FailedConsole Output

Started by GitHub push by djcomlab
[EnvInject] - Loading node environment variables.
Building remotely on docker-packer-ansible (ansible docker) in workspace /home/ubuntu/workspace/container-isatab-create
 > 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-isatab-create # timeout=10
Fetching upstream changes from https://github.com/phnmnl/container-isatab-create
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/phnmnl/container-isatab-create +refs/heads/*:refs/remotes/origin/*
Seen branch in repository origin/develop
Seen branch in repository origin/master
Seen 2 remote branches
Checking out Revision 7cd86ba07a8f45227d11919dec16ff081b02cf19 (origin/develop)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 7cd86ba07a8f45227d11919dec16ff081b02cf19
 > git branch -a -v --no-abbrev # timeout=10
 > git branch -D develop # timeout=10
 > git checkout -b develop 7cd86ba07a8f45227d11919dec16ff081b02cf19
 > git rev-list 8084cd1ec8d112e7705747498166e0a629e30dc8 # 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=isatab-create

[EnvInject] - Variables injected successfully.
[container-isatab-create] $ /bin/bash -xe /tmp/jenkins2665139026898881250.sh
+ wget -O make-versions-file https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
--2018-05-03 16:16:03--  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% 34.9M=0s

2018-05-03 16:16:03 (34.9 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: Trying command LABEL...
DEBUG: Trying variable name software.version...
DEBUG: Trying command ENV...
DEBUG: Trying command LABEL...
DEBUG: Found line "LABEL software.version="0.9.5"" for variable TOOL_VERSION.
DEBUG: Replaced variable name: "LABEL TOOL_VERSION="0.9.5"".
DEBUG: New version variable definition: TOOL_VERSION="0.9.5"
DEBUG: Looking for variable CONTAINER_VERSION...
DEBUG: Trying variable name CONTAINER_VERSION...
DEBUG: Trying command ENV...
DEBUG: Trying command LABEL...
DEBUG: Trying variable name version...
DEBUG: Trying command ENV...
DEBUG: Trying command LABEL...
DEBUG: Found line "LABEL version="0.4.0"" for variable CONTAINER_VERSION.
DEBUG: Replaced variable name: "LABEL CONTAINER_VERSION="0.4.0"".
DEBUG: New version variable definition: CONTAINER_VERSION="0.4.0"
DEBUG: Sourcing written file "PhenoMeNal_Versions.txt"...
DEBUG: TOOL_VERSION=0.9.5
DEBUG: CONTAINER_VERSION=0.4.0
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_v0.9.5_cv0.4.0
[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-isatab-create] $ docker build -t docker-registry-v2.local:30750/phnmnl/isatab-create:dev_v0.9.5_cv0.4.0.64 --no-cache=true --pull=true /home/ubuntu/workspace/container-isatab-create
Sending build context to Docker daemon  518.7kB

Step 1/15 : FROM isatools/isatools:3.6-alpine-0.9.5
3.6-alpine-0.9.5: Pulling from isatools/isatools
Digest: sha256:6cb00fbda4298d50b2be6f308392b52eeaaa68fd4c08bad145a98cbba2858591
Status: Image is up to date for isatools/isatools:3.6-alpine-0.9.5
 ---> 491e12196adc
Step 2/15 : LABEL maintainer "PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )"
 ---> Running in 55a295958a3b
 ---> d67f30adbf6e
Removing intermediate container 55a295958a3b
Step 3/15 : LABEL description "Tools to create ISA-Tab from experiment plans"
 ---> Running in f117dc69c0a0
 ---> 2bb8c76c3b96
Removing intermediate container f117dc69c0a0
Step 4/15 : LABEL software.version "0.9.5"
 ---> Running in 3a76f1cad0d7
 ---> 95fe43ef7a5c
Removing intermediate container 3a76f1cad0d7
Step 5/15 : LABEL version "0.4.0"
 ---> Running in a35c373d3741
 ---> 2f173bc75431
Removing intermediate container a35c373d3741
Step 6/15 : LABEL software "isatab-create"
 ---> Running in 4c808f7eaaf1
 ---> 11f5c5d4bf79
Removing intermediate container 4c808f7eaaf1
Step 7/15 : RUN pip3 install click==6.7
 ---> Running in dc9b376d9935
Collecting click==6.7
  Downloading https://files.pythonhosted.org/packages/34/c1/8806f99713ddb993c5366c362b2f908f18269f8d792aff1abfd700775a77/click-6.7-py2.py3-none-any.whl (71kB)
Installing collected packages: click
Successfully installed click-6.7
You are using pip version 9.0.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
 ---> 7d83fa51bb71
Removing intermediate container dc9b376d9935
Step 8/15 : RUN pip3 uninstall isatools -y
 ---> Running in ce986005c814
Uninstalling isatools-0.9.5:
  Successfully uninstalled isatools-0.9.5
You are using pip version 9.0.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
 ---> 59015f416bb9
Removing intermediate container ce986005c814
Step 9/15 : RUN apk add --no-cache --virtual git-deps git openssh     && git clone --depth 1 --single-branch -b develop https://github.com/ISA-tools/isatools-galaxy /files/galaxy     && pip3 install git+git://github.com/ISA-tools/isa-api.git@develop#egg=isatools     && apk del git-deps     && rm -rf /var/cache/apk/*     && rm -rf /tmp/* /var/tmp/*
 ---> Running in 61aec37f6f7f
fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/community/x86_64/APKINDEX.tar.gz
(1/11) Installing ca-certificates (20161130-r2)
(2/11) Installing libssh2 (1.8.0-r1)
(3/11) Installing libcurl (7.59.0-r0)
(4/11) Installing pcre (8.41-r0)
(5/11) Installing git (2.13.5-r0)
(6/11) Installing openssh-keygen (7.5_p1-r2)
(7/11) Installing openssh-client (7.5_p1-r2)
(8/11) Installing openssh-sftp-server (7.5_p1-r2)
(9/11) Installing openssh-server (7.5_p1-r2)
(10/11) Installing openssh (7.5_p1-r2)
(11/11) Installing git-deps (0)
Executing busybox-1.26.2-r9.trigger
Executing ca-certificates-20161130-r2.trigger
OK: 99 MiB in 42 packages
Cloning into '/files/galaxy'...
Collecting isatools from git+git://github.com/ISA-tools/isa-api.git@develop#egg=isatools
  Cloning git://github.com/ISA-tools/isa-api.git (to develop) to /tmp/pip-build-tdaslpro/isatools
Requirement already satisfied: numpy in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: jsonschema in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: pandas in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: networkx in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: lxml in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: requests in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: chardet in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: iso8601 in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: jinja2 in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: beautifulsoup4 in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: mzml2isa in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: biopython in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: progressbar2 in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: deepdiff in /usr/lib/python3.6/site-packages (from isatools)
Requirement already satisfied: python-dateutil>=2 in /usr/lib/python3.6/site-packages (from pandas->isatools)
Requirement already satisfied: pytz>=2011k in /usr/lib/python3.6/site-packages (from pandas->isatools)
Requirement already satisfied: decorator>=4.1.0 in /usr/lib/python3.6/site-packages (from networkx->isatools)
Requirement already satisfied: urllib3<1.23,>=1.21.1 in /usr/lib/python3.6/site-packages (from requests->isatools)
Requirement already satisfied: certifi>=2017.4.17 in /usr/lib/python3.6/site-packages (from requests->isatools)
Requirement already satisfied: idna<2.7,>=2.5 in /usr/lib/python3.6/site-packages (from requests->isatools)
Requirement already satisfied: MarkupSafe>=0.23 in /usr/lib/python3.6/site-packages (from jinja2->isatools)
Requirement already satisfied: six in /usr/lib/python3.6/site-packages (from mzml2isa->isatools)
Requirement already satisfied: openpyxl in /usr/lib/python3.6/site-packages (from mzml2isa->isatools)
Requirement already satisfied: pronto>=0.6.0 in /usr/lib/python3.6/site-packages (from mzml2isa->isatools)
Requirement already satisfied: python-utils>=2.1.0 in /usr/lib/python3.6/site-packages (from progressbar2->isatools)
Requirement already satisfied: jsonpickle in /usr/lib/python3.6/site-packages (from deepdiff->isatools)
Requirement already satisfied: jdcal in /usr/lib/python3.6/site-packages (from openpyxl->mzml2isa->isatools)
Requirement already satisfied: et_xmlfile in /usr/lib/python3.6/site-packages (from openpyxl->mzml2isa->isatools)
Installing collected packages: isatools
  Running setup.py install for isatools: started
    Running setup.py install for isatools: finished with status 'done'
Successfully installed isatools-0.9.5
You are using pip version 9.0.1, however version 10.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
WARNING: Ignoring APKINDEX.84815163.tar.gz: No such file or directory
WARNING: Ignoring APKINDEX.24d64ab1.tar.gz: No such file or directory
(1/11) Purging git-deps (0)
(2/11) Purging git (2.13.5-r0)
(3/11) Purging openssh (7.5_p1-r2)
(4/11) Purging openssh-client (7.5_p1-r2)
(5/11) Purging openssh-sftp-server (7.5_p1-r2)
(6/11) Purging openssh-server (7.5_p1-r2)
(7/11) Purging openssh-keygen (7.5_p1-r2)
(8/11) Purging libcurl (7.59.0-r0)
(9/11) Purging ca-certificates (20161130-r2)
Executing ca-certificates-20161130-r2.post-deinstall
(10/11) Purging libssh2 (1.8.0-r1)
(11/11) Purging pcre (8.41-r0)
Executing busybox-1.26.2-r9.trigger
OK: 75 MiB in 31 packages
 ---> 5faf6a70355f
Removing intermediate container 61aec37f6f7f
Step 10/15 : ENV PATH $PATH:/files/galaxy
 ---> Running in 3ea16b3d5d0c
 ---> d54aa7a38c9b
Removing intermediate container 3ea16b3d5d0c
Step 11/15 : ADD run_test.sh /usr/local/bin/run_test.sh
 ---> 8923afacd83d
Removing intermediate container 6a0764c5c70e
Step 12/15 : RUN chmod +x /usr/local/bin/run_test.sh
 ---> Running in 4081015aa58f
 ---> f81e94c938c1
Removing intermediate container 4081015aa58f
Step 13/15 : RUN cp /files/galaxy/tools/isacreator_metabo/isacreator_metabo.py /usr/local/bin/isacreator_metabo.py
 ---> Running in 7706b025a4f9
 ---> 24bea320ab2b
Removing intermediate container 7706b025a4f9
Step 14/15 : RUN chmod a+x /usr/local/bin/isacreator_metabo.py
 ---> Running in b742e154da54
 ---> ce002bc9f2a4
Removing intermediate container b742e154da54
Step 15/15 : ENTRYPOINT isacreator_metabo.py
 ---> Running in 44d80608f3e3
 ---> 11b7d1c2eaea
Removing intermediate container 44d80608f3e3
Successfully built 11b7d1c2eaea
Successfully tagged docker-registry-v2.local:30750/phnmnl/isatab-create:dev_v0.9.5_cv0.4.0.64
[container-isatab-create] $ docker tag 11b7d1c2eaea docker-registry-v2.local:30750/phnmnl/isatab-create:latest
[container-isatab-create] $ docker inspect 11b7d1c2eaea
[container-isatab-create] $ /bin/bash -xe /tmp/jenkins4567945590833516612.sh
+ wget -O test-built-container https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
--2018-05-03 16:16:28--  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% 66.1M=0s

2018-05-03 16:16:28 (66.1 MB/s) - ‘test-built-container’ saved [3877/3877]

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