SuccessConsole Output

Started by GitHub push by bmerlet90
[EnvInject] - Loading node environment variables.
Building remotely on docker-packer-ansible2 (packer ansible docker) in workspace /home/ubuntu/workspace/container-SBML2MetexploreJsonGraph
 > 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-SBML2MetexploreJsonGraph # timeout=10
Fetching upstream changes from https://github.com/phnmnl/container-SBML2MetexploreJsonGraph
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/phnmnl/container-SBML2MetexploreJsonGraph +refs/heads/*:refs/remotes/origin/*
Seen branch in repository origin/develop
Seen branch in repository origin/master
Seen 2 remote branches
Checking out Revision ab215c6c5dd03e20744edba7ad63c011a6c57bef (origin/develop)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f ab215c6c5dd03e20744edba7ad63c011a6c57bef
 > git branch -a -v --no-abbrev # timeout=10
 > git branch -D develop # timeout=10
 > git checkout -b develop ab215c6c5dd03e20744edba7ad63c011a6c57bef
 > git rev-list b5da2a352e25cb17d4a2340ddf3c29f0e9d80285 # 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=sbml2metexplorejsongraph

[EnvInject] - Variables injected successfully.
[container-SBML2MetexploreJsonGraph] $ /bin/bash -xe /tmp/hudson293135072704252461.sh
+ wget -O make-versions-file https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
--2017-08-10 11:35:55--  https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.128.133, 151.101.0.133, 151.101.192.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.128.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 5705 (5.6K) [text/plain]
Saving to: ‘make-versions-file’

     0K .....                                                 100% 82.8M=0s

2017-08-10 11:35:55 (82.8 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: Trying command LABEL...
DEBUG: Trying variable name software.version...
DEBUG: Trying command ENV...
DEBUG: Trying command LABEL...
DEBUG: Found line "LABEL software.version="1.2"" for variable TOOL_VERSION.
DEBUG: Replaced variable name: "LABEL TOOL_VERSION="1.2"".
DEBUG: New version variable definition: TOOL_VERSION="1.2"
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="1.1"" for variable CONTAINER_VERSION.
DEBUG: Replaced variable name: "LABEL CONTAINER_VERSION="1.1"".
DEBUG: New version variable definition: CONTAINER_VERSION="1.1"
DEBUG: Sourcing written file "PhenoMeNal_Versions.txt"...
DEBUG: TOOL_VERSION=1.2
DEBUG: CONTAINER_VERSION=1.1
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_v1.2_cv1.1
[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-SBML2MetexploreJsonGraph] $ docker build -t docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph:dev_v1.2_cv1.1.9 --no-cache=true --pull=true /home/ubuntu/workspace/container-SBML2MetexploreJsonGraph
Sending build context to Docker daemon   169 kB

Step 1 : FROM java:8
8: Pulling from library/java
5040bd298390: Pulling fs layer
fce5728aad85: Pulling fs layer
76610ec20bf5: Pulling fs layer
60170fec2151: Pulling fs layer
e98f73de8f0d: Pulling fs layer
11f7af24ed9c: Pulling fs layer
49e2d6393f32: Pulling fs layer
bb9cdec9c7f3: Pulling fs layer
60170fec2151: Waiting
11f7af24ed9c: Waiting
49e2d6393f32: Waiting
e98f73de8f0d: Waiting
fce5728aad85: Verifying Checksum
fce5728aad85: Download complete
60170fec2151: Verifying Checksum
60170fec2151: Download complete
76610ec20bf5: Verifying Checksum
76610ec20bf5: Download complete
e98f73de8f0d: Verifying Checksum
e98f73de8f0d: Download complete
5040bd298390: Verifying Checksum
5040bd298390: Download complete
11f7af24ed9c: Verifying Checksum
11f7af24ed9c: Download complete
bb9cdec9c7f3: Verifying Checksum
bb9cdec9c7f3: Download complete
49e2d6393f32: Verifying Checksum
49e2d6393f32: Download complete
5040bd298390: Pull complete
fce5728aad85: Pull complete
76610ec20bf5: Pull complete
60170fec2151: Pull complete
e98f73de8f0d: Pull complete
11f7af24ed9c: Pull complete
49e2d6393f32: Pull complete
bb9cdec9c7f3: Pull complete
Digest: sha256:c1ff613e8ba25833d2e1940da0940c3824f03f802c449f3d1815a66b7f8c0e9d
Status: Downloaded newer image for java:8
 ---> d23bdf5b1b1b
Step 2 : MAINTAINER PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )
 ---> Running in b9d9d187384b
 ---> ab1aea8821c8
Removing intermediate container b9d9d187384b
Step 3 : LABEL software.version "1.2"
 ---> Running in 4fee539a0fae
 ---> 07746b4d2f1a
Removing intermediate container 4fee539a0fae
Step 4 : LABEL version "1.1"
 ---> Running in 480a95ba38a8
 ---> 1cdd6f090952
Removing intermediate container 480a95ba38a8
Step 5 : LABEL software "SBML2MetexploreJsonGraph"
 ---> Running in a3e5197c2580
 ---> ab2ec09b3884
Removing intermediate container a3e5197c2580
Step 6 : ENV TAG_NUMBER 1.2.3
 ---> Running in f2063291921d
 ---> b6d817f82651
Removing intermediate container f2063291921d
Step 7 : ADD digicertca.crt /usr/local/share/ca-certificates/digicertca.crt
 ---> 1180c43ce6da
Removing intermediate container 26c03edf046b
Step 8 : RUN apt-get update && 	apt-get install -y --no-install-recommends ant ca-certificates ant-optional && 	apt-get -y clean && 	apt-get -y autoremove && 	rm -rf /var/lib/{cache,log}/ /tmp/* /var/tmp/* && 	git clone  --depth 1 --single-branch --branch v$TAG_NUMBER https://github.com/bmerlet90/tool-SBML2MetexploreJsonGraph.git javaDir && 	cd javaDir && 	git checkout v$TAG_NUMBER && 	ant jar && 	cp dist/SBML2MetexploreJsonGraph/SBML2MetexploreJsonGraph.jar / && 	cd / && rm -rf javaDir
 ---> Running in 2bfef7d6b442
Get:1 http://security.debian.org jessie/updates InRelease [63.1 kB]
Ign http://deb.debian.org jessie InRelease
Get:2 http://deb.debian.org jessie-updates InRelease [145 kB]
Get:3 http://deb.debian.org jessie-backports InRelease [166 kB]
Get:4 http://deb.debian.org jessie Release.gpg [2373 B]
Get:5 http://deb.debian.org jessie Release [148 kB]
Get:6 http://security.debian.org jessie/updates/main amd64 Packages [549 kB]
Get:7 http://deb.debian.org jessie-updates/main amd64 Packages [17.8 kB]
Get:8 http://deb.debian.org jessie-backports/main amd64 Packages [1169 kB]
Get:9 http://deb.debian.org jessie/main amd64 Packages [9063 kB]
Fetched 11.3 MB in 1s (7846 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Suggested packages:
  ant-doc ant-gcj ant-optional-gcj antlr javacc junit jython libbcel-java
  libbsf-java libcommons-logging-java libcommons-net-java libmail-java
  libjaxp1.3-java libjdepend-java libjsch-java liblog4j1.2-java liboro-java
  libregexp-java libxalan2-java libxml-commons-resolver1.1-java
The following NEW packages will be installed:
  ant ant-optional
The following packages will be upgraded:
  ca-certificates
1 upgraded, 2 newly installed, 0 to remove and 48 not upgraded.
Need to get 2411 kB of archives.
After this operation, 2981 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian/ jessie/main ant all 1.9.4-3 [1888 kB]
Get:2 http://deb.debian.org/debian/ jessie/main ant-optional all 1.9.4-3 [316 kB]
Get:3 http://deb.debian.org/debian/ jessie/main ca-certificates all 20141019+deb8u3 [207 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2411 kB in 0s (5803 kB/s)
Selecting previously unselected package ant.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 17571 files and directories currently installed.)
Preparing to unpack .../archives/ant_1.9.4-3_all.deb ...
Unpacking ant (1.9.4-3) ...
Selecting previously unselected package ant-optional.
Preparing to unpack .../ant-optional_1.9.4-3_all.deb ...
Unpacking ant-optional (1.9.4-3) ...
Preparing to unpack .../ca-certificates_20141019+deb8u3_all.deb ...
Unpacking ca-certificates (20141019+deb8u3) over (20141019+deb8u2) ...
Setting up ant (1.9.4-3) ...
Setting up ant-optional (1.9.4-3) ...
Setting up ca-certificates (20141019+deb8u3) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
Updating certificates in /etc/ssl/certs... 1 added, 0 removed; done.
Processing triggers for ca-certificates (20141019+deb8u3) ...
Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d....
done.
done.
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
Cloning into 'javaDir'...
Note: checking out '620b31c4df2d2c7ceea0cfdf355da9cd21bf35ee'.

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

HEAD is now at 620b31c... Merge branch 'release/v1.2.3'
Buildfile: /javaDir/build.xml

git.build.number:

init:
     [echo] ----------- SBML2MetexploreJsonGraph 1-Dev-snapshot [2017] ------------
     [echo] -----------  August 10 2017   ------------
     [echo] -----------  20170810 1136  ------------
     [echo] ----------- git hash 620b31c4df2d2c7ceea0cfdf355da9cd21bf35ee  ------------
     [echo] ----------- git url https://github.com/bmerlet90/tool-SBML2MetexploreJsonGraph.git  ------------

prepare:
    [mkdir] Created dir: /javaDir/build
    [mkdir] Created dir: /javaDir/build/classes
    [mkdir] Created dir: /javaDir/build/src
    [mkdir] Created dir: /javaDir/tests/reports
     [echo] Directories created

compile:
    [javac] Compiling 18 source files to /javaDir/build/classes

copy-dependencies:
    [mkdir] Created dir: /javaDir/dist/lib
      [jar] Building jar: /javaDir/dist/lib/dependencies-all.jar

junit:
    [junit] Running phnmnl.tests.Test1_Reader
    [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.524 sec
    [junit] Running phnmnl.tests.Test2_NotesReader
    [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.045 sec
    [junit] Running phnmnl.tests.Test3_Converter
    [junit] Tests run: 14, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.02 sec
    [junit] Running phnmnl.tests.Test4_DataConvertion
    [junit] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.516 sec
    [junit] Running phnmnl.tests.Test5_Main
    [junit] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.546 sec

jar:
      [jar] Building jar: /javaDir/dist/SBML2MetexploreJsonGraph/SBML2MetexploreJsonGraph.jar
      [jar] Warning: selected jar files include a META-INF/INDEX.LIST which will be replaced by a newly generated one.

clean-up:
   [delete] Deleting directory /javaDir/dist/lib

BUILD SUCCESSFUL
Total time: 6 seconds
 ---> abbf39260153
Removing intermediate container 2bfef7d6b442
Step 9 : ADD runTest1.sh /usr/local/bin/runTest1.sh
 ---> ce1c1b50e06b
Removing intermediate container 9704f5882d98
Step 10 : RUN chmod a+x /usr/local/bin/runTest1.sh
 ---> Running in 6d2b93695232
 ---> bc854dd63a06
Removing intermediate container 6d2b93695232
Step 11 : ENTRYPOINT java -jar SBML2MetexploreJsonGraph.jar
 ---> Running in b3c8d4cd3346
 ---> 0a2c44474d31
Removing intermediate container b3c8d4cd3346
Successfully built 0a2c44474d31
[container-SBML2MetexploreJsonGraph] $ docker tag 0a2c44474d31 docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph:latest
[container-SBML2MetexploreJsonGraph] $ docker inspect 0a2c44474d31
[container-SBML2MetexploreJsonGraph] $ /bin/bash -xe /tmp/hudson3782773322951958844.sh
+ wget -O test-built-container https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
--2017-08-10 11:37:01--  https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.128.133, 151.101.0.133, 151.101.192.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.128.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2760 (2.7K) [text/plain]
Saving to: ‘test-built-container’

     0K ..                                                    100% 82.7M=0s

2017-08-10 11:37:01 (82.7 MB/s) - ‘test-built-container’ saved [2760/2760]

+ bash test-built-container docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph
Application Usage:
 -flux2Mapp   : Convert Flux data contained in the SBML as mapping data
                (default: false)
 -h           : Prints this help. (default: true)
 -inFile VAL  : [Required] Input SBML file.
 -outFile VAL : [Required] Output json file name.
 -validate    : Validate input SBML file. Default to false (default: false)
[container-SBML2MetexploreJsonGraph] $ docker tag ${CONTAINER_REGISTRY}/phnmnl/${CONTAINER} docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph:dev_v1.2_cv1.1.9
[container-SBML2MetexploreJsonGraph] $ docker tag ${CONTAINER_REGISTRY}/phnmnl/${CONTAINER} docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph:latest
[container-SBML2MetexploreJsonGraph] $ docker push docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph:dev_v1.2_cv1.1.9
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph]
86a5d2e512e2: Preparing
292f1e32b705: Preparing
10390817fa4c: Preparing
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35c20f26d188: Preparing
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ce6c8756685b: Preparing
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0eb22bfb707d: Preparing
a2ae92ffcd29: Preparing
6ed1a81ba5b6: Waiting
a3483ce177ce: Waiting
ce6c8756685b: Waiting
30339f20ced0: Waiting
0eb22bfb707d: Waiting
a2ae92ffcd29: Waiting
c3fe59dd9556: Waiting
35c20f26d188: Layer already exists
c3fe59dd9556: Layer already exists
6ed1a81ba5b6: Layer already exists
a3483ce177ce: Layer already exists
ce6c8756685b: Layer already exists
30339f20ced0: Layer already exists
0eb22bfb707d: Layer already exists
292f1e32b705: Pushed
fabae99fb1db: Pushed
a2ae92ffcd29: Layer already exists
86a5d2e512e2: Pushed
10390817fa4c: Pushed
dev_v1.2_cv1.1.9: digest: sha256:45cc8c5b7a0e0a02f5595f3477a692ea10f41279fde864d861ff661877556056 size: 2834
[container-SBML2MetexploreJsonGraph] $ docker push docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph:latest
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/sbml2metexplorejsongraph]
86a5d2e512e2: Preparing
292f1e32b705: Preparing
10390817fa4c: Preparing
fabae99fb1db: Preparing
35c20f26d188: Preparing
c3fe59dd9556: Preparing
6ed1a81ba5b6: Preparing
a3483ce177ce: Preparing
ce6c8756685b: Preparing
30339f20ced0: Preparing
0eb22bfb707d: Preparing
a2ae92ffcd29: Preparing
ce6c8756685b: Waiting
30339f20ced0: Waiting
0eb22bfb707d: Waiting
a2ae92ffcd29: Waiting
6ed1a81ba5b6: Waiting
c3fe59dd9556: Waiting
a3483ce177ce: Waiting
fabae99fb1db: Layer already exists
35c20f26d188: Layer already exists
86a5d2e512e2: Layer already exists
292f1e32b705: Layer already exists
10390817fa4c: Layer already exists
c3fe59dd9556: Layer already exists
a3483ce177ce: Layer already exists
30339f20ced0: Layer already exists
6ed1a81ba5b6: Layer already exists
ce6c8756685b: Layer already exists
0eb22bfb707d: Layer already exists
a2ae92ffcd29: Layer already exists
latest: digest: sha256:1544663219c29f20a909b5ab5b919d3f92893b4531576008d10899f6df08f3ef size: 2812
Strings match run condition: string 1=[origin/develop], string 2=[origin/master]
Run condition [Strings match] preventing perform for step [BuilderChain]
Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Triggering a new build of test-SBML2MetexploreJsonGraph-t3t1
Finished: SUCCESS