Issues with building AFNI neurodocker #673

jankaWIS · 2025-04-23T15:47:27Z

Hi,

I have had a few issues with trying to create and build neurodocker container with AFNI. I'm new to neurodocker, so I don't know if maybe I'm doing something wrong and what is or isn't relevant, so I will try to be concise.

I followed the protocol at https://www.repronim.org/neurodocker/user_guide/examples.html, and while the first method worked, the second, which also installs R packages, failed. The initial command worked:

neurodocker generate docker \
    --pkg-manager yum \
    --base-image fedora:40 \
    --afni method=binaries version=latest install_r_pkgs=true \
> afni-binaries-r.Dockerfile

but the build failed after about 40 mins of building (I had to cut some of the output for size limitations):

docker build --tag afni:latest-with-r --file afni-binaries-r.Dockerfile .
[+] Building 2816.3s (6/7)                                                                                                                  docker:desktop-linux
 => [internal] load build definition from afni-binaries-r.Dockerfile                                                                                        0.0s
 => => transferring dockerfile: 5.83kB                                                                                                                      0.0s
 => [internal] load metadata for docker.io/library/fedora:40                                                                                                1.3s
 => [internal] load .dockerignore                                                                                                                           0.0s
 => => transferring context: 2B                                                                                                                             0.0s
 => [1/4] FROM docker.io/library/fedora:40@sha256:3c86d25fef9d2001712bc3d9b091fc40cf04be4767e48f1aa3b785bf58d300ed                                          0.0s
 => => resolve docker.io/library/fedora:40@sha256:3c86d25fef9d2001712bc3d9b091fc40cf04be4767e48f1aa3b785bf58d300ed                                          0.0s
 => CACHED [2/4] RUN export ND_ENTRYPOINT="/neurodocker/startup.sh"     && if ls /etc/yum.repos.d/CentOS-* >/dev/null 2>&1; then            sed -i 's/mirr  0.0s
 => ERROR [3/4] RUN yum install -y -q            R            cmake            curl            ed            gsl            libGLU            libXp      2814.9s
------                                                                                                                                                           
 > [3/4] RUN yum install -y -q            R            cmake            curl            ed            gsl            libGLU            libXp            libXpm            libcurl-devel            libgomp            libjpeg-turbo-devel            libpng12            mesa-dri-drivers            mesa-dri-drivers            mesa-libGLw            ncurses-compat-libs            netpbm-progs            openmotif            openssl-devel            python-is-python3            python3-pip            tcsh            udunits2-devel            unzip            wget            which            which            xorg-x11-fonts-misc            xorg-x11-server-Xvfb     && yum clean all     && rm -rf /var/cache/yum/*     && gsl_path="$(find / -name 'libgsl.so.??' || printf '')"     && if [ -n "$gsl_path" ]; then          ln -sfv "$gsl_path" "$(dirname $gsl_path)/libgsl.so.0";     fi     && ldconfig     && mkdir -p /opt/afni-latest     && echo "Downloading AFNI ..."     && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar -xz -C /opt/afni-latest --strip-components 1     &&   yum install -y -q            R-devel     && yum clean all     && rm -rf /var/cache/yum/*     &&   rPkgsInstall -pkgs ALL:
528.2 
528.2 Upgraded:
528.2   elfutils-libelf-0.192-9.fc40.aarch64    elfutils-libs-0.192-9.fc40.aarch64   
528.2   gnutls-3.8.9-1.fc40.aarch64             libxcrypt-4.4.38-7.fc40.aarch64      
528.2   openssl-libs-1:3.2.4-1.fc40.aarch64     python3-3.12.9-3.fc40.aarch64        
528.2   python3-libs-3.12.9-3.fc40.aarch64     
528.2 Installed:
528.2   ModemManager-glib-1.22.0-3.fc40.aarch64                                       
528.2   NetworkManager-libnm-1:1.46.6-1.fc40.aarch64                                  
528.2   R-4.4.3-1.fc40.aarch64                                                        
528.2   R-core-4.4.3-1.fc40.aarch64                                                   
528.2   R-core-devel-4.4.3-1.fc40.aarch64                                             
528.2   R-devel-4.4.3-1.fc40.aarch64                                                  
528.2   R-java-4.4.3-1.fc40.aarch64                                                   
528.2   R-java-devel-4.4.3-1.fc40.aarch64                                             
528.2   R-rpm-macros-1.2.1-10.fc40.noarch                                             
528.2   abattis-cantarell-vf-fonts-0.301-12.fc40.noarch       
                        
...

528.3 
528.4 17 files removed
528.5 '/usr/lib64/libgsl.so.0' -> '/usr/lib64/libgsl.so.27'
528.5 Downloading AFNI ...
528.5   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
528.5                                  Dload  Upload   Total   Spent    Left  Speed
100 1080M  100 1080M    0     0   487k      0  0:37:51  0:37:51 --:--:--  649k
2814.7 17 files removed
2814.8 
2814.8 oo Warning: 
2814.8    Failed to load R_io.so with this error message: 
2814.8  /opt/afni-latest/R_io.so
2814.8 Error in dyn.load(ll) : 
2814.8   unable to load shared object '/opt/afni-latest/R_io.so':
2814.8   /opt/afni-latest/R_io.so: cannot open shared object file: No such file or directory
2814.8 Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
2814.8 Execution halted
------
afni-binaries-r.Dockerfile:32
--------------------
  31 |         AFNI_PLUGINPATH="/opt/afni-latest"
  32 | >>> RUN yum install -y -q \
  33 | >>>            R \
  34 | >>>            cmake \
  35 | >>>            curl \
  36 | >>>            ed \
  37 | >>>            gsl \
  38 | >>>            libGLU \
  39 | >>>            libXp \
  40 | >>>            libXpm \
  41 | >>>            libcurl-devel \
  42 | >>>            libgomp \
  43 | >>>            libjpeg-turbo-devel \
  44 | >>>            libpng12 \
  45 | >>>            mesa-dri-drivers \
  46 | >>>            mesa-dri-drivers \
  47 | >>>            mesa-libGLw \
  48 | >>>            ncurses-compat-libs \
  49 | >>>            netpbm-progs \
  50 | >>>            openmotif \
  51 | >>>            openssl-devel \
  52 | >>>            python-is-python3 \
  53 | >>>            python3-pip \
  54 | >>>            tcsh \
  55 | >>>            udunits2-devel \
  56 | >>>            unzip \
  57 | >>>            wget \
  58 | >>>            which \
  59 | >>>            which \
  60 | >>>            xorg-x11-fonts-misc \
  61 | >>>            xorg-x11-server-Xvfb \
  62 | >>>     && yum clean all \
  63 | >>>     && rm -rf /var/cache/yum/* \
  64 | >>>     && gsl_path="$(find / -name 'libgsl.so.??' || printf '')" \
  65 | >&
8000
gt;>     && if [ -n "$gsl_path" ]; then \
  66 | >>>          ln -sfv "$gsl_path" "$(dirname $gsl_path)/libgsl.so.0"; \
  67 | >>>     fi \
  68 | >>>     && ldconfig \
  69 | >>>     && mkdir -p /opt/afni-latest \
  70 | >>>     && echo "Downloading AFNI ..." \
  71 | >>>     && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
  72 | >>>     | tar -xz -C /opt/afni-latest --strip-components 1 \
  73 | >>>     &&   yum install -y -q \
  74 | >>>            R-devel \
  75 | >>>     && yum clean all \
  76 | >>>     && rm -rf /var/cache/yum/* \
  77 | >>>     &&   rPkgsInstall -pkgs ALL
  78 |     ENTRYPOINT ["/neurodocker/startup.sh"]
--------------------
ERROR: failed to solve: process "/bin/sh -c yum install -y -q            R            cmake            curl            ed            gsl            libGLU            libXp            libXpm            libcurl-devel            libgomp            libjpeg-turbo-devel            libpng12            mesa-dri-drivers            mesa-dri-drivers            mesa-libGLw            ncurses-compat-libs            netpbm-progs            openmotif            openssl-devel            python-is-python3            python3-pip            tcsh            udunits2-devel            unzip            wget            which            which            xorg-x11-fonts-misc            xorg-x11-server-Xvfb     && yum clean all     && rm -rf /var/cache/yum/*     && gsl_path=\"$(find / -name 'libgsl.so.??' || printf '')\"     && if [ -n \"$gsl_path\" ]; then          ln -sfv \"$gsl_path\" \"$(dirname $gsl_path)/libgsl.so.0\";     fi     && ldconfig     && mkdir -p /opt/afni-latest     && echo \"Downloading AFNI ...\"     && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar -xz -C /opt/afni-latest --strip-components 1     &&   yum install -y -q            R-devel     && yum clean all     && rm -rf /var/cache/yum/*     &&   rPkgsInstall -pkgs ALL" did not complete successfully: exit code: 1

I was unable to run neurodocker with specifying AFNI version, e.g.:

neurodocker generate docker \
    --pkg-manager yum \
    --base-image fedora:40 \
    --afni method=binaries version=25.1.03 \
> version.Dockerfile

Traceback (most recent call last):
  File "/opt/anaconda3/lib/python3.11/site-packages/neurodocker/reproenv/renderers.py", line 76, in _render_string_from_template
    source = tmpl.render(template=template)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/jinja2/environment.py", line 1301, in render
    self.environment.handle_exception()
  File "/opt/anaconda3/lib/python3.11/site-packages/jinja2/environment.py", line 936, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "<template>", line 13, in top-level template code
jinja2.exceptions.UndefinedError: 'dict object' has no attribute '25.1.03'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/anaconda3/bin/neurodocker", line 8, in <module>
    sys.exit(cli())
             ^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/neurodocker/cli/generate.py", line 478, in docker
    _base_generate(
  File "/opt/anaconda3/lib/python3.11/site-packages/neurodocker/cli/generate.py", line 455, in _base_generate
    r = renderer.from_dict(renderer_dict)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/neurodocker/reproenv/renderers.py", line 212, in from_dict
    renderer.add_registered_template(method_or_template, **kwds)
  File "/opt/anaconda3/lib/python3.11/site-packages/neurodocker/reproenv/renderers.py", line 364, in add_registered_template
    self.add_template(template=template, method=method)
  File "/opt/anaconda3/lib/python3.11/site-packages/neurodocker/reproenv/renderers.py", line 328, in add_template
    command = _render_string_from_template(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/site-packages/neurodocker/reproenv/renderers.py", line 78, in _render_string_from_template
    raise RendererError(err) from e
neurodocker.reproenv.exceptions.RendererError: A template included in this renderer raised an error. Please check the template definition. A required argument might not be included in the required arguments part of the template. Variables in the template should start with `self.`.

Maybe similar to this issue, AFNI out of date in distributed version, and maybe its build is broken? #662. I first tried building it with Ubuntu 22.04 and 24.04. The first issue is that it fails on multiarch-support, so the file generation is fine:

neurodocker generate docker \
  --pkg-manager apt \
  --base-image ubuntu:22.04 \
  --afni version=latest \
  --miniconda version=latest \
    env_name=neuro \
    conda_install='python=3.11 nipype nilearn pandas matplotlib' \
  --user=neuro \
  > Dockerfile_neurodocker

but the build failed on:

  76 | >>>     | tar -xz -C /opt/afni-latest --strip-components 1
  77 |     ENV CONDA_DIR="/opt/miniconda-latest" \
--------------------
ERROR: failed to solve: process "/bin/sh -c apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            curl            ed            gsl-bin            libcurl4-openssl-dev            libgl1-mesa-dri            libglib2.0-0            libglu1-mesa-dev            libglw1-mesa            libgomp1            libjpeg-turbo8-dev            libjpeg62            libssl-dev            libudunits2-dev            libxm4            multiarch-support            netpbm            python-is-python3            python3-pip            tcsh            xfonts-base            xvfb     && rm -rf /var/lib/apt/lists/*     && _reproenv_tmppath=\"$(mktemp -t tmp.XXXXXXXXXX.deb)\"     && curl -fsSL --retry 5 -o \"${_reproenv_tmppath}\" http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb     && apt-get install --yes -q \"${_reproenv_tmppath}\"     && rm \"${_reproenv_tmppath}\"     && _reproenv_tmppath=\"$(mktemp -t tmp.XXXXXXXXXX.deb)\"     && curl -fsSL --retry 5 -o \"${_reproenv_tmppath}\" http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb     && apt-get install --yes -q \"${_reproenv_tmppath}\"     && rm \"${_reproenv_tmppath}\"     && apt-get update -qq     && apt-get install --yes --quiet --fix-missing     && rm -rf /var/lib/apt/lists/*     && gsl_path=\"$(find / -name 'libgsl.so.??' || printf '')\"     && if [ -n \"$gsl_path\" ]; then          ln -sfv \"$gsl_path\" \"$(dirname $gsl_path)/libgsl.so.0\";     fi     && ldconfig     && mkdir -p /opt/afni-latest     && echo \"Downloading AFNI ...\"     && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar -xz -C /opt/afni-latest --strip-components 1" did not complete successfully: exit code: 100

This can be fixed by removing the multiarch-support flag from the build file but when you do that, it fails on yet another thing - curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz which is the reason it might be related to the other issue I mentioned.

 82 | >>>     &&   rPkgsInstall -pkgs ALL
  83 |     ENV CONDA_DIR="/opt/miniconda-latest" \
--------------------
ERROR: failed to solve: process "/bin/sh -c apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            curl            ed            gsl-bin            libcurl4-openssl-dev            libgl1-mesa-dri            libglib2.0-0            libglu1-mesa-dev            libglw1-mesa            libgomp1            libjpeg-turbo8-dev            libjpeg62            libssl-dev            libudunits2-dev            libxm4            netpbm            python-is-python3            python3-pip            tcsh            xfonts-base            xvfb     && rm -rf /var/lib/apt/lists/*     && _reproenv_tmppath=\"$(mktemp -t tmp.XXXXXXXXXX.deb)\"     && curl -fsSL --retry 5 -o \"${_reproenv_tmppath}\" http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb     && apt-get install --yes -q \"${_reproenv_tmppath}\"     && rm \"${_reproenv_tmppath}\"     && _reproenv_tmppath=\"$(mktemp -t tmp.XXXXXXXXXX.deb)\"     && curl -fsSL --retry 5 -o \"${_reproenv_tmppath}\" http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb     && apt-get install --yes -q \"${_reproenv_tmppath}\"     && rm \"${_reproenv_tmppath}\"     && apt-get update -qq     && apt-get install --yes --quiet --fix-missing     && rm -rf /var/lib/apt/lists/*     && gsl_path=\"$(find / -name 'libgsl.so.??' || printf '')\"     && if [ -n \"$gsl_path\" ]; then          ln -sfv \"$gsl_path\" \"$(dirname $gsl_path)/libgsl.so.0\";     fi     && ldconfig     && mkdir -p /opt/afni-latest     && echo \"Downloading AFNI ...\"     && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar -xz -C /opt/afni-latest --strip-components 1     &&   apt-get update -qq     && apt-get install -y -q --no-install-recommends            libnlopt-dev            r-base            r-base-dev     && rm -rf /var/lib/apt/lists/*     &&   rPkgsInstall -pkgs ALL" did not complete successfully: exit code: 22

I didn't manage to get any further than that, and I'd welcome any tips and advice on how to proceed.

Thanks for helping.

The text was updated successfully, but these errors were encountered:

jankaWIS changed the title ~~Issues with building neurodocker AFNI~~ Issues with building AFNI neurodocker Apr 23, 2025

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Issues with building AFNI neurodocker #673

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Issues with building AFNI neurodocker #673

Issues with building AFNI neurodocker #673

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