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/master
Seen 2 remote branches
Checking out Revision 50a13ceecbb124b2bf366e44bb22311f946fad7a (origin/develop)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 50a13ceecbb124b2bf366e44bb22311f946fad7a
 > git branch -a -v --no-abbrev # timeout=10
 > git branch -D develop # timeout=10
 > git checkout -b develop 50a13ceecbb124b2bf366e44bb22311f946fad7a
 > git rev-list f611d607abb427fdb0d10a48d39727b917697a82 # timeout=10
[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/jenkins486710271850480905.sh
+ wget -O make-versions-file https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
--2018-06-29 16:53:39--  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% 35.6M=0s

2018-06-29 16:53:40 (35.6 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="0.1.0"" for variable TOOL_VERSION.
DEBUG: Replaced variable name: "LABEL TOOL_VERSION="0.1.0"".
DEBUG: New version variable definition: TOOL_VERSION="0.1.0"
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=0.1.0
DEBUG: CONTAINER_VERSION=0.1
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_v0.1.0_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:dev_v0.1.0_cv0.1.11 --no-cache=true --pull=true /home/ubuntu/workspace/container-nmr-integrals
Sending build context to Docker daemon  355.8kB

Step 1/17 : FROM artemklevtsov/r-alpine:3.3.1
3.3.1: Pulling from artemklevtsov/r-alpine
Digest: sha256:a49980621dc8dae8e29f87e2125bb6520f5b813aea7c08ca3979c0b4c3283d0c
Status: Image is up to date for artemklevtsov/r-alpine:3.3.1
 ---> 218ef88601b1
Step 2/17 : MAINTAINER PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )
 ---> Running in 4798b5935edb
 ---> 9ff32de3b615
Removing intermediate container 4798b5935edb
Step 3/17 : LABEL Description "R-based script to compute NMR spectrum deviation for sample QC"
 ---> Running in efff1224e6e3
 ---> dc1c1f359093
Removing intermediate container efff1224e6e3
Step 4/17 : LABEL software.version "0.1.0"
 ---> Running in 9f595c1e0681
 ---> e6c0ec8ede6c
Removing intermediate container 9f595c1e0681
Step 5/17 : LABEL version "0.1"
 ---> Running in 6ba8eab29e7b
 ---> cbd6098e3fe0
Removing intermediate container 6ba8eab29e7b
Step 6/17 : LABEL software "nmr-integrals"
 ---> Running in d6cf5a0456d6
 ---> 5fcc41324251
Removing intermediate container d6cf5a0456d6
Step 7/17 : LABEL base.image "artemklevtsov/r-alpine:3.3.1"
 ---> Running in d05890d0f376
 ---> a406a2eee6fb
Removing intermediate container d05890d0f376
Step 8/17 : LABEL website "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in 6007dc739a62
 ---> c37bd9207e4d
Removing intermediate container 6007dc739a62
Step 9/17 : LABEL documentation "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in 83e6054b393d
 ---> e549f485fda9
Removing intermediate container 83e6054b393d
Step 10/17 : LABEL license "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in 060abd9954bb
 ---> 47af54c3d2c6
Removing intermediate container 060abd9954bb
Step 11/17 : LABEL tags "Metabolomics"
 ---> Running in 835ed7b7ec15
 ---> f4cda336dcc1
Removing intermediate container 835ed7b7ec15
Step 12/17 : RUN apk update   && apk add ca-certificates unzip wget   && rm -rf /var/cache/apk/*
 ---> Running in 24b343c12ca1
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
v3.4.6-299-ge10ec9b [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-r2)
Executing busybox-1.24.2-r9.trigger
OK: 244 MiB in 70 packages
 ---> 7df45da344bd
Removing intermediate container 24b343c12ca1
Step 13/17 : RUN Rscript -e 'install.packages(c("caTools", "optparse"))'
 ---> Running in bc1d5e04bed8
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.tar.gz'
Content type 'application/x-gzip' length 63358 bytes (61 KB)
==================================================
downloaded 61 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/RtmpiChBPa/downloaded_packages’
 ---> 8510559aa336
Removing intermediate container bc1d5e04bed8
Step 14/17 : WORKDIR /nmr-integrals
 ---> 9046e382662f
Removing intermediate container 67d8bfd1b69c
Step 15/17 : COPY integrals.R integrals_galaxy_wrapper.sh runTest1.sh /usr/local/bin/
 ---> 26d3f95ae65c
Removing intermediate container 041e54f41434
Step 16/17 : RUN chmod a+rx      /usr/local/bin/integrals.R      /usr/local/bin/integrals_galaxy_wrapper.sh      /usr/local/bin/runTest1.sh
 ---> Running in 1da7c82373d4
 ---> b99c390c17dd
Removing intermediate container 1da7c82373d4
Step 17/17 : ENTRYPOINT integrals_galaxy_wrapper.sh
 ---> Running in 4d39c01f3e96
 ---> 4801ab6eb542
Removing intermediate container 4d39c01f3e96
Successfully built 4801ab6eb542
Successfully tagged docker-registry-v2.local:30750/phnmnl/nmr-integrals:dev_v0.1.0_cv0.1.11
[container-nmr-integrals] $ docker tag 4801ab6eb542 docker-registry-v2.local:30750/phnmnl/nmr-integrals:latest
[container-nmr-integrals] $ docker inspect 4801ab6eb542
[container-nmr-integrals] $ /bin/bash -xe /tmp/jenkins328422908495906106.sh
+ wget -O test-built-container https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
--2018-06-29 16:53:55--  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% 70.2M=0s

2018-06-29 16:53:55 (70.2 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:dev_v0.1.0_cv0.1.11
[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:dev_v0.1.0_cv0.1.11
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/nmr-integrals]
91675eaa6550: Preparing
5fe78246a993: Preparing
b8ef651c0380: Preparing
bc622a6817a5: Preparing
e13848f4c030: Preparing
853e0cddde7d: Preparing
4fe15f8d0ae6: Preparing
853e0cddde7d: Waiting
4fe15f8d0ae6: Waiting
b8ef651c0380: Pushed
5fe78246a993: Pushed
91675eaa6550: Pushed
bc622a6817a5: Pushed
853e0cddde7d: Layer already exists
e13848f4c030: Pushed
4fe15f8d0ae6: Layer already exists
dev_v0.1.0_cv0.1.11: digest: sha256:dbcede4c18783fad7671cad26aa0da78d85c584c041167ec198f6a4fa52af818 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]
91675eaa6550: Preparing
5fe78246a993: Preparing
b8ef651c0380: Preparing
bc622a6817a5: Preparing
e13848f4c030: Preparing
853e0cddde7d: Preparing
4fe15f8d0ae6: Preparing
853e0cddde7d: Waiting
4fe15f8d0ae6: Waiting
91675eaa6550: Layer already exists
5fe78246a993: Layer already exists
b8ef651c0380: Layer already exists
bc622a6817a5: Layer already exists
e13848f4c030: Layer already exists
853e0cddde7d: Layer already exists
4fe15f8d0ae6: Layer already exists
latest: digest: sha256:dbcede4c18783fad7671cad26aa0da78d85c584c041167ec198f6a4fa52af818 size: 1784
Triggering a new build of test-container-nmr-integrals
Finished: SUCCESS