Error building from Dockerfile

[paulflang]

I am using Docker version 19.03.8 and Ubuntu 20.04 in a VirtualBox on Windows host. When running sudo docker build -f Dockerfile Dockerfile_assets --tag karrlab/bpforms:latest I was prompted to select my geographical location. After adding ENV DEBIAN_FRONTEND=noninteractive before the first RUN command, this issue was resolved, but I got the following error instead:

...
Step 8/15 : RUN apt-get update -y     && apt-get install --no-install-recommends -y         build-essential         libpython3-dev         swig         && pip3 install openbabel         && apt-get remove -y           build-essential           libpython3-dev           swig     && apt-get autoremove -y     && rm -rf /var/lib/apt/lists/*
 ---> Running in b48d92427e63
Get:1 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]
Get:2 http://security.ubuntu.com/ubuntu focal-security InRelease [107 kB]
Get:3 http://archive.ubuntu.com/ubuntu focal-updates InRelease [111 kB]
Get:4 http://archive.ubuntu.com/ubuntu focal-backports InRelease [98.3 kB]
Get:5 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB]
Get:6 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]
Get:7 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [1,078 B]
Get:8 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [248 kB]
Get:9 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [51.0 kB]
Get:10 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [73.3 kB]
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Get:12 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1,275 kB]
Get:13 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [17.3 kB]
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Get:15 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [485 kB]
Get:16 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [214 kB]
Get:17 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [3,195 B]
Fetched 14.6 MB in 6s (2,317 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-9 dpkg-dev g++
  g++-9 gcc gcc-9 gcc-9-base libasan5 libatomic1 libbinutils libc-dev-bin
  libc6-dev libcc1-0 libcrypt-dev libctf-nobfd0 libctf0 libdpkg-perl
  libexpat1-dev libgcc-9-dev libgdbm-compat4 libgdbm6 libgomp1 libisl22
  libitm1 liblsan0 libmpc3 libmpfr6 libperl5.30 libpython3.8 libpython3.8-dev
  libquadmath0 libstdc++-9-dev libtsan0 libubsan1 linux-libc-dev make patch
  perl perl-modules-5.30 swig4.0
Suggested packages:
  binutils-doc cpp-doc gcc-9-locales debian-keyring g++-multilib
  g++-9-multilib gcc-9-doc gcc-multilib manpages-dev autoconf automake libtool
  flex bison gdb gcc-doc gcc-9-multilib glibc-doc gnupg | gnupg2 git bzr
  gdbm-l10n libstdc++-9-doc make-doc ed diffutils-doc perl-doc
  libterm-readline-gnu-perl | libterm-readline-perl-perl libb-debug-perl
  liblocale-codes-perl swig-doc swig-examples swig4.0-examples swig4.0-doc
Recommended packages:
  fakeroot gnupg | gnupg2 libalgorithm-merge-perl manpages manpages-dev
  libfile-fcntllock-perl liblocale-gettext-perl netbase
The following NEW packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu build-essential cpp cpp-9
  dpkg-dev g++ g++-9 gcc gcc-9 gcc-9-base libasan5 libatomic1 libbinutils
  libc-dev-bin libc6-dev libcc1-0 libcrypt-dev libctf-nobfd0 libctf0
  libdpkg-perl libexpat1-dev libgcc-9-dev libgdbm-compat4 libgdbm6 libgomp1
  libisl22 libitm1 liblsan0 libmpc3 libmpfr6 libperl5.30 libpython3-dev
  libpython3.8 libpython3.8-dev libquadmath0 libstdc++-9-dev libtsan0
  libubsan1 linux-libc-dev make patch perl perl-modules-5.30 swig swig4.0
0 upgraded, 47 newly installed, 0 to remove and 23 not upgraded.
Need to get 51.6 MB of archives.
After this operation, 250 MB of additional disk space will be used.
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Get:4 http://archive.ubuntu.com/ubuntu focal/main amd64 libperl5.30 amd64 5.30.0-9build1 [3,943 kB]
Get:5 http://archive.ubuntu.com/ubuntu focal/main amd64 perl amd64 5.30.0-9build1 [224 kB]
Get:6 http://archive.ubuntu.com/ubuntu focal/main amd64 binutils-common amd64 2.34-6ubuntu1 [207 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal/main amd64 libbinutils amd64 2.34-6ubuntu1 [474 kB]
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Get:25 http://archive.ubuntu.com/ubuntu focal/main amd64 libatomic1 amd64 10-20200411-0ubuntu1 [9,284 B]
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Get:27 http://archive.ubuntu.com/ubuntu focal/main amd64 liblsan0 amd64 10-20200411-0ubuntu1 [144 kB]
Get:28 http://archive.ubuntu.com/ubuntu focal/main amd64 libtsan0 amd64 10-20200411-0ubuntu1 [319 kB]
Get:29 http://archive.ubuntu.com/ubuntu focal/main amd64 libubsan1 amd64 10-20200411-0ubuntu1 [136 kB]
Get:30 http://archive.ubuntu.com/ubuntu focal/main amd64 libquadmath0 amd64 10-20200411-0ubuntu1 [146 kB]
Get:31 http://archive.ubuntu.com/ubuntu focal/main amd64 libgcc-9-dev amd64 9.3.0-10ubuntu2 [2,359 kB]
Get:32 http://archive.ubuntu.com/ubuntu focal/main amd64 gcc-9 amd64 9.3.0-10ubuntu2 [8,234 kB]
Get:33 http://archive.ubuntu.com/ubuntu focal/main amd64 gcc amd64 4:9.3.0-1ubuntu2 [5,208 B]
Get:34 http://archive.ubuntu.com/ubuntu focal/main amd64 libstdc++-9-dev amd64 9.3.0-10ubuntu2 [1,711 kB]
Get:35 http://archive.ubuntu.com/ubuntu focal/main amd64 g++-9 amd64 9.3.0-10ubuntu2 [8,404 kB]
Get:36 http://archive.ubuntu.com/ubuntu focal/main amd64 g++ amd64 4:9.3.0-1ubuntu2 [1,604 B]
Get:37 http://archive.ubuntu.com/ubuntu focal/main amd64 make amd64 4.2.1-1.2 [162 kB]
Get:38 http://archive.ubuntu.com/ubuntu focal/main amd64 libdpkg-perl all 1.19.7ubuntu3 [230 kB]
Get:39 http://archive.ubuntu.com/ubuntu focal/main amd64 patch amd64 2.7.6-6 [105 kB]
Get:40 http://archive.ubuntu.com/ubuntu focal/main amd64 dpkg-dev all 1.19.7ubuntu3 [679 kB]
Get:41 http://archive.ubuntu.com/ubuntu focal/main amd64 build-essential amd64 12.8ubuntu1 [4,624 B]
Get:42 http://archive.ubuntu.com/ubuntu focal/main amd64 libexpat1-dev amd64 2.2.9-1build1 [116 kB]
Get:43 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8 amd64 3.8.2-1ubuntu1.2 [1,620 kB]
Get:44 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-dev amd64 3.8.2-1ubuntu1.2 [3,940 kB]
Get:45 http://archive.ubuntu.com/ubuntu focal/main amd64 libpython3-dev amd64 3.8.2-0ubuntu2 [7,236 B]
Get:46 http://archive.ubuntu.com/ubuntu focal/universe amd64 swig4.0 amd64 4.0.1-5build1 [1,081 kB]
Get:47 http://archive.ubuntu.com/ubuntu focal/universe amd64 swig all 4.0.1-5build1 [5,528 B]
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Setting up g++ (4:9.3.0-1ubuntu2) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/c++.1.gz because associated file /usr/share/man/man1/g++.1.gz (of link group c++) doesn't exist
Setting up build-essential (12.8ubuntu1) ...
Processing triggers for libc-bin (2.31-0ubuntu9) ...
Collecting openbabel
  Downloading openbabel-3.1.1.1.tar.gz (82 kB)
Building wheels for collected packages: openbabel
  Building wheel for openbabel (setup.py): started
  Building wheel for openbabel (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kvretdmq/openbabel/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kvretdmq/openbabel/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-bwouv2mb
       cwd: /tmp/pip-install-kvretdmq/openbabel/
  Complete output (66 lines):
  running bdist_wheel
  running build
  running build_ext
  Warning: invalid version number '3.1.1.1'.
  Guessing Open Babel location:
  - include_dirs: ['/usr/include/python3.8', '/usr/local/include/openbabel3']
  - library_dirs: ['/usr/local/lib']
  building 'openbabel._openbabel' extension
  swigging openbabel/openbabel-python.i to openbabel/openbabel-python_wrap.cpp
  swig -python -c++ -small -O -templatereduce -naturalvar -I/usr/include/python3.8 -I/usr/local/include/openbabel3 -o openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i
  openbabel/openbabel-python.i:246: Error: Unable to find 'openbabel/babelconfig.h'
  openbabel/openbabel-python.i:248: Error: Unable to find 'openbabel/data.h'
  openbabel/openbabel-python.i:249: Error: Unable to find 'openbabel/obutil.h'
  openbabel/openbabel-python.i:250: Error: Unable to find 'openbabel/math/vector3.h'
  openbabel/openbabel-python.i:252: Error: Unable to find 'openbabel/math/matrix3x3.h'
  openbabel/openbabel-python.i:253: Error: Unable to find 'openbabel/math/transform3d.h'
  openbabel/openbabel-python.i:254: Error: Unable to find 'openbabel/math/spacegroup.h'
  openbabel/openbabel-python.i:256: Error: Unable to find 'openbabel/bitvec.h'
  openbabel/openbabel-python.i:260: Error: Unable to find 'openbabel/base.h'
  openbabel/openbabel-python.i:262: Error: Unable to find 'openbabel/generic.h'
  openbabel/openbabel-python.i:265: Error: Unable to find 'openbabel/griddata.h'
  openbabel/openbabel-python.i:267: Error: Unable to find 'openbabel/chains.h'
  openbabel/openbabel-python.i:268: Error: Unable to find 'openbabel/typer.h'
  openbabel/openbabel-python.i:276: Error: Unable to find 'openbabel/plugin.h'
  openbabel/openbabel-python.i:281: Error: Unable to find 'openbabel/oberror.h'
  openbabel/openbabel-python.i:282: Error: Unable to find 'openbabel/format.h'
  openbabel/openbabel-python.i:283: Error: Unable to find 'openbabel/obconversion.h'
  openbabel/openbabel-python.i:284: Error: Unable to find 'openbabel/obfunctions.h'
  openbabel/openbabel-python.i:295: Error: Unable to find 'openbabel/elements.h'
  openbabel/openbabel-python.i:296: Error: Unable to find 'openbabel/residue.h'
  openbabel/openbabel-python.i:297: Error: Unable to find 'openbabel/internalcoord.h'
  openbabel/openbabel-python.i:298: Error: Unable to find 'openbabel/atom.h'
  openbabel/openbabel-python.i:299: Error: Unable to find 'openbabel/bond.h'
  openbabel/openbabel-python.i:300: Error: Unable to find 'openbabel/reaction.h'
  openbabel/openbabel-python.i:301: Error: Unable to find 'openbabel/reactionfacade.h'
  openbabel/openbabel-python.i:319: Error: Unable to find 'openbabel/mol.h'
  openbabel/openbabel-python.i:326: Error: Unable to find 'openbabel/ring.h'
  openbabel/openbabel-python.i:327: Error: Unable to find 'openbabel/parsmart.h'
  openbabel/openbabel-python.i:328: Error: Unable to find 'openbabel/alias.h'
  openbabel/openbabel-python.i:330: Error: Unable to find 'openbabel/fingerprint.h'
  openbabel/openbabel-python.i:332: Error: Unable to find 'openbabel/descriptor.h'
  openbabel/openbabel-python.i:343: Error: Unable to find 'openbabel/forcefield.h'
  openbabel/openbabel-python.i:345: Error: Unable to find 'openbabel/builder.h'
  openbabel/openbabel-python.i:346: Error: Unable to find 'openbabel/op.h'
  openbabel/openbabel-python.i:348: Error: Unable to find 'openbabel/chargemodel.h'
  openbabel/openbabel-python.i:351: Error: Unable to find 'openbabel/phmodel.h'
  openbabel/openbabel-python.i:352: Error: Unable to find 'openbabel/graphsym.h'
  openb  Running setup.py clean for openbabel
abel/openbabel-python.i:353: Error: Unable to find 'openbabel/isomorphism.h'
  openbabel/openbabel-python.i:354: Error: Unable to find 'openbabel/query.h'
  openbabel/openbabel-python.i:355: Error: Unable to find 'openbabel/canon.h'
  openbabel/openbabel-python.i:357: Error: Unable to find 'openbabel/stereo/stereo.h'
  openbabel/openbabel-python.i:361: Error: Unable to find 'openbabel/rotor.h'
  openbabel/openbabel-python.i:363: Error: Unable to find 'openbabel/rotamer.h'
  openbabel/openbabel-python.i:364: Error: Unable to find 'openbabel/spectrophore.h'
  openbabel/openbabel-python.i:435: Error: Unable to find 'openbabel/obiter.h'
  openbabel/stereo.i:1: Error: Unable to find 'openbabel/stereo/tetranonplanar.h'
  openbabel/stereo.i:2: Error: Unable to find 'openbabel/stereo/tetraplanar.h'
  openbabel/stereo.i:3: Error: Unable to find 'openbabel/stereo/tetrahedral.h'
  openbabel/stereo.i:4: Error: Unable to find 'openbabel/stereo/cistrans.h'
  openbabel/stereo.i:5: Error: Unable to find 'openbabel/stereo/squareplanar.h'
  openbabel/stereo.i:6: Error: Unable to find 'openbabel/stereo/bindings.h'
  
  Error: SWIG failed. Is Open Babel installed?
  You may need to manually specify the location of Open Babel include and library directories. For example:
    python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib
    python setup.py install
  ----------------------------------------
  ERROR: Failed building wheel for openbabel
Failed to build openbabel
Installing collected packages: openbabel
    Running setup.py install for openbabel: started
    Running setup.py install for openbabel: finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kvretdmq/openbabel/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kvretdmq/openbabel/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-v73bgpul/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.8/openbabel
         cwd: /tmp/pip-install-kvretdmq/openbabel/
    Complete output (65 lines):
    running install
    running build_ext
    Warning: invalid version number '3.1.1.1'.
    Guessing Open Babel location:
    - include_dirs: ['/usr/include/python3.8', '/usr/local/include/openbabel3']
    - library_dirs: ['/usr/local/lib']
    building 'openbabel._openbabel' extension
    swigging openbabel/openbabel-python.i to openbabel/openbabel-python_wrap.cpp
    swig -python -c++ -small -O -templatereduce -naturalvar -I/usr/include/python3.8 -I/usr/local/include/openbabel3 -o openbabel/openbabel-python_wrap.cpp openbabel/openbabel-python.i
    openbabel/openbabel-python.i:246: Error: Unable to find 'openbabel/babelconfig.h'
    openbabel/openbabel-python.i:248: Error: Unable to find 'openbabel/data.h'
    openbabel/openbabel-python.i:249: Error: Unable to find 'openbabel/obutil.h'
    openbabel/openbabel-python.i:250: Error: Unable to find 'openbabel/math/vector3.h'
    openbabel/openbabel-python.i:252: Error: Unable to find 'openbabel/math/matrix3x3.h'
    openbabel/openbabel-python.i:253: Error: Unable to find 'openbabel/math/transform3d.h'
    openbabel/openbabel-python.i:254: Error: Unable to find 'openbabel/math/spacegroup.h'
    openbabel/openbabel-python.i:256: Error: Unable to find 'openbabel/bitvec.h'
    openbabel/openbabel-python.i:260: Error: Unable to find 'openbabel/base.h'
    openbabel/openbabel-python.i:262: Error: Unable to find 'openbabel/generic.h'
    openbabel/openbabel-python.i:265: Error: Unable to find 'openbabel/griddata.h'
    openbabel/openbabel-python.i:267: Error: Unable to find 'openbabel/chains.h'
    openbabel/openbabel-python.i:268: Error: Unable to find 'openbabel/typer.h'
    openbabel/openbabel-python.i:276: Error: Unable to find 'openbabel/plugin.h'
    openbabel/openbabel-python.i:281: Error: Unable to find 'openbabel/oberror.h'
    openbabel/openbabel-python.i:282: Error: Unable to find 'openbabel/format.h'
    openbabel/openbabel-python.i:283: Error: Unable to find 'openbabel/obconversion.h'
    openbabel/openbabel-python.i:284: Error: Unable to find 'openbabel/obfunctions.h'
    openbabel/openbabel-python.i:295: Error: Unable to find 'openbabel/elements.h'
    openbabel/openbabel-python.i:296: Error: Unable to find 'openbabel/residue.h'
    openbabel/openbabel-python.i:297: Error: Unable to find 'openbabel/internalcoord.h'
    openbabel/openbabel-python.i:298: Error: Unable to find 'openbabel/atom.h'
    openbabel/openbabel-python.i:299: Error: Unable to find 'openbabel/bond.h'
    openbabel/openbabel-python.i:300: Error: Unable to find 'openbabel/reaction.h'
    openbabel/openbabel-python.i:301: Error: Unable to find 'openbabel/reactionfacade.h'
    openbabel/openbabel-python.i:319: Error: Unable to find 'openbabel/mol.h'
    openbabel/openbabel-python.i:326: Error: Unable to find 'openbabel/ring.h'
    openbabel/openbabel-python.i:327: Error: Unable to find 'openbabel/parsmart.h'
    openbabel/openbabel-python.i:328: Error: Unable to find 'openbabel/alias.h'
    openbabel/openbabel-python.i:330: Error: Unable to find 'openbabel/fingerprint.h'
    openbabel/openbabel-python.i:332: Error: Unable to find 'openbabel/descriptor.h'
    openbabel/openbabel-python.i:343: Error: Unable to find 'openbabel/forcefield.h'
    openbabel/openbabel-python.i:345: Error: Unable to find 'openbabel/builder.h'
    openbabel/openbabel-python.i:346: Error: Unable to find 'openbabel/op.h'
    openbabel/openbabel-python.i:348: Error: Unable to find 'openbabel/chargemodel.h'
    openbabel/openbabel-python.i:351: Error: Unable to find 'openbabel/phmodel.h'
    openbabel/openbabel-python.i:352: Error: Unable to find 'openbabel/graphsym.h'
    openbabel/openbabel-python.i:353: Error: Unable to find 'openbabel/isomorphism.h'
    openbabel/openbabel-python.i:354: Error: Unable to find 'openbabel/query.h'
    openbabel/openbabel-python.i:355: Error: Unable to find 'openbabel/canon.h'
    openbabel/openbabel-python.i:357: Error: Unable to find 'openbabel/stereo/stereo.h'
    openbabel/openbabel-python.i:361: Error: Unable to find 'openbabel/rotor.h'
    openbabel/openbabel-python.i:363: Error: Unable to find 'openbabel/rotamer.h'
    openbabel/openbabel-python.i:364: Error: Unable to find 'openbabel/spectrophore.h'
    openbabel/openbabel-python.i:435: Error: Unable to find 'openbabel/obiter.h'
    openbabel/stereo.i:1: Error: Unable to find 'openbabel/stereo/tetranonplanar.h'
    openbabel/stereo.i:2: Error: Unable to find 'openbabel/stereo/tetraplanar.h'
    openbabel/stereo.i:3: Error: Unable to find 'openbabel/stereo/tetrahedral.h'
    openbabel/stereo.i:4: Error: Unable to find 'openbabel/stereo/cistrans.h'
    openbabel/stereo.i:5: Error: Unable to find 'openbabel/stereo/squareplanar.h'
    openbabel/stereo.i:6: Error: Unable to find 'openbabel/stereo/bindings.h'
    
    Error: SWIG failed. Is Open Babel installed?
    You may need to manually specify the location of Open Babel include and library directories. For example:
      python setup.py build_ext -I/usr/local/include/openbabel3 -L/usr/local/lib
      python setup.py install
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-kvretdmq/openbabel/setup.py'"'"'; __file__='"'"'/tmp/pip-install-kvretdmq/openbabel/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-v73bgpul/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/python3.8/openbabel Check the logs for full command output.
The command '/bin/sh -c apt-get update -y     && apt-get install --no-install-recommends -y         build-essential         libpython3-dev         swig         && pip3 install openbabel         && apt-get remove -y           build-essential           libpython3-dev           swig     && apt-get autoremove -y     && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 1
paul@paul-VirtualBox:/media/sf_DPhil_Project/Project05_WCM/bpforms$

[jonrkarr]

This is breaking due to a new version of the open babel python binding. The open babel requirement needs to be set to openbabel < 3 in requirements.txt.

[paulflang]

Thanks. I needed to make a few minor other changes, too, but it runs now on my machine.