 to remove and 5 not upgraded.
Need to get 2,133 kB of archives.
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Get:3 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssl-dev amd64 1.1.1f-1ubuntu2.9 [1,583 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 28482 files and directories currently installed.)
Removing libcurl4-openssl-dev:amd64 (7.68.0-1ubuntu2.7) ...
Selecting previously unselected package libcurl3-gnutls:amd64.
(Reading database ... 28461 files and directories currently installed.)
Preparing to unpack .../libcurl3-gnutls_7.68.0-1ubuntu2.7_amd64.deb ...
Unpacking libcurl3-gnutls:amd64 (7.68.0-1ubuntu2.7) ...
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Unpacking libcurl4-gnutls-dev:amd64 (7.68.0-1ubuntu2.7) ...
Selecting previously unselected package libssl-dev:amd64.
Preparing to unpack .../libssl-dev_1.1.1f-1ubuntu2.9_amd64.deb ...
Unpacking libssl-dev:amd64 (1.1.1f-1ubuntu2.9) ...
Setting up libcurl3-gnutls:amd64 (7.68.0-1ubuntu2.7) ...
Setting up libcurl4-gnutls-dev:amd64 (7.68.0-1ubuntu2.7) ...
Setting up libssl-dev:amd64 (1.1.1f-1ubuntu2.9) ...
Processing triggers for libc-bin (2.31-0ubuntu9.2) ...
Removing intermediate container 515da4fd96ed
 ---> 7b8562863b1b
Step 21/26 : RUN R -e 'install.packages(c(              "shiny",               "shinyFiles",               "GGIR",               "jsonlite",               "DT",               "waiter",               "activityCounts",               "remotes"             ),             repos="https://packagemanager.rstudio.com/cran/__linux__/focal/latest"          )'
 ---> Running in 442af5913f70
/root/.bashrc: line 1: activate: No such file or directory

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.

* DONE (bit)
* installing *binary* package ‘purrr’ ...
* DONE (purrr)
* installing *binary* package ‘prettyunits’ ...
* DONE (prettyunits)
* installing *binary* package ‘cli’ ...
* DONE (cli)
* installing *binary* package ‘utf8’ ...
* DONE (utf8)
* installing *binary* package ‘fansi’ ...
* DONE (fansi)
* installing *binary* package ‘pkgconfig’ ...
* DONE (pkgconfig)
* installing *binary* package ‘vctrs’ ...
* DONE (vctrs)
* installing *binary* package ‘iterators’ ...
* DONE (iterators)
* installing *binary* package ‘mmap’ ...
* DONE (mmap)
* installing *binary* package ‘XML’ ...
* DONE (XML)
* installing *binary* package ‘hexView’ ...
* DONE (hexView)
* installing *binary* package ‘lazyeval’ ...
* DONE (lazyeval)
* installing *binary* package ‘generics’ ...
* DONE (generics)
* installing *binary* package ‘cpp11’ ...
* DONE (cpp11)
* installing *binary* package ‘data.table’ ...
* DONE (data.table)
* installing *binary* package ‘signal’ ...
* DONE (signal)
* installing *binary* package ‘zoo’ ...
* DONE (zoo)
* installing *binary* package ‘bitops’ ...
* DONE (bitops)
* installing *binary* package ‘matlab’ ...
* DONE (matlab)
* installing *binary* package ‘ineq’ ...
* DONE (ineq)
* installing *binary* package ‘jsonlite’ ...
* DONE (jsonlite)
* installing *binary* package ‘remotes’ ...
* DONE (remotes)
* installing *binary* package ‘bit64’ ...
* DONE (bit64)
* installing *binary* package ‘hms’ ...
* DONE (hms)
* installing *binary* package ‘tzdb’ ...
* DONE (tzdb)
* installing *binary* package ‘tidyselect’ ...
* DONE (tidyselect)
* installing *binary* package ‘pillar’ ...
* DONE (pillar)
* installing *binary* package ‘foreach’ ...
* DONE (foreach)
* installing *binary* package ‘GENEAread’ ...
* DONE (GENEAread)
* installing *binary* package ‘tuneR’ ...
* DONE (tuneR)
* installing *binary* package ‘htmlwidgets’ ...
* DONE (htmlwidgets)
* installing *binary* package ‘crosstalk’ ...
* DONE (crosstalk)
* installing *binary* package ‘lubridate’ ...
* DONE (lubridate)
* installing *binary* package ‘shiny’ ...
* DONE (shiny)
* installing *binary* package ‘progress’ ...
* DONE (progress)
* installing *binary* package ‘tibble’ ...
* DONE (tibble)
* installing *binary* package ‘doParallel’ ...
* DONE (doParallel)
* installing *binary* package ‘seewave’ ...
* DONE (seewave)
* installing *binary* package ‘DT’ ...
* DONE (DT)
* installing *binary* package ‘waiter’ ...
* DONE (waiter)
* installing *binary* package ‘vroom’ ...
* DONE (vroom)
* installing *binary* package ‘shinyFiles’ ...
* DONE (shinyFiles)
* installing *binary* package ‘activityCounts’ ...
* DONE (activityCounts)
* installing *binary* package ‘unisensR’ ...
* DONE (unisensR)
* installing *binary* package ‘GGIR’ ...
* DONE (GGIR)

The downloaded source packages are in
	‘/tmp/RtmpGUq9vf/downloaded_packages’
>
>
Removing intermediate container 442af5913f70
 ---> 3b3cf39bada7
Step 22/26 : RUN R -e 'remotes::install_github("rstudio/bslib")' # development version because CRAN version has bug that affects us
 ---> Running in e1e484ae03a9
/root/.bashrc: line 1: activate: No such file or directory

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> remotes::install_github("rstudio/bslib")
Downloading GitHub repo rstudio/bslib@HEAD
memoise (NA -> 2.0.1) [CRAN]
Installing 1 packages: memoise
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest/src/contrib/memoise_2.0.1.tar.gz'
Content type 'binary/octet-stream' length 46466 bytes (45 KB)
==================================================
downloaded 45 KB

* installing *binary* package ‘memoise’ ...
* DONE (memoise)

The downloaded source packages are in
	‘/tmp/RtmpmZZ8Hf/downloaded_packages’
Running `R CMD build`...
* checking for file ‘/tmp/RtmpmZZ8Hf/remotes121d2edaf/rstudio-bslib-888fbe0/DESCRIPTION’ ... OK
* preparing ‘bslib’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘bslib/inst/lib/bs3/assets/images’
* looking to see if a ‘data/datalist’ file should be added
* building ‘bslib_<IP_ADDRESS>00.tar.gz’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘bslib’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bslib)
>
>
Removing intermediate container e1e484ae03a9
 ---> 4cd1fc228172
Step 23/26 : RUN R -e 'remotes::install_github("habitus-eu/HabitusGUI", ref = "adding_real_palmspy")'
 ---> Running in 0b3fe9d0157b
/root/.bashrc: line 1: activate: No such file or directory

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> remotes::install_github("habitus-eu/HabitusGUI", ref = "adding_real_palmspy")
Downloading GitHub repo habitus-eu/HabitusGUI@adding_real_palmspy

Running `R CMD build`...
* checking for file ‘/tmp/RtmpoT9edf/remotes14cd6d9e/habitus-eu-HabitusGUI-8d393e9/DESCRIPTION’ ... OK
* preparing ‘HabitusGUI’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘HabitusGUI_0.1.2.tar.gz’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘HabitusGUI’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HabitusGUI)
>
>
Removing intermediate container 0b3fe9d0157b
 ---> b1077e9f9ee3
Step 24/26 : RUN mkdir -p /code
 ---> Running in 47c9eabc9c34
/root/.bashrc: line 1: activate: No such file or directory
Removing intermediate container 47c9eabc9c34
 ---> 966591db9431
Step 25/26 : COPY /code/app.R /srv/shiny-server/
 ---> 668f7e65d2b6
Step 26/26 : CMD ["/usr/bin/shiny-server"]
 ---> Running in 81baa5bb4ede
Removing intermediate container 81baa5bb4ede
 ---> cbac6a9b3989
Successfully built cbac6a9b3989
Successfully tagged habitus-app:latest