SuccessConsole Output

Started by GitHub push by ilveroluca
[EnvInject] - Loading node environment variables.
Building remotely on docker-packer-ansible (ansible docker) in workspace /home/ubuntu/workspace/container-nmr-integrals
 > 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-nmr-integrals/ # timeout=10
Fetching upstream changes from https://github.com/phnmnl/container-nmr-integrals/
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/phnmnl/container-nmr-integrals/ +refs/heads/*:refs/remotes/origin/*
Seen branch in repository origin/develop
Seen branch in repository origin/jbradbury-patch-1
Seen branch in repository origin/master
Seen branch in repository origin/test-jenkins
Seen 4 remote branches
Checking out Revision fd23d6bc02d34ce2a2c6ad8ec7a4369210070245 (origin/test-jenkins)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f fd23d6bc02d34ce2a2c6ad8ec7a4369210070245
 > git branch -a -v --no-abbrev # timeout=10
 > git checkout -b test-jenkins fd23d6bc02d34ce2a2c6ad8ec7a4369210070245
First time build. Skipping changelog.
[EnvInject] - Executing scripts and injecting environment variables after the SCM step.
[EnvInject] - Injecting as environment variables the properties content 
CONTAINER=nmr-integrals

[EnvInject] - Variables injected successfully.
[container-nmr-integrals] $ /bin/bash -xe /tmp/jenkins1230022780554522636.sh
+ wget -O make-versions-file https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
--2018-12-12 10:07:21--  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%  127M=0s

2018-12-12 10:07:22 (127 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="0.1.1"" for variable TOOL_VERSION.
DEBUG: Replaced variable name: "LABEL TOOL_VERSION="0.1.1"".
DEBUG: New version variable definition: TOOL_VERSION="0.1.1"
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="0.1"" for variable CONTAINER_VERSION.
DEBUG: Replaced variable name: "LABEL CONTAINER_VERSION="0.1"".
DEBUG: New version variable definition: CONTAINER_VERSION="0.1"
DEBUG: Sourcing written file "PhenoMeNal_Versions.txt"...
DEBUG: TOOL_VERSION=0.1.1
DEBUG: CONTAINER_VERSION=0.1
DEBUG: Looking for git branch...
DEBUG: Found git as "/usr/bin/git".
DEBUG: Current git branch is "test-jenkins".
DEBUG: CONTAINER_TAG_PREFIX=v0.1.1_cv0.1
[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-nmr-integrals] $ docker build -t docker-registry-v2.local:30750/phnmnl/nmr-integrals:v0.1.1_cv0.1.18 --no-cache=true --pull=true /home/ubuntu/workspace/container-nmr-integrals
Sending build context to Docker daemon  413.7kB

Step 1/18 : FROM artemklevtsov/r-alpine:3.3.1
3.3.1: Pulling from artemklevtsov/r-alpine
e110a4a17941: Pulling fs layer
d36d2dbde5a0: Pulling fs layer
e110a4a17941: Verifying Checksum
e110a4a17941: Download complete
e110a4a17941: Pull complete
d36d2dbde5a0: Verifying Checksum
d36d2dbde5a0: Download complete
d36d2dbde5a0: Pull complete
Digest: sha256:a49980621dc8dae8e29f87e2125bb6520f5b813aea7c08ca3979c0b4c3283d0c
Status: Downloaded newer image for artemklevtsov/r-alpine:3.3.1
 ---> 218ef88601b1
Step 2/18 : MAINTAINER PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )
 ---> Running in 1721debb1016
 ---> c4cd696f05ee
Removing intermediate container 1721debb1016
Step 3/18 : LABEL Description "R-based script to compute NMR spectrum deviation for sample QC"
 ---> Running in 5540a8d0fa20
 ---> bac1f9a9bf8b
Removing intermediate container 5540a8d0fa20
Step 4/18 : LABEL software.version "0.1.1"
 ---> Running in 0a8c34bbe1a0
 ---> 507feab87d75
Removing intermediate container 0a8c34bbe1a0
Step 5/18 : LABEL version "0.1"
 ---> Running in d927ef848255
 ---> 2b1269153b7d
Removing intermediate container d927ef848255
Step 6/18 : LABEL software "nmr-integrals"
 ---> Running in 786581127cb2
 ---> d74969135bf0
Removing intermediate container 786581127cb2
Step 7/18 : LABEL my.test.label "hello"
 ---> Running in 7d4f80c969b0
 ---> dc2a0248bdbd
Removing intermediate container 7d4f80c969b0
Step 8/18 : LABEL base.image "artemklevtsov/r-alpine:3.3.1"
 ---> Running in 2cbf9e5cf1fb
 ---> 27930666debe
Removing intermediate container 2cbf9e5cf1fb
Step 9/18 : LABEL website "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in eedc69f6c059
 ---> 99166ecfb7d8
Removing intermediate container eedc69f6c059
Step 10/18 : LABEL documentation "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in 77faed13ddab
 ---> 62ba0503e318
Removing intermediate container 77faed13ddab
Step 11/18 : LABEL license "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in aa59d7750730
 ---> c5e1a190302d
Removing intermediate container aa59d7750730
Step 12/18 : LABEL tags "Metabolomics"
 ---> Running in ee184965dc49
 ---> 08032d128aaf
Removing intermediate container ee184965dc49
Step 13/18 : RUN apk update   && apk add ca-certificates unzip wget   && rm -rf /var/cache/apk/*
 ---> Running in 4b5ced093b3e
fetch http://dl-cdn.alpinelinux.org/alpine/v3.4/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.4/community/x86_64/APKINDEX.tar.gz
v3.4.6-316-g63ea6d0 [http://dl-cdn.alpinelinux.org/alpine/v3.4/main]
v3.4.6-160-g14ad2a3 [http://dl-cdn.alpinelinux.org/alpine/v3.4/community]
OK: 5998 distinct packages available
(1/2) Installing unzip (6.0-r1)
(2/2) Installing wget (1.18-r3)
Executing busybox-1.24.2-r9.trigger
OK: 244 MiB in 70 packages
 ---> 083d77ee5795
Removing intermediate container 4b5ced093b3e
Step 14/18 : RUN Rscript -e 'install.packages(c("caTools", "optparse"))'
 ---> Running in f96fb0a7d141
Installing packages into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘bitops’, ‘getopt’

trying URL 'https://cloud.r-project.org/src/contrib/bitops_1.0-6.tar.gz'
Content type 'application/x-gzip' length 8734 bytes
==================================================
downloaded 8734 bytes

trying URL 'https://cloud.r-project.org/src/contrib/getopt_1.20.2.tar.gz'
Content type 'application/x-gzip' length 17521 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://cloud.r-project.org/src/contrib/caTools_1.17.1.1.tar.gz'
Content type 'application/x-gzip' length 63565 bytes (62 KB)
==================================================
downloaded 62 KB

trying URL 'https://cloud.r-project.org/src/contrib/optparse_1.6.0.tar.gz'
Content type 'application/x-gzip' length 34931 bytes (34 KB)
==================================================
downloaded 34 KB

* installing *source* package ‘bitops’ ...
** package ‘bitops’ successfully unpacked and MD5 sums checked
** libs
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c bit-ops.c -o bit-ops.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cksum.c -o cksum.o
gcc -shared -L/usr/lib/R/lib -L/usr/local/lib -o bitops.so bit-ops.o cksum.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/bitops/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (bitops)
* installing *source* package ‘getopt’ ...
** package ‘getopt’ successfully unpacked and MD5 sums checked
** R
** exec
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (getopt)
* installing *source* package ‘caTools’ ...
** package ‘caTools’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -D__MUSL__  -c Gif2R.cpp -o Gif2R.o
g++ -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -D__MUSL__  -c GifTools.cpp -o GifTools.o
gcc -I/usr/include/R -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c runfunc.c -o runfunc.o
g++ -shared -L/usr/lib/R/lib -L/usr/local/lib -o caTools.so Gif2R.o GifTools.o runfunc.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/caTools/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (caTools)
* installing *source* package ‘optparse’ ...
** package ‘optparse’ successfully unpacked and MD5 sums checked
** R
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (optparse)

The downloaded source packages are in
	‘/tmp/RtmpAKnBIa/downloaded_packages’
 ---> 37c86318e5e0
Removing intermediate container f96fb0a7d141
Step 15/18 : WORKDIR /nmr-integrals
 ---> 4ffc066dbf69
Removing intermediate container 0dd50f358ebe
Step 16/18 : COPY integrals.R integrals_galaxy_wrapper.sh runTest1.sh /usr/local/bin/
 ---> 4f8913eadd39
Removing intermediate container 9abb86f74d1f
Step 17/18 : RUN chmod a+rx      /usr/local/bin/integrals.R      /usr/local/bin/integrals_galaxy_wrapper.sh      /usr/local/bin/runTest1.sh
 ---> Running in 991d46de3eb0
 ---> bccb10e45fd3
Removing intermediate container 991d46de3eb0
Step 18/18 : ENTRYPOINT integrals_galaxy_wrapper.sh
 ---> Running in d012b60b52a9
 ---> 48d833b9739f
Removing intermediate container d012b60b52a9
Successfully built 48d833b9739f
Successfully tagged docker-registry-v2.local:30750/phnmnl/nmr-integrals:v0.1.1_cv0.1.18
[container-nmr-integrals] $ docker tag 48d833b9739f docker-registry-v2.local:30750/phnmnl/nmr-integrals:latest
[container-nmr-integrals] $ docker inspect 48d833b9739f
[container-nmr-integrals] $ /bin/bash -xe /tmp/jenkins3651815731804456522.sh
+ wget -O test-built-container https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
--2018-12-12 10:07:50--  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% 61.5M=0s

2018-12-12 10:07:50 (61.5 MB/s) - ‘test-built-container’ saved [3877/3877]

+ bash test-built-container docker-registry-v2.local:30750/phnmnl/nmr-integrals
INFO: Try loading R package caTools

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library('caTools')
> 
> 
INFO: R package caTools loaded successfully.
INFO: Try loading R package optparse

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library('optparse')
> 
> 
INFO: R package optparse loaded successfully.
/usr/local/bin/integrals.R
INFO: Container docker-registry-v2.local:30750/phnmnl/nmr-integrals tested successfully.
Usage: /usr/local/bin/integrals.R [options] METABOLITES_TABLE REFERENCE_SPECTRUM TEST_SPECTRUM


Options:
	--left=N
		Left

	--right=N
		Right

	--where=N
		Where

	--plotfile=FILE.PDF
		Plot file

	--metabolites=METABOLITES.TSV
		Metabolites table in tab-separated format

	-h, --help
		Show this help message and exit

	REFERENCE_SPECTRUM
		Reference dataset (Bruker NMR)

	TEST_SPECTRUM
		Test dataset (Bruker NMR)


INFO: Container docker-registry-v2.local:30750/phnmnl/nmr-integrals tested successfully.
[container-nmr-integrals] $ docker tag ${CONTAINER_REGISTRY}/phnmnl/${CONTAINER} docker-registry-v2.local:30750/phnmnl/nmr-integrals:v0.1.1_cv0.1.18
[container-nmr-integrals] $ docker tag ${CONTAINER_REGISTRY}/phnmnl/${CONTAINER} docker-registry-v2.local:30750/phnmnl/nmr-integrals:latest
[container-nmr-integrals] $ docker push docker-registry-v2.local:30750/phnmnl/nmr-integrals:v0.1.1_cv0.1.18
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/nmr-integrals]
941a6578c020: Preparing
52aaca014b76: Preparing
182f4cb2b2b7: Preparing
c1ee9029a69e: Preparing
d63607b6ee39: Preparing
853e0cddde7d: Preparing
4fe15f8d0ae6: Preparing
853e0cddde7d: Waiting
4fe15f8d0ae6: Waiting
941a6578c020: Pushed
182f4cb2b2b7: Pushed
52aaca014b76: Pushed
d63607b6ee39: Pushed
c1ee9029a69e: Pushed
4fe15f8d0ae6: Layer already exists
853e0cddde7d: Layer already exists
v0.1.1_cv0.1.18: digest: sha256:18861fb9c869aa3831d47d2da1bbacd0c55a3ef38729ed38f76fe737ea86c9e7 size: 1784
[container-nmr-integrals] $ docker push docker-registry-v2.local:30750/phnmnl/nmr-integrals:latest
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/nmr-integrals]
941a6578c020: Preparing
52aaca014b76: Preparing
182f4cb2b2b7: Preparing
c1ee9029a69e: Preparing
d63607b6ee39: Preparing
853e0cddde7d: Preparing
4fe15f8d0ae6: Preparing
853e0cddde7d: Waiting
4fe15f8d0ae6: Waiting
941a6578c020: Layer already exists
52aaca014b76: Layer already exists
182f4cb2b2b7: Layer already exists
c1ee9029a69e: Layer already exists
d63607b6ee39: Layer already exists
4fe15f8d0ae6: Layer already exists
853e0cddde7d: Layer already exists
latest: digest: sha256:18861fb9c869aa3831d47d2da1bbacd0c55a3ef38729ed38f76fe737ea86c9e7 size: 1784
Triggering a new build of test-container-nmr-integrals
Finished: SUCCESS