No Java Runtime Environment(JRE) was found on this system.

[mianasbat]

Hi,
I followed the following steps on centos 7 and end up in "No Java Runtime Environment (JRE) was found on this system".
Here are the steps:

sudo yum update && sudo yum install -y build-essential libssl-dev uuid-dev libgpgme11-dev squashfs-tools libseccomp-dev wget pkg-config git


wget https://dl.google.com/go/go1.12.7.linux-amd64.tar.gz

tar -C /usr/local -zxvf go1.12.7.linux-amd64.tar.gz

export PATH=$PATH:/usr/local/go/bin

source ~/.bashrc

git clone /~https://github.com/sylabs/singularity.git

cd singularity

yum install openssl-devel -y

yum install libuuid-devel -y

./mconfig
cd /root/singularity/builddir
make
make install

export PATH=$PATH:/root/singularity/builddir
export PATH=$PATH:/usr/local/bin

source ~/.bashrc

singularity help

cd
wget /~https://github.com/kaczmarj/neurodocker/files/3462171/singularity_recipe_neuro.txt
singularity build neurosing.sif singularity_recipe_neuro.txt

Here is the error

[kaczmarj]

hi @mianasbat - thanks for the report. can you please give the command you used to create the file singularity_recipe_neuro.txt? thanks.

[mianasbat]

Hi Kaczmarj, Thanks for reply. Attached is the recipe.txt. #
singularity_recipe_neuro.txt

[kaczmarj]

hi @mianasbat - i was able to reproduce your issue. are you attached to ubuntu:latest as a base image? switching debian:stretch works.

[mianasbat]

@kaczmarg, I will give it a try and let you know. Many thanks.

[mianasbat]

@kaczmarj I tried it today in new centos vm in virtualbox. Running it with sudo switching to debian:stretch image I got some permission errors. The final part of terminal log is attached.

termianllog.txt

[kaczmarj]

Thanks, can you paste the neurodocker command you used? This looks like a bug. I will fix that soon. The problem is that I wrote rm -rf /tmp* but singularity uses /tmp for the build, so it doesn’t like when you try to delete it...

…

On Sep 5, 2019, at 7:12 AM, Mian Asbat Ahmad ***@***.***> wrote: @kaczmarj I tried it today in new centos vm in virtualbox. Running it with sudo switching to debian:stretch image I got some permission errors. The final part of terminal log is attached. termianllog.txt — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[mianasbat]

@kaczmarj thanks for reply. Not sure about neurodocker ?
I just ran as root

singularity build neurosing.sif singularity_recipe_neuro.txt

I also did

singularity build neurosing.sif singularity_recipe_neuro.txt> run_log.txt

run_log1.txt

[kaczmarj]

@mianasbat - can you please try again with the latest neurodocker container? kaczmarj/neurodocker:master

[mianasbat]

@kaczmarj - for the above image I got the error

[root@localhost ~]# singularity build neurosing.sif singularity_recipe_neuro.txt
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:5d20c808ce198565ff70b3ed23a991dd49afac45dece63474b27ce6ed036adc6
Skipping fetch of repeat blob sha256:2525790be8a30b7ba1055f21c57a2acc666a930d7450fbc07295e4c51b392474
Skipping fetch of repeat blob sha256:cfebb70eb20ab32386beb1a013404b3872b9403702c8da348abbe9d00571322d
Skipping fetch of repeat blob sha256:92cd4890849ca69a3f6ad4891a0dc7bbc974d24a105bb9570a1692459cde5a9c
Copying config sha256:421136a398dcb5cd17ade3d4de7b6f4f7155cf985985cab2cb85f7c07a699d66
 1.88 KiB / 1.88 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
2019/09/19 13:07:17  info unpack layer: sha256:5d20c808ce198565ff70b3ed23a991dd49afac45dece63474b27ce6ed036adc6
2019/09/19 13:07:17  info unpack layer: sha256:2525790be8a30b7ba1055f21c57a2acc666a930d7450fbc07295e4c51b392474
2019/09/19 13:07:20  info unpack layer: sha256:cfebb70eb20ab32386beb1a013404b3872b9403702c8da348abbe9d00571322d
2019/09/19 13:07:21  info unpack layer: sha256:92cd4890849ca69a3f6ad4891a0dc7bbc974d24a105bb9570a1692459cde5a9c
INFO:    Running post scriptlet
+ export ND_ENTRYPOINT=/neurodocker/startup.sh
+ apt-get update -qq
/bin/sh: apt-get: not found
FATAL:   failed to execute %post proc: exit status 127
FATAL:   While performing build: while running engine: exit status 255

The image is centos I believe and it is expecting Ubuntu may be?

[kaczmarj]

yes looks like you are using centos but requesting the apt-get package manager, which is only for debian/ubuntu images.

can you build the image using debian:stretch as a base image and apt as package manager?

[kaczmarj]

hi @mianasbat - the command below should work for you. i know your original dockerfile installs more than spm12, but this should demonstrate how spm12 can be successfully installed.

docker run --rm kaczmarj/neurodocker:master generate docker --base=debian:jessie --pkg-manager=apt --spm version=r7219

[mianasbat]

@kaczmarj
It spit the following text. Also it is not addressing the issue with the recipe.

docker run --rm kaczmarj/neurodocker:master generate docker --base=debian:jessie --pkg-manager=apt --spm version=r7219

Unable to find image 'kaczmarj/neurodocker:master' locally
master: Pulling from kaczmarj/neurodocker
5d20c808ce19: Pull complete 
2525790be8a3: Pull complete 
800717a55ae4: Pull complete 
8494bd0b800b: Pull complete 
Digest: sha256:75ebbd7a6b8c46de1913c71cc5dfbb5d0a5b33822c4152e0e509c1e530d42e8c
Status: Downloaded newer image for kaczmarj/neurodocker:master
# Your version: 0.5.0-9-gaaa7671 Latest version: 0.5.0
# Generated by Neurodocker version 0.5.0-9-gaaa7671
# Timestamp: 2019-10-03 13:00:12 UTC
# 
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
# 
#     /~https://github.com/kaczmarj/neurodocker

FROM debian:jessie

ARG DEBIAN_FRONTEND="noninteractive"

ENV LANG="en_US.UTF-8" \
    LC_ALL="en_US.UTF-8" \
    ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           apt-utils \
           bzip2 \
           ca-certificates \
           curl \
           locales \
           unzip \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
    && dpkg-reconfigure --frontend=noninteractive locales \
    && update-locale LANG="en_US.UTF-8" \
    && chmod 777 /opt && chmod a+s /opt \
    && mkdir -p /neurodocker \
    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
    fi \
    && chmod -R 777 /neurodocker && chmod a+s /neurodocker

ENTRYPOINT ["/neurodocker/startup.sh"]

ENV FORCE_SPMMCR="1" \
    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
    MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
RUN export TMPDIR="$(mktemp -d)" \
    && apt-get update -qq \
    && apt-get install -y -q --no-install-recommends \
           bc \
           libncurses5 \
           libxext6 \
           libxmu6 \
           libxpm-dev \
           libxt6 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && echo "Downloading MATLAB Compiler Runtime ..." \
    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
    && dpkg -i /tmp/toinstall.deb \
    && rm /tmp/toinstall.deb \
    && apt-get install -f \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/* \
    && curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
    && chmod +x "$TMPDIR/MCRInstaller.bin" \
    && "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a" \
    && rm -rf "$TMPDIR" \
    && unset TMPDIR \
    && echo "Downloading standalone SPM ..." \
    && curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip \
    && unzip -q /tmp/spm12.zip -d /tmp \
    && mkdir -p /opt/spm12-r7219 \
    && mv /tmp/spm12/* /opt/spm12-r7219/ \
    && chmod -R 777 /opt/spm12-r7219 \
    && rm -rf /tmp/spm* \
    && /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
    && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT

RUN echo '{ \
    \n  "pkg_manager": "apt", \
    \n  "instructions": [ \
    \n    [ \
    \n      "base", \
    \n      "debian:jessie" \
    \n    ], \
    \n    [ \
    \n      "spm12", \
    \n      { \
    \n        "version": "r7219" \
    \n      } \
    \n    ] \
    \n  ] \
    \n}' > /neurodocker/neurodocker_specs.json