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AFNI docker build fails #478

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spurani opened this issue Nov 22, 2022 · 18 comments
Closed

AFNI docker build fails #478

spurani opened this issue Nov 22, 2022 · 18 comments
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AFNI stale

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@spurani
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spurani commented Nov 22, 2022 

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:buster-slim \
    --afni method=binaries version=latest \
> afni-binaries.Dockerfile

This command successfully generated the dockerfile
Here is the dockerfile

# Generated by Neurodocker and Reproenv.

FROM debian:buster-slim
ENV PATH="/opt/afni-latest:$PATH" \
    AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ca-certificates \
           cmake \
           curl \
           ed \
           gsl-bin \
           libcurl4-openssl-dev \
           libgl1-mesa-dri \
           libglib2.0-0 \
           libglu1-mesa-dev \
           libglw1-mesa \
           libgomp1 \
           libjpeg-turbo8-dev \
           libjpeg62 \
           libssl-dev \
           libudunits2-dev \
           libxm4 \
           multiarch-support \
           netpbm \
           python-is-python3 \
           python3-pip \
           tcsh \
           xfonts-base \
           xvfb \
    && rm -rf /var/lib/apt/lists/* \
    && _reproenv_tmppath="$(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

# Save specification to JSON.
RUN printf '{ \
  "pkg_manager": "apt", \
  "existing_users": [ \
    "root" \
  ], \
  "instructions": [ \
    { \
      "name": "from_", \
      "kwds": { \
        "base_image": "debian:buster-slim" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "PATH": "/opt/afni-latest:$PATH", \
        "AFNI_PLUGINPATH": "/opt/afni-latest" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    ca-certificates \\\\\\n    cmake \\\\\\n    curl \\\\\\n    ed \\\\\\n    gsl-bin \\\\\\n    libcurl4-openssl-dev \\\\\\n    libgl1-mesa-dri \\\\\\n    libglib2.0-0 \\\\\\n    libglu1-mesa-dev \\\\\\n    libglw1-mesa \\\\\\n    libgomp1 \\\\\\n    libjpeg-turbo8-dev \\\\\\n    libjpeg62 \\\\\\n    libssl-dev \\\\\\n    libudunits2-dev \\\\\\n    libxm4 \\\\\\n    multiarch-support \\\\\\n    netpbm \\\\\\n    python-is-python3 \\\\\\n    python3-pip \\\\\\n    tcsh \\\\\\n    xfonts-base \\\\\\n    xvfb\\nrm -rf /var/lib/apt/lists/*\\n_reproenv_tmppath=\\"$\(mktemp -t tmp.XXXXXXXXXX.deb\)\\"\\ncurl -fsSL --retry 5 -o \\"${_reproenv_tmppath}\\" http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb\\napt-get install --yes -q \\"${_reproenv_tmppath}\\"\\nrm \\"${_reproenv_tmppath}\\"\\n_reproenv_tmppath=\\"$\(mktemp -t tmp.XXXXXXXXXX.deb\)\\"\\ncurl -fsSL --retry 5 -o \\"${_reproenv_tmppath}\\" http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%%2Bdeb7u2_amd64.deb\\napt-get install --yes -q \\"${_reproenv_tmppath}\\"\\nrm \\"${_reproenv_tmppath}\\"\\napt-get update -qq\\napt-get install --yes --quiet --fix-missing\\nrm -rf /var/lib/apt/lists/*\\n\\ngsl_path=\\"$\(find / -name '"'"'libgsl.so.??'"'"' || printf '"'"''"'"'\)\\"\\nif [ -n \\"$gsl_path\\" ]; then \\\\\\n  ln -sfv \\"$gsl_path\\" \\"$\(dirname $gsl_path\)/libgsl.so.0\\"; \\\\\\nfi\\nldconfig\\nmkdir -p /opt/afni-latest\\necho \\"Downloading AFNI ...\\"\\ncurl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \\\\\\n| tar -xz -C /opt/afni-latest --strip-components 1" \
      } \
    } \
  ] \
}' > /.reproenv.json
# End saving to specification to JSON.

docker build --tag afni:latest --file afni-binaries.Dockerfile .
This commad fails with the below error

[+] Building 3.3s (5/6)
 => [internal] load build definition from afni-binaries.Dockerfile                                                 0.0s
 => => transferring dockerfile: 4.34kB                                                                             0.0s
 => [internal] load .dockerignore                                                                                  0.0s
 => => transferring context: 2B                                                                                    0.0s
 => [internal] load metadata for docker.io/library/debian:buster-slim                                              2.6s
 => CACHED [1/3] FROM docker.io/library/debian:buster-slim@sha256:5dbce817ee72802025a38a388237b0ea576aa164bc90b71  0.0s
 => ERROR [2/3] RUN apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certifi  0.5s
------
 > [2/3] RUN 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 $gsl_path)/libgsl.so.0";     fi     && ldconfig     && mkdir -p /opt/afni-latest     && echo "Downloading AFNI ..."     && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar -xz -C /opt/afni-latest --strip-components 1:
#5 0.495 /bin/sh: 1: Syntax error: "&&" unexpected
------
executor failed running [/bin/sh -c apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            curl            ed            gsl-bin            libcurl4-openssl-dev            libgl1-mesa-dri            libglib2.0-0            libglu1-mesa-dev            libglw1-mesa            libgomp1            libjpeg-turbo8-dev            libjpeg62            libssl-dev            libudunits2-dev            libxm4            multiarch-support            netpbm            python-is-python3            python3-pip            tcsh            xfonts-base            xvfb     && rm -rf /var/lib/apt/lists/*     && _reproenv_tmppath="$(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]: exit code: 2

Can anyone please guide me?
@stebo85
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stebo85 commented Nov 23, 2022

Dear @spurani,

It looks like you are facing a bug that was fixed a few weeks ago. The problem was that the AFNI recipe added an empty line and this is causing the && error.

I submitted a pull request to fix this and it was merged:
stebo85@3da4e04

Can you check if you are using the latest version of Neurodocker and if this fix is included?

Cheers
Steffen

@spurani
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spurani commented Nov 23, 2022

Dear @spurani,

It looks like you are facing a bug that was fixed a few weeks ago. The problem was that the AFNI recipe added an empty line and this is causing the && error.

I submitted a pull request to fix this and it was merged: NeuroDesk@3da4e04

Can you check if you are using the latest version of Neurodocker and if this fix is included?

Cheers Steffen
Hello @stebo85,

Thank you for your quick response. Basically, I installed neurodocker using this command pip install neurodocker and my current version is 0.9.1. Earlier, I tried the preferred installation using docker run --rm repronim/neurodocker:0.7.0 --help it did not install neurodocker nor it gave any errors or warnings. is this page still active and updated repronim/neurodocker Tags? because the last update I see is 3years ago.

@kaczmarj
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thanks @stebo85 and @spurani. looks like we need to cut a new release and upload to pypi and dockerhub.

@djarecka @satra - I do not have permissions to upload to repronim/neurodocker on dockerhub. Can you please give me permissions to do this?

@stebo85
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stebo85 commented Nov 23, 2022

Dear @spurani,

You should be able to install the latest version of Neurodocker via:
pip install --no-cache-dir https://github.com/repronim/neurodocker/tarball/master

and that should include the fix

Cheers
Steffen

@satra
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satra commented Nov 23, 2022

@kaczmarj - sent an invite, but also set up automatic building for this repo (we can add version based building as well). we may have to disconnect you as the org has only 5 seats. we do have a service account that we can use.

@spurani
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spurani commented Nov 24, 2022

Hello @stebo85
Here are the steps I followed

  1. Uninstalled neurodocker pip uninstall neurodocker from my current os environment

  2. Fresh install of Neurodocker pip install --no-cache-dir https://github.com/repronim/neurodocker/tarball/master and generated the Dockerfile with this command

neurodocker --version
neurodocker version 0.9.1

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:stable \
    --afni method=binaries version=latest \
    --fsl version='6.0.5.1' > AFNI_FSL_Dockerfile.Dockerfile

it generated this Dockerfile

# Generated by Neurodocker and Reproenv.

FROM debian:stable
ENV PATH="/opt/afni-latest:$PATH" \
    AFNI_PLUGINPATH="/opt/afni-latest"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           ca-certificates \
           cmake \
           curl \
           ed \
           gsl-bin \
           libcurl4-openssl-dev \
           libgl1-mesa-dri \
           libglib2.0-0 \
           libglu1-mesa-dev \
           libglw1-mesa \
           libgomp1 \
           libjpeg-turbo8-dev \
           libjpeg62 \
           libssl-dev \
           libudunits2-dev \
           libxm4 \
           multiarch-support \
           netpbm \
           python-is-python3 \
           python3-pip \
           tcsh \
           xfonts-base \
           xvfb \
    && rm -rf /var/lib/apt/lists/* \
    && _reproenv_tmppath="$(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 $gsl_path)/libgsl.so.0"; \
    fi \
    && ldconfig \
    && mkdir -p /opt/afni-latest \
    && echo "Downloading AFNI ..." \
    && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
    | tar -xz -C /opt/afni-latest --strip-components 1
ENV FSLDIR="/opt/fsl-6.0.5.1" \
    PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
    FSLOUTPUTTYPE="NIFTI_GZ" \
    FSLMULTIFILEQUIT="TRUE" \
    FSLTCLSH="/opt/fsl-6.0.5.1/bin/fsltclsh" \
    FSLWISH="/opt/fsl-6.0.5.1/bin/fslwish" \
    FSLLOCKDIR="" \
    FSLMACHINELIST="" \
    FSLREMOTECALL="" \
    FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           ca-certificates \
           curl \
           dc \
           file \
           libfontconfig1 \
           libfreetype6 \
           libgl1-mesa-dev \
           libgl1-mesa-dri \
           libglu1-mesa-dev \
           libgomp1 \
           libice6 \
           libopenblas-base \
           libxcursor1 \
           libxft2 \
           libxinerama1 \
           libxrandr2 \
           libxrender1 \
           libxt6 \
           nano \
           sudo \
           wget \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading FSL ..." \
    && mkdir -p /opt/fsl-6.0.5.1 \
    && curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
    | tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
    && echo "Installing FSL conda environment ..." \
    && bash /opt/fsl-6.0.5.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.5.1

# Save specification to JSON.
RUN printf '{ \
  "pkg_manager": "apt", \
  "existing_users": [ \
    "root" \
  ], \
  "instructions": [ \
    { \
      "name": "from_", \
      "kwds": { \
        "base_image": "debian:stable" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "PATH": "/opt/afni-latest:$PATH", \
        "AFNI_PLUGINPATH": "/opt/afni-latest" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    ca-certificates \\\\\\n    cmake \\\\\\n    curl \\\\\\n    ed \\\\\\n    gsl-bin \\\\\\n    libcurl4-openssl-dev \\\\\\n    libgl1-mesa-dri \\\\\\n    libglib2.0-0 \\\\\\n    libglu1-mesa-dev \\\\\\n    libglw1-mesa \\\\\\n    libgomp1 \\\\\\n    libjpeg-turbo8-dev \\\\\\n    libjpeg62 \\\\\\n    libssl-dev \\\\\\n    libudunits2-dev \\\\\\n    libxm4 \\\\\\n    multiarch-support \\\\\\n    netpbm \\\\\\n    python-is-python3 \\\\\\n    python3-pip \\\\\\n    tcsh \\\\\\n    xfonts-base \\\\\\n    xvfb\\nrm -rf /var/lib/apt/lists/*\\n_reproenv_tmppath=\\"$\(mktemp -t tmp.XXXXXXXXXX.deb\)\\"\\ncurl -fsSL --retry 5 -o \\"${_reproenv_tmppath}\\" http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb\\napt-get install --yes -q \\"${_reproenv_tmppath}\\"\\nrm \\"${_reproenv_tmppath}\\"\\n_reproenv_tmppath=\\"$\(mktemp -t tmp.XXXXXXXXXX.deb\)\\"\\ncurl -fsSL --retry 5 -o \\"${_reproenv_tmppath}\\" http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%%2Bdeb7u2_amd64.deb\\napt-get install --yes -q \\"${_reproenv_tmppath}\\"\\nrm \\"${_reproenv_tmppath}\\"\\napt-get update -qq\\napt-get install --yes --quiet --fix-missing\\nrm -rf /var/lib/apt/lists/*\\n\\ngsl_path=\\"$\(find / -name '"'"'libgsl.so.??'"'"' || printf '"'"''"'"'\)\\"\\nif [ -n \\"$gsl_path\\" ]; then \\\\\\n  ln -sfv \\"$gsl_path\\" \\"$\(dirname $gsl_path\)/libgsl.so.0\\"; \\\\\\nfi\\nldconfig\\nmkdir -p /opt/afni-latest\\necho \\"Downloading AFNI ...\\"\\ncurl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \\\\\\n| tar -xz -C /opt/afni-latest --strip-components 1" \
      } \
    }, \
    { \
      "name": "env", \
      "kwds": { \
        "FSLDIR": "/opt/fsl-6.0.5.1", \
        "PATH": "/opt/fsl-6.0.5.1/bin:$PATH", \
        "FSLOUTPUTTYPE": "NIFTI_GZ", \
        "FSLMULTIFILEQUIT": "TRUE", \
        "FSLTCLSH": "/opt/fsl-6.0.5.1/bin/fsltclsh", \
        "FSLWISH": "/opt/fsl-6.0.5.1/bin/fslwish", \
        "FSLLOCKDIR": "", \
        "FSLMACHINELIST": "", \
        "FSLREMOTECALL": "", \
        "FSLGECUDAQ": "cuda.q" \
      } \
    }, \
    { \
      "name": "run", \
      "kwds": { \
        "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n    bc \\\\\\n    ca-certificates \\\\\\n    curl \\\\\\n    dc \\\\\\n    file \\\\\\n    libfontconfig1 \\\\\\n    libfreetype6 \\\\\\n    libgl1-mesa-dev \\\\\\n    libgl1-mesa-dri \\\\\\n    libglu1-mesa-dev \\\\\\n    libgomp1 \\\\\\n    libice6 \\\\\\n    libopenblas-base \\\\\\n    libxcursor1 \\\\\\n    libxft2 \\\\\\n    libxinerama1 \\\\\\n    libxrandr2 \\\\\\n    libxrender1 \\\\\\n    libxt6 \\\\\\n    nano \\\\\\n    sudo \\\\\\n    wget\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FSL ...\\"\\nmkdir -p /opt/fsl-6.0.5.1\\ncurl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \\\\\\n| tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \\necho \\"Installing FSL conda environment ...\\"\\nbash /opt/fsl-6.0.5.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.5.1" \
      } \
    } \
  ] \
}' > /.reproenv.json
# End saving to specification to JSON.

This is the error

Sending build context to Docker daemon  8.704kB
Step 1/6 : FROM debian:stable
 ---> 096ef7a0068a
Step 2/6 : ENV PATH="/opt/afni-latest:$PATH"     AFNI_PLUGINPATH="/opt/afni-latest"
 ---> Using cache
 ---> 1ef720b7f33d
Step 3/6 : RUN apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            curl            ed            gsl-bin            libcurl4-openssl-dev            libgl1-mesa-dri            libglib2.0-0            libglu1-mesa-dev            libglw1-mesa            libgomp1            libjpeg-turbo8-dev            libjpeg62            libssl-dev            libudunits2-dev            libxm4            multiarch-support            netpbm            python-is-python3            python3-pip            tcsh            xfonts-base            xvfb     && rm -rf /var/lib/apt/lists/*     && _reproenv_tmppath="$(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 $gsl_path)/libgsl.so.0";     fi     && ldconfig     && mkdir -p /opt/afni-latest     && echo "Downloading AFNI ..."     && curl -fL https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz     | tar -xz -C /opt/afni-latest --strip-components 1
 ---> Running in f5cfaafa2678
/bin/sh: 1: Syntax error: "&&" unexpected
The command '/bin/sh -c apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            curl            ed            gsl-bin            libcurl4-openssl-dev            libgl1-mesa-dri            libglib2.0-0            libglu1-mesa-dev            libglw1-mesa            libgomp1            libjpeg-turbo8-dev            libjpeg62            libssl-dev            libudunits2-dev            libxm4            multiarch-support            netpbm            python-is-python3            python3-pip            tcsh            xfonts-base            xvfb     && rm -rf /var/lib/apt/lists/*     && _reproenv_tmppath="$(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' returned a non-zero code: 2

@spurani
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spurani commented Nov 24, 2022 •
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When I am removing && \ from line 43
image

here is the error I get

Sending build context to Docker daemon  16.38kB
Step 1/6 : FROM debian:stable
 ---> 096ef7a0068a
Step 2/6 : ENV PATH="/opt/afni-latest:$PATH"     AFNI_PLUGINPATH="/opt/afni-latest"
 ---> Using cache
 ---> 1ef720b7f33d
Step 3/6 : RUN apt-get update -qq     && apt-get install -y -q --no-install-recommends            ca-certificates            cmake            curl            ed            gsl-bin            libcurl4-openssl-dev            libgl1-mesa-dri            libglib2.0-0            libglu1-mesa-dev            libglw1-mesa            libgomp1            libjpeg-turbo8-dev            libjpeg62            libssl-dev            libudunits2-dev            libxm4            multiarch-support            netpbm            python-is-python3            python3-pip            tcsh            xfonts-base            xvfb     && rm -rf /var/lib/apt/lists/*     && _reproenv_tmppath="$(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 "${_reproenv_tmppath}"     && apt-get update -qq     && apt-get install --yes --quiet --fix-missing     && rm -rf /var/lib/apt/lists/*     && > dev/null     && gsl_path="$(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
 ---> Running in 62cc348ce22c
Reading package lists...
Building dependency tree...
Reading state information...
Package libjpeg-turbo8-dev is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'libjpeg-turbo8-dev' has no installation candidate
E: Unable to locate package multiarch-support
The command '/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/*     && > dev/null     && 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' returned a non-zero code: 100

Debian does not have libjpeg-turbo8-dev and multiarchsupport
multiarch issue neurodocker

debian packages it has libjpeg62-turbo-dev

@anandsaini024
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Hello,

I am also getting the same error while building afni as described on official example page.

Further, when tried the workaround mentioned in issue,the error message is:

dpkg-deb: error: '/tmp/toinstall.deb' is not a Debian format archive
dpkg: error processing archive /tmp/toinstall.deb (--install):
dpkg-deb --control subprocess returned error exit status 2
Errors were encountered while processing:
/tmp/toinstall.deb

my neurodocker version is 0.9.1 and installed as instructed above i.e pip install --no-cache-dir https://github.com/repronim/neurodocker/tarball/master.

Is there any step i am missing?

@stebo85
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stebo85 commented Nov 29, 2022

Dear @spurani and @anandsaini024

can you try this:

yes | pip uninstall neurodocker

pip install --no-cache-dir https://github.com/NeuroDesk/neurodocker/tarball/fix-afni-recipe-spaces-python-R-packages  --upgrade

and as a base container I found that fedora:36 works best for AFNI.

Here you can find how we build AFNI for the neurodesk project:
https://github.com/NeuroDesk/neurocontainers/tree/master/recipes/afni

You could also directly use the neurodesk AFNI container if you like - then you don't have to build it yourself :)
https://www.neurodesk.org/docs/neurocontainers/docker/

This would give you the current afni docker container (we also provide singularity containers):

docker pull vnmd/afni_22.3.06

Thank you
Steffen

@satra satra mentioned this issue Jan 3, 2023
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@djarecka
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@spurani and @anandsaini024 - have you tried the @stebo85 suggestions? did it work?

@stebo85
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stebo85 commented Feb 20, 2023

A little addition to my previous recommendation: There is a little bug in suma that crashes it when changing the t-statistic slider in Fedora 36, Fedora 35 however works ... so we are now installing afni in a Fedora 35 container.

@Remi-Gau Remi-Gau added the AFNI label Mar 13, 2023
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This issue is stale because it has been open for 30 days with no activity.

@github-actions github-actions bot added the stale label Aug 24, 2023
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This issue was closed because it has been inactive for 14 days since being marked as stale.

@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Oct 23, 2023
@yarikoptic yarikoptic reopened this Mar 27, 2024
@yarikoptic
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issue was not automagically addressed!

debian packages it has libjpeg62-turbo-dev

Different releases of debian/ubuntu might have different packages. BUT in this case it seems that indeed

so when added in 3da4e04 I guess @stebo85 used ubuntu and thus that package.

multiarch-support is in general no longer needed AFAIK since long ago and could be removed.

but then there is also use of

neurodocker/templates/afni.yaml:      - http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
neurodocker/templates/afni.yaml:      - http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
neurodocker/templates/spm12.yaml:    - http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb

which is no longer there since not present in any supported currently debian release... https://snapshot.debian.org/archive/debian/20140820T220424Z/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb should be there forever... but that package does require that elderly multiarch-support so it would then need to be also attempted to be downloaded/installed.

Current problem is afni/afni#596 ... I will draft a PR with what I have so far

@yarikoptic yarikoptic mentioned this issue Mar 27, 2024
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@github-actions github-actions bot removed the stale label Mar 28, 2024
@stebo85
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stebo85 commented Apr 1, 2024

that's great!

@kaczmarj
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kaczmarj commented Apr 4, 2024

thanks @yarikoptic :)

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github-actions bot commented Jun 4, 2024

This issue is stale because it has been open for 30 days with no activity.

@github-actions github-actions bot added the stale label Jun 4, 2024
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github-actions bot commented Aug 3, 2024

This issue was closed because it has been inactive for 14 days since being marked as stale.

@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Aug 3, 2024
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@yarikoptic @satra @djarecka @stebo85 @Remi-Gau @kaczmarj @spurani @anandsaini024