FailedConsole Output

Started by GitHub push by pkrog
[EnvInject] - Loading node environment variables.
Building remotely on docker-packer-ansible (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 fetch --tags --progress https://github.com/phnmnl/container-nmrml2isa +refs/heads/*:refs/remotes/origin/*
Seen branch in repository origin/develop
Seen branch in repository origin/master
Seen 2 remote branches
Checking out Revision efb24c4530a10b97c7ec765750823d611c3de4fa (origin/develop)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f efb24c4530a10b97c7ec765750823d611c3de4fa
 > git branch -a -v --no-abbrev # timeout=10
 > git branch -D develop # timeout=10
 > git checkout -b develop efb24c4530a10b97c7ec765750823d611c3de4fa
 > git rev-list 25b2b37ac05ab2631807fb17be4f9184393d1352 # timeout=10
Run condition [Strings match] enabling prebuild for step [BuilderChain]
[EnvInject] - Executing scripts and injecting environment variables after the SCM step.
[EnvInject] - Injecting as environment variables the properties content 
CONTAINER=nmrml2isa

[EnvInject] - Variables injected successfully.
[container-nmrml2isa] $ /bin/bash -xe /tmp/jenkins4441939480469764781.sh
+ wget -O make-versions-file https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
--2018-06-15 14:10:45--  https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 5705 (5.6K) [text/plain]
Saving to: ‘make-versions-file’

     0K .....                                                 100% 33.8M=0s

2018-06-15 14:10:45 (33.8 MB/s) - ‘make-versions-file’ saved [5705/5705]

+ bash make-versions-file -ggtb
DEBUG: Arguments are : -ggtb
DEBUG: Looking for variable TOOL_VERSION...
DEBUG: Trying variable name TOOL_VERSION...
DEBUG: Trying command ENV...
DEBUG: Found line "ENV TOOL_VERSION=1.1.0" for variable TOOL_VERSION.
DEBUG: Replaced variable name: "ENV TOOL_VERSION=1.1.0".
DEBUG: New version variable definition: TOOL_VERSION=1.1.0
DEBUG: Looking for variable CONTAINER_VERSION...
DEBUG: Trying variable name CONTAINER_VERSION...
DEBUG: Trying command ENV...
DEBUG: Found line "ENV CONTAINER_VERSION=0.3" for variable CONTAINER_VERSION.
DEBUG: Replaced variable name: "ENV CONTAINER_VERSION=0.3".
DEBUG: New version variable definition: CONTAINER_VERSION=0.3
DEBUG: Sourcing written file "PhenoMeNal_Versions.txt"...
DEBUG: TOOL_VERSION=1.1.0
DEBUG: CONTAINER_VERSION=0.3
DEBUG: Looking for git branch...
DEBUG: Found git as "/usr/bin/git".
DEBUG: Current git branch is "develop".
DEBUG: Adding prefix "dev_" to tag.
DEBUG: CONTAINER_TAG_PREFIX=dev_v1.1.0_cv0.3
[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:dev_v1.1.0_cv0.3.13 --no-cache=true --pull=true /home/ubuntu/workspace/container-nmrml2isa
Sending build context to Docker daemon  193.5kB

Step 1/26 : FROM ubuntu:16.04
16.04: Pulling from library/ubuntu
b234f539f7a1: Pulling fs layer
55172d420b43: Pulling fs layer
5ba5bbeb6b91: Pulling fs layer
43ae2841ad7a: Pulling fs layer
f6c9c6de4190: Pulling fs layer
43ae2841ad7a: Waiting
f6c9c6de4190: Waiting
5ba5bbeb6b91: Verifying Checksum
5ba5bbeb6b91: Download complete
55172d420b43: Verifying Checksum
55172d420b43: Download complete
f6c9c6de4190: Verifying Checksum
f6c9c6de4190: Download complete
43ae2841ad7a: Verifying Checksum
43ae2841ad7a: Download complete
b234f539f7a1: Verifying Checksum
b234f539f7a1: Download complete
b234f539f7a1: Pull complete
55172d420b43: Pull complete
5ba5bbeb6b91: Pull complete
43ae2841ad7a: Pull complete
f6c9c6de4190: Pull complete
Digest: sha256:b050c1822d37a4463c01ceda24d0fc4c679b0dd3c43e742730e2884d3c582e3a
Status: Downloaded newer image for ubuntu:16.04
 ---> 5e8b97a2a082
Step 2/26 : MAINTAINER PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )
 ---> Running in 9689ff698c3a
 ---> 90c879aa1148
Removing intermediate container 9689ff698c3a
Step 3/26 : ENV TOOL_NAME nmrml2isa
 ---> Running in ae60291557b4
 ---> 36f70cce42c8
Removing intermediate container ae60291557b4
Step 4/26 : ENV TOOL_VERSION 1.1.0
 ---> Running in 2e4393c803ea
 ---> 1c3c1bd2144c
Removing intermediate container 2e4393c803ea
Step 5/26 : ENV CONTAINER_VERSION 0.3
 ---> Running in 7a51f5814519
 ---> a72f4da081e4
Removing intermediate container 7a51f5814519
Step 6/26 : ENV CONTAINER_GITHUB "https://github.com/isa-tools/nmrml2isa"
 ---> Running in 6f1a05578729
 ---> 5db62ec905da
Removing intermediate container 6f1a05578729
Step 7/26 : LABEL maintainer "PhenoMeNal-H2020 Project (phenomenal-h2020-users@googlegroups.com)"
 ---> Running in ec8d8e574d5e
 ---> 04818b91758a
Removing intermediate container ec8d8e574d5e
Step 8/26 : LABEL version 
 ---> Running in 731bbc2cee18
 ---> 913aef1c45ce
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Step 9/26 : LABEL software 
 ---> Running in 5a2545db0bcc
 ---> 2fbcd04426e3
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Step 10/26 : LABEL version "${CONTAINER_VERSION}"
 ---> Running in 48d1c14d771b
 ---> e1cfed3cc8de
Removing intermediate container 48d1c14d771b
Step 11/26 : LABEL software.version "${TOOL_VERSION}"
 ---> Running in 9b00e49520d7
 ---> e60bddcbfa71
Removing intermediate container 9b00e49520d7
Step 12/26 : LABEL description "Creates ISA metadata files based on a collection of nmrML files."
 ---> Running in ecf59e581eda
 ---> bfb9f1e60ad4
Removing intermediate container ecf59e581eda
Step 13/26 : LABEL website "${CONTAINER_GITHUB}"
 ---> Running in 4c7bdbb87101
 ---> 7e6dca75a7d9
Removing intermediate container 4c7bdbb87101
Step 14/26 : LABEL documentation "https://github.com/isa-tools/nmrml2isa-galaxy"
 ---> Running in 7ae29ec909c0
 ---> 0d08a3db46a5
Removing intermediate container 7ae29ec909c0
Step 15/26 : LABEL license "https://github.com/ISA-tools/nmrml2isa/blob/master/LICENSE"
 ---> Running in 48316c81c50d
 ---> 993ea1ddc34f
Removing intermediate container 48316c81c50d
Step 16/26 : LABEL tags "Metabolomics"
 ---> Running in 42451d6bbce4
 ---> d885d3cff0d3
Removing intermediate container 42451d6bbce4
Step 17/26 : ENV WRAPPER_REVISION 4c85371042feda978278498f25ae89d6582a5aee
 ---> Running in 62c7b0bda8ad
 ---> 5e68cce41f51
Removing intermediate container 62c7b0bda8ad
Step 18/26 : RUN apt-get -y update && apt-get -y install --no-install-recommends python python-setuptools python-pip git unzip &&     pip install nmrml2isa==0.3.0 &&     git clone --depth 1 --recursive --single-branch -b v${TOOL_VERSION} https://github.com/pkrog/nmrml2isa-galaxy /files/nmrml2isa-galaxy &&     apt-get purge -y git python-pip python-setuptools &&     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 ---> Running in 3fcd1564b501
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  ca-certificates git-man libasn1-8-heimdal libcurl3-gnutls liberror-perl
  libexpat1 libffi6 libgdbm3 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 libperl5.22 libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules-db libsqlite3-0 libssl1.0.0 libtasn1-6 libwind0-heimdal
  mime-support openssl perl perl-base perl-modules-5.22 python-minimal
  python-pip-whl python-pkg-resources python2.7 python2.7-minimal
Suggested packages:
  gettext-base git-daemon-run | git-daemon-sysvinit git-doc git-el git-email
  git-gui gitk gitweb git-arch git-cvs git-mediawiki git-svn gnutls-bin
  krb5-doc krb5-user perl-doc libterm-readline-gnu-perl
  | libterm-readline-perl-perl make python-doc python-tk python-setuptools-doc
  python2.7-doc binutils binfmt-support zip
Recommended packages:
  patch less rsync ssh-client krb5-locales libsasl2-modules file netbase
  rename build-essential python-all-dev python-wheel
The following NEW packages will be installed:
  ca-certificates git git-man libasn1-8-heimdal libcurl3-gnutls liberror-perl
  libexpat1 libffi6 libgdbm3 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 libperl5.22 libpython-stdlib libpython2.7-minimal
  libpython2.7-stdlib libroken18-heimdal librtmp1 libsasl2-2
  libsasl2-modules-db libsqlite3-0 libssl1.0.0 libtasn1-6 libwind0-heimdal
  mime-support openssl perl perl-modules-5.22 python python-minimal python-pip
  python-pip-whl python-pkg-resources python-setuptools python2.7
  python2.7-minimal unzip
The following packages will be upgraded:
  perl-base
1 upgraded, 52 newly installed, 0 to remove and 2 not upgraded.
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Updating certificates in /etc/ssl/certs...
148 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Collecting nmrml2isa==0.3.0
  Downloading https://files.pythonhosted.org/packages/61/87/eb7ed3b5dfcdaa5109355daf7ccab722ce984cf49283bead437d6a51cd8a/nmrml2isa-0.3.0.tar.gz (53kB)
Collecting lxml (from nmrml2isa==0.3.0)
  Downloading https://files.pythonhosted.org/packages/57/38/25b2acd2a179cb1900a32ab2daeec2967e511192c9ce0763ce16cece6366/lxml-4.2.1-cp27-cp27mu-manylinux1_x86_64.whl (5.6MB)
Collecting pronto (from nmrml2isa==0.3.0)
  Downloading https://files.pythonhosted.org/packages/cd/09/584862c1d8c6e66b5d3f9f7a2d068ab0412e1ad4bb3cd57b2d7e930d92ed/pronto-0.10.2-py2.py3-none-any.whl
Collecting chainmap (from nmrml2isa==0.3.0)
  Downloading https://files.pythonhosted.org/packages/6a/53/795ce18439a067eea1b233152985c0e67fd7dcc4edf102fb30f8cca6bad0/chainmap-1.0.2-py2.py3-none-any.whl
Collecting six (from pronto->nmrml2isa==0.3.0)
  Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Building wheels for collected packages: nmrml2isa
  Running setup.py bdist_wheel for nmrml2isa: started
  Running setup.py bdist_wheel for nmrml2isa: finished with status 'error'
  Complete output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-vCJqhr/nmrml2isa/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmpdz6gnvpip-wheel- --python-tag cp27:
  usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: -c --help [cmd1 cmd2 ...]
     or: -c --help-commands
     or: -c cmd --help
  
  error: invalid command 'bdist_wheel'
  
  ----------------------------------------
  Failed building wheel for nmrml2isa
  Running setup.py clean for nmrml2isa
Failed to build nmrml2isa
Installing collected packages: lxml, six, 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-4.2.1 nmrml2isa-0.3.0 pronto-0.10.2 six-1.11.0
You are using pip version 8.1.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Cloning into '/files/nmrml2isa-galaxy'...
Note: checking out '07555aa546859e36f32527c16a7dc3112e78a051'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

Submodule 'bash-testthat' (https://github.com/pkrog/bash-testthat) registered for path 'bash-testthat'
Cloning into 'bash-testthat'...
Submodule path 'bash-testthat': checked out '95d9b43159c0bc71573c5a11d41c79034944c9d0'
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates git-man libasn1-8-heimdal libcurl3-gnutls liberror-perl
  libgdbm3 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 libperl5.22
  libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libtasn1-6
  libwind0-heimdal openssl perl perl-modules-5.22 python-pip-whl
  python-pkg-resources
Use 'apt autoremove' to remove them.
The following packages will be REMOVED:
  git* python-pip* python-setuptools*
0 upgraded, 0 newly installed, 3 to remove and 2 not upgraded.
After this operation, 25.3 MB disk space will be freed.
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Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
  ca-certificates git-man libasn1-8-heimdal libcurl3-gnutls liberror-perl
  libgdbm3 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 libperl5.22
  libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libtasn1-6
  libwind0-heimdal openssl perl perl-modules-5.22 python-pip-whl
  python-pkg-resources
0 upgraded, 0 newly installed, 36 to remove and 2 not upgraded.
After this operation, 53.6 MB disk space will be freed.
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Removing python-pip-whl (8.1.1-2ubuntu0.4) ...
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Removing dangling symlinks from /etc/ssl/certs... done.
Removing git-man (1:2.7.4-0ubuntu1.4) ...
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Removing libldap-2.4-2:amd64 (2.4.42+dfsg-2ubuntu3.3) ...
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Removing librtmp1:amd64 (2.4+20151223.gitfa8646d-1ubuntu0.1) ...
Removing libgnutls30:amd64 (3.4.10-4ubuntu1.4) ...
Removing libhogweed4:amd64 (3.2-1ubuntu0.16.04.1) ...
Removing libgmp10:amd64 (2:6.1.0+dfsg-2) ...
Removing libgssapi-krb5-2:amd64 (1.13.2+dfsg-5ubuntu2) ...
Removing libhcrypto4-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Removing libheimbase1-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Removing libidn11:amd64 (1.32-3ubuntu1.2) ...
Removing libkrb5-3:amd64 (1.13.2+dfsg-5ubuntu2) ...
Removing libk5crypto3:amd64 (1.13.2+dfsg-5ubuntu2) ...
Removing libkeyutils1:amd64 (1.5.9-8ubuntu1) ...
Removing libkrb5support0:amd64 (1.13.2+dfsg-5ubuntu2) ...
Removing libnettle6:amd64 (3.2-1ubuntu0.16.04.1) ...
Removing libp11-kit0:amd64 (0.23.2-5~ubuntu16.04.1) ...
Removing libwind0-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Removing libsasl2-2:amd64 (2.1.26.dfsg1-14build1) ...
Removing libsasl2-modules-db:amd64 (2.1.26.dfsg1-14build1) ...
Removing libtasn1-6:amd64 (4.7-3ubuntu0.16.04.3) ...
Removing openssl (1.0.2g-1ubuntu4.12) ...
Removing perl-modules-5.22 (5.22.1-9ubuntu0.5) ...
Removing python-pkg-resources (20.7.0-1) ...
Removing libasn1-8-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Removing libroken18-heimdal:amd64 (1.7~git20150920+dfsg-4ubuntu1.16.04.1) ...
Processing triggers for libc-bin (2.23-0ubuntu10) ...
 ---> 78b89fdc3c5f
Removing intermediate container 3fcd1564b501
Step 19/26 : ENV PATH $PATH:/files/nmrml2isa-galaxy/galaxy/nmrml2isa
 ---> Running in 634a630b2259
 ---> 323f5a4ae352
Removing intermediate container 634a630b2259
Step 20/26 : RUN chmod u+x "/files/nmrml2isa-galaxy/galaxy/nmrml2isa/wrapper.py"
 ---> Running in 1a3c0d213f01
 ---> dedba27a4b0f
Removing intermediate container 1a3c0d213f01
Step 21/26 : RUN echo "#!/bin/bash" >/files/test-nmrml2isa
 ---> Running in bbe60a7b0110
 ---> f00d319f8590
Removing intermediate container bbe60a7b0110
Step 22/26 : RUN echo "cd /files/nmrml2isa-galaxy/test" >>/files/test-nmrml2isa
 ---> Running in d27a0f9f8571
 ---> 0b771b011f42
Removing intermediate container d27a0f9f8571
Step 23/26 : RUN echo "testthat.sh test-wrapper.sh" >>/files/test-nmrml2isa
 ---> Running in 1aa8c33e8c90
 ---> 236b38817706
Removing intermediate container 1aa8c33e8c90
Step 24/26 : RUN chmod u+x "/files/test-nmrml2isa"
 ---> Running in c87b3191e91d
 ---> 0282b9df5b79
Removing intermediate container c87b3191e91d
Step 25/26 : ENV PATH $PATH:/files:/files/nmrml2isa-galaxy/bash-testthat
 ---> Running in bd2fb8ca8242
 ---> 30977ca68154
Removing intermediate container bd2fb8ca8242
Step 26/26 : ENTRYPOINT /files/nmrml2isa-galaxy/galaxy/nmrml2isa/wrapper.py
 ---> Running in 20c260bc95cc
 ---> f8fa885711b4
Removing intermediate container 20c260bc95cc
Successfully built f8fa885711b4
Successfully tagged docker-registry-v2.local:30750/phnmnl/nmrml2isa:dev_v1.1.0_cv0.3.13
[container-nmrml2isa] $ docker tag f8fa885711b4 docker-registry-v2.local:30750/phnmnl/nmrml2isa:latest
[container-nmrml2isa] $ docker inspect f8fa885711b4
[container-nmrml2isa] $ /bin/bash -xe /tmp/jenkins6232275210782262675.sh
+ wget -O test-built-container https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
--2018-06-15 14:11:56--  https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3877 (3.8K) [text/plain]
Saving to: ‘test-built-container’

     0K ...                                                   100% 89.3M=0s

2018-06-15 14:11:56 (89.3 MB/s) - ‘test-built-container’ saved [3877/3877]

+ bash test-built-container docker-registry-v2.local:30750/phnmnl/nmrml2isa
/usr/local/bin/nmrml2isa
INFO: Container docker-registry-v2.local:30750/phnmnl/nmrml2isa tested successfully.
INFO: Failure when testing container docker-registry-v2.local:30750/phnmnl/nmrml2isa.
Build step 'Execute shell' marked build as failure
Finished: FAILURE