SuccessConsole Output

Started by user pmoreno@ebi.ac.uk
[EnvInject] - Loading node environment variables.
Building remotely on docker-packer-ansible (packer ansible docker) in workspace /home/ubuntu/workspace/container-nmrml2isa
 > git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > git config remote.origin.url https://github.com/phnmnl/container-nmrml2isa/ # timeout=10
Fetching upstream changes from https://github.com/phnmnl/container-nmrml2isa/
 > git --version # timeout=10
 > git -c core.askpass=true fetch --tags --progress https://github.com/phnmnl/container-nmrml2isa/ +refs/heads/*:refs/remotes/origin/*
 > git rev-parse refs/remotes/origin/develop^{commit} # timeout=10
 > git rev-parse refs/remotes/origin/origin/develop^{commit} # timeout=10
Checking out Revision 6bbdd220eaa31a5efe8f4f13608227b970a19bcd (refs/remotes/origin/develop)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 6bbdd220eaa31a5efe8f4f13608227b970a19bcd
 > git rev-list 6bbdd220eaa31a5efe8f4f13608227b970a19bcd # timeout=10
[container-nmrml2isa] $ /bin/bash -xe /tmp/hudson5752174940519074947.sh
+ wget https://raw.githubusercontent.com/phnmnl/jenkins-scripts/develop/make-versions-file
--2016-11-24 22:03:27--  https://raw.githubusercontent.com/phnmnl/jenkins-scripts/develop/make-versions-file
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.60.133
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.60.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2652 (2.6K) [text/plain]
Saving to: ‘make-versions-file.4’

     0K ..                                                    100% 64.3M=0s

2016-11-24 22:03:27 (64.3 MB/s) - ‘make-versions-file.4’ saved [2652/2652]

+ bash make-versions-file
[EnvInject] - Injecting environment variables from a build step.
[EnvInject] - Injecting as environment variables the properties file path 'PhenoMeNal_Versions.txt'
[EnvInject] - Variables injected successfully.
[container-nmrml2isa] $ docker build -t docker-registry-v2.local:30750/phnmnl/nmrml2isa:v0.3.0_cv0.1.6 --no-cache=true /home/ubuntu/workspace/container-nmrml2isa
Sending build context to Docker daemon 144.9 kB

Step 1 : FROM ubuntu:16.04
 ---> f753707788c5
Step 2 : MAINTAINER PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )
 ---> Running in 59d9ceaeb2d6
 ---> e9102b0742f5
Removing intermediate container 59d9ceaeb2d6
Step 3 : LABEL version "0.1"
 ---> Running in 97d84dacb614
 ---> 6dbdcbe77c0a
Removing intermediate container 97d84dacb614
Step 4 : LABEL software "nmrml2isa"
 ---> Running in f770bc60432f
 ---> 9b450da52089
Removing intermediate container f770bc60432f
Step 5 : LABEL software.version "0.3.0"
 ---> Running in f98c9f01be49
 ---> 8ec2b24c620e
Removing intermediate container f98c9f01be49
Step 6 : RUN apt-get -y update && apt-get -y install --no-install-recommends python-pip &&     pip install --upgrade pip && pip install -U setuptools && pip install six &&     pip install nmrml2isa==0.3.0 &&     pip uninstall -y pip &&     apt-get purge -y python-pip &&     apt-get install --no-install-recommends python &&     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ---> Running in d3bd37f96965
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Reading package lists...
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Building dependency tree...
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The following additional packages will be installed:
  ca-certificates libexpat1 libffi6 libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support openssl python
  python-minimal python-pip-whl python2.7 python2.7-minimal
Suggested packages:
  python-doc python-tk python2.7-doc binutils binfmt-support
Recommended packages:
  file build-essential python-all-dev python-setuptools python-wheel
The following NEW packages will be installed:
  ca-certificates libexpat1 libffi6 libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support openssl python
  python-minimal python-pip python-pip-whl python2.7 python2.7-minimal
0 upgraded, 16 newly installed, 0 to remove and 18 not upgraded.
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debconf: delaying package configuration, since apt-utils is not installed
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Setting up python-pip-whl (8.1.1-2ubuntu0.4) ...
Setting up python-pip (8.1.1-2ubuntu0.4) ...
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Processing triggers for ca-certificates (20160104ubuntu1) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Collecting pip
  Downloading pip-9.0.1-py2.py3-none-any.whl (1.3MB)
Installing collected packages: pip
  Found existing installation: pip 8.1.1
    Not uninstalling pip at /usr/lib/python2.7/dist-packages, outside environment /usr
Successfully installed pip-9.0.1
Collecting setuptools
  Downloading setuptools-28.8.0-py2.py3-none-any.whl (472kB)
Installing collected packages: setuptools
Successfully installed setuptools-28.8.0
Collecting six
  Downloading six-1.10.0-py2.py3-none-any.whl
Installing collected packages: six
Successfully installed six-1.10.0
Collecting nmrml2isa==0.3.0
  Downloading nmrml2isa-0.3.0.tar.gz (53kB)
Collecting lxml (from nmrml2isa==0.3.0)
  Downloading lxml-3.6.4-cp27-cp27mu-manylinux1_x86_64.whl (4.2MB)
Collecting pronto (from nmrml2isa==0.3.0)
  Downloading pronto-0.6.2-py2.py3-none-any.whl
Collecting chainmap (from nmrml2isa==0.3.0)
  Downloading chainmap-1.0.2-py2.py3-none-any.whl
Installing collected packages: lxml, pronto, chainmap, nmrml2isa
  Running setup.py install for nmrml2isa: started
    Running setup.py install for nmrml2isa: finished with status 'done'
Successfully installed chainmap-1.0.2 lxml-3.6.4 nmrml2isa-0.3.0 pronto-0.6.2
Uninstalling pip-9.0.1:
  Successfully uninstalled pip-9.0.1
You are using pip version 8.1.1, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates libexpat1 libffi6 libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libsqlite3-0 libssl1.0.0 mime-support openssl python
  python-minimal python-pip-whl python2.7 python2.7-minimal
Use 'apt autoremove' to remove them.
The following packages will be REMOVED:
  python-pip*
0 upgraded, 0 newly installed, 1 to remove and 18 not upgraded.
After this operation, 635 kB disk space will be freed.
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Reading package lists...
Building dependency tree...
Reading state information...
python is already the newest version (2.7.11-1).
python set to manually installed.
The following packages were automatically installed and are no longer required:
  ca-certificates openssl python-pip-whl
Use 'apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
  ca-certificates openssl python-pip-whl
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Removing dangling symlinks from /etc/ssl/certs... done.
Removing openssl (1.0.2g-1ubuntu4.5) ...
 ---> f5bb9385c669
Removing intermediate container d3bd37f96965
Step 7 : ENV WRAPPER_REVISION 4c85371042feda978278498f25ae89d6582a5aee
 ---> Running in 231643a01b41
 ---> 93dac8a6e50a
Removing intermediate container 231643a01b41
Step 8 : RUN apt-get -y update && apt-get -y install --no-install-recommends curl zip &&     curl https://raw.githubusercontent.com/ISA-tools/nmrml2isa-galaxy/$WRAPPER_REVISION/galaxy/nmrml2isa/wrapper.py -o /usr/local/bin/wrapper.py &&     curl https://raw.githubusercontent.com/ISA-tools/nmrml2isa-galaxy/$WRAPPER_REVISION/galaxy/nmrml2isa/pub_role.loc -o /usr/local/bin/pub_role.loc &&     curl https://raw.githubusercontent.com/ISA-tools/nmrml2isa-galaxy/$WRAPPER_REVISION/galaxy/nmrml2isa/pub_role.loc -o /usr/local/bin/pub_status.loc &&     chmod a+x /usr/local/bin/wrapper.py &&     apt-get purge -y curl &&     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ---> Running in 82d714ee1ca5
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libasn1-8-heimdal libcurl3-gnutls libgmp10 libgnutls30 libgssapi-krb5-2
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libk5crypto3
  libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2
  libnettle6 libp11-kit0 libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules-db libtasn1-6 libwind0-heimdal
Suggested packages:
  gnutls-bin krb5-doc krb5-user
Recommended packages:
  ca-certificates krb5-locales libsasl2-modules unzip
The following NEW packages will be installed:
  curl libasn1-8-heimdal libcurl3-gnutls libgmp10 libgnutls30 libgssapi-krb5-2
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libk5crypto3
  libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2
  libnettle6 libp11-kit0 libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules-db libtasn1-6 libwind0-heimdal zip
0 upgraded, 28 newly installed, 0 to remove and 18 not upgraded.
Need to get 3282 kB of archives.
After this operation, 10.7 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgmp10 amd64 2:6.1.0+dfsg-2 [240 kB]
Get:2 http://archive.ubuntu.com/ubuntu xenial/main amd64 libnettle6 amd64 3.2-1 [93.2 kB]
Get:3 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhogweed4 amd64 3.2-1 [135 kB]
Get:4 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libidn11 amd64 1.32-3ubuntu1.1 [45.6 kB]
Get:5 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libp11-kit0 amd64 0.23.2-5~ubuntu16.04.1 [105 kB]
Get:6 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtasn1-6 amd64 4.7-3ubuntu0.16.04.1 [43.2 kB]
Get:7 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libgnutls30 amd64 3.4.10-4ubuntu1.1 [547 kB]
Get:8 http://archive.ubuntu.com/ubuntu xenial/main amd64 libroken18-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [41.2 kB]
Get:9 http://archive.ubuntu.com/ubuntu xenial/main amd64 libasn1-8-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [174 kB]
Get:10 http://archive.ubuntu.com/ubuntu xenial/main amd64 libkrb5support0 amd64 1.13.2+dfsg-5 [30.7 kB]
Get:11 http://archive.ubuntu.com/ubuntu xenial/main amd64 libk5crypto3 amd64 1.13.2+dfsg-5 [81.0 kB]
Get:12 http://archive.ubuntu.com/ubuntu xenial/main amd64 libkeyutils1 amd64 1.5.9-8ubuntu1 [9904 B]
Get:13 http://archive.ubuntu.com/ubuntu xenial/main amd64 libkrb5-3 amd64 1.13.2+dfsg-5 [273 kB]
Get:14 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgssapi-krb5-2 amd64 1.13.2+dfsg-5 [120 kB]
Get:15 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhcrypto4-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [84.9 kB]
Get:16 http://archive.ubuntu.com/ubuntu xenial/main amd64 libheimbase1-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [29.2 kB]
Get:17 http://archive.ubuntu.com/ubuntu xenial/main amd64 libwind0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [48.2 kB]
Get:18 http://archive.ubuntu.com/ubuntu xenial/main amd64 libhx509-5-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [107 kB]
Get:19 http://archive.ubuntu.com/ubuntu xenial/main amd64 libkrb5-26-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [202 kB]
Get:20 http://archive.ubuntu.com/ubuntu xenial/main amd64 libheimntlm0-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [15.1 kB]
Get:21 http://archive.ubuntu.com/ubuntu xenial/main amd64 libgssapi3-heimdal amd64 1.7~git20150920+dfsg-4ubuntu1 [96.1 kB]
Get:22 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-14build1 [14.5 kB]
Get:23 http://archive.ubuntu.com/ubuntu xenial/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-14build1 [48.7 kB]
Get:24 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2ubuntu3.1 [161 kB]
Get:25 http://archive.ubuntu.com/ubuntu xenial/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d-1build1 [53.9 kB]
Get:26 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 libcurl3-gnutls amd64 7.47.0-1ubuntu2.2 [184 kB]
Get:27 http://archive.ubuntu.com/ubuntu xenial-updates/main amd64 curl amd64 7.47.0-1ubuntu2.2 [139 kB]
Get:28 http://archive.ubuntu.com/ubuntu xenial/main amd64 zip amd64 3.0-11 [158 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking zip (3.0-11) ...
Processing triggers for libc-bin (2.23-0ubuntu3) ...
Setting up libgmp10:amd64 (2:6.1.0+dfsg-2) ...
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Setting up libtasn1-6:amd64 (4.7-3ubuntu0.16.04.1) ...
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Setting up libroken18-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libasn1-8-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libkrb5support0:amd64 (1.13.2+dfsg-5) ...
Setting up libk5crypto3:amd64 (1.13.2+dfsg-5) ...
Setting up libkeyutils1:amd64 (1.5.9-8ubuntu1) ...
Setting up libkrb5-3:amd64 (1.13.2+dfsg-5) ...
Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-5) ...
Setting up libhcrypto4-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libheimbase1-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libwind0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libhx509-5-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libkrb5-26-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libheimntlm0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libgssapi3-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-14build1) ...
Setting up libsasl2-2:amd64 (2.1.26.dfsg1-14build1) ...
Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2ubuntu3.1) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d-1build1) ...
Setting up libcurl3-gnutls:amd64 (7.47.0-1ubuntu2.2) ...
Setting up curl (7.47.0-1ubuntu2.2) ...
Setting up zip (3.0-11) ...
Processing triggers for libc-bin (2.23-0ubuntu3) ...
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Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libasn1-8-heimdal libcurl3-gnutls libgmp10 libgnutls30 libgssapi-krb5-2
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libk5crypto3
  libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2
  libnettle6 libp11-kit0 libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules-db libtasn1-6 libwind0-heimdal
Use 'apt autoremove' to remove them.
The following packages will be REMOVED:
  curl*
0 upgraded, 0 newly installed, 1 to remove and 18 not upgraded.
After this operation, 338 kB disk space will be freed.
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Removing curl (7.47.0-1ubuntu2.2) ...
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
  libasn1-8-heimdal libcurl3-gnutls libgmp10 libgnutls30 libgssapi-krb5-2
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libidn11 libk5crypto3
  libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2
  libnettle6 libp11-kit0 libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules-db libtasn1-6 libwind0-heimdal
0 upgraded, 0 newly installed, 26 to remove and 18 not upgraded.
After this operation, 9736 kB disk space will be freed.
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Removing libcurl3-gnutls:amd64 (7.47.0-1ubuntu2.2) ...
Removing libldap-2.4-2:amd64 (2.4.42+dfsg-2ubuntu3.1) ...
Removing libgssapi3-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing libheimntlm0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing libkrb5-26-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing libhx509-5-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing librtmp1:amd64 (2.4+20151223.gitfa8646d-1build1) ...
Removing libgnutls30:amd64 (3.4.10-4ubuntu1.1) ...
Removing libhogweed4:amd64 (3.2-1) ...
Removing libgmp10:amd64 (2:6.1.0+dfsg-2) ...
Removing libgssapi-krb5-2:amd64 (1.13.2+dfsg-5) ...
Removing libhcrypto4-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing libheimbase1-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing libidn11:amd64 (1.32-3ubuntu1.1) ...
Removing libkrb5-3:amd64 (1.13.2+dfsg-5) ...
Removing libk5crypto3:amd64 (1.13.2+dfsg-5) ...
Removing libkeyutils1:amd64 (1.5.9-8ubuntu1) ...
Removing libkrb5support0:amd64 (1.13.2+dfsg-5) ...
Removing libnettle6:amd64 (3.2-1) ...
Removing libp11-kit0:amd64 (0.23.2-5~ubuntu16.04.1) ...
Removing libwind0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing libsasl2-2:amd64 (2.1.26.dfsg1-14build1) ...
Removing libsasl2-modules-db:amd64 (2.1.26.dfsg1-14build1) ...
Removing libtasn1-6:amd64 (4.7-3ubuntu0.16.04.1) ...
Removing libasn1-8-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Removing libroken18-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1) ...
Processing triggers for libc-bin (2.23-0ubuntu3) ...
 ---> eb1c3716d74e
Removing intermediate container 82d714ee1ca5
Step 9 : ADD runTest1.sh /usr/local/bin/runTest1.sh
 ---> 03b27905f8ce
Removing intermediate container 98437e6533ec
Step 10 : RUN chmod +x /usr/local/bin/runTest1.sh
 ---> Running in 795127ddec5a
 ---> 29e63e51a9bb
Removing intermediate container 795127ddec5a
Step 11 : ENTRYPOINT nmrml2isa
 ---> Running in c5b0737c3594
 ---> 933f1e1b4ecf
Removing intermediate container c5b0737c3594
Successfully built 933f1e1b4ecf
[container-nmrml2isa] $ docker tag 933f1e1b4ecf docker-registry-v2.local:30750/phnmnl/nmrml2isa:latest
[container-nmrml2isa] $ docker inspect 933f1e1b4ecf
[container-nmrml2isa] $ docker push docker-registry-v2.local:30750/phnmnl/nmrml2isa:v0.3.0_cv0.1.6
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/nmrml2isa]
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v0.3.0_cv0.1.6: digest: sha256:405d0ba95cf535dc573d2188b47f8f25f8abd621a89e6eda945c4d1e1aa3c745 size: 2193
[container-nmrml2isa] $ docker push docker-registry-v2.local:30750/phnmnl/nmrml2isa:latest
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/nmrml2isa]
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latest: digest: sha256:1b955280e8159a3700b8dde3b3512c55c86219ff6342c6a01128dac806b8f551 size: 2171
Finished: SUCCESS