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 258211cbb750e9411f1aa97b03841ef5836a1c42 (origin/develop)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 258211cbb750e9411f1aa97b03841ef5836a1c42
 > git branch -a -v --no-abbrev # timeout=10
 > git branch -D develop # timeout=10
 > git checkout -b develop 258211cbb750e9411f1aa97b03841ef5836a1c42
 > git rev-list 0fb1afd05a5d30de91c86abbc92650be61f15d25 # 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/jenkins416760756384121522.sh
+ wget -O make-versions-file https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/make-versions-file
--2018-06-22 16:42:53--  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% 26.7M=0s

2018-06-22 16:42:53 (26.7 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_cv0.1.2 --no-cache=true --pull=true /home/ubuntu/workspace/container-nmr-integrals
Sending build context to Docker daemon    212kB

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 6fdc8e69deab
 ---> 36d260c9f007
Removing intermediate container 6fdc8e69deab
Step 3/17 : LABEL Description "R-based script to compute NMR spectrum deviation for sample QC"
 ---> Running in 8764c657bae4
 ---> e0a1d035c1ab
Removing intermediate container 8764c657bae4
Step 4/17 : LABEL software.version "0.1.0"
 ---> Running in fbd6a438ee74
 ---> 19fad33633f7
Removing intermediate container fbd6a438ee74
Step 5/17 : LABEL version "0.1"
 ---> Running in e133b86b5473
 ---> ec3a43dda20b
Removing intermediate container e133b86b5473
Step 6/17 : LABEL software "nmr-integrals"
 ---> Running in 91541fa5de83
 ---> ec3196ae9628
Removing intermediate container 91541fa5de83
Step 7/17 : LABEL base.image "artemklevtsov/r-alpine:3.3.1"
 ---> Running in 2505ca95e68d
 ---> 3e84dc7007d4
Removing intermediate container 2505ca95e68d
Step 8/17 : LABEL website "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in a9ed5b129be9
 ---> 7770c33c9cc3
Removing intermediate container a9ed5b129be9
Step 9/17 : LABEL documentation "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in c6b55e6597b3
 ---> acf6dfc34b5f
Removing intermediate container c6b55e6597b3
Step 10/17 : LABEL license "https://github.com/phnmnl/container-nmr-integrals"
 ---> Running in ec36e0f056f5
 ---> 7712c6996bc3
Removing intermediate container ec36e0f056f5
Step 11/17 : LABEL tags "Metabolomics"
 ---> Running in d86be6e9aba8
 ---> 035b14a02cb7
Removing intermediate container d86be6e9aba8
Step 12/17 : RUN apk update   && apk add unzip    && rm -rf /var/cache/apk/*
 ---> Running in f97f1fac7a2a
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
(1/1) Installing unzip (6.0-r1)
Executing busybox-1.24.2-r9.trigger
OK: 244 MiB in 69 packages
 ---> d6f07cf98e39
Removing intermediate container f97f1fac7a2a
Step 13/17 : RUN Rscript -e 'install.packages(c("caTools", "optparse"))'
 ---> Running in 8175d86824b5
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/RtmpBaapLh/downloaded_packages’
 ---> ac61601fc42e
Removing intermediate container 8175d86824b5
Step 14/17 : WORKDIR /nmr-integrals
 ---> 931390267750
Removing intermediate container 9d3ce5380730
Step 15/17 : COPY integrals.R integrals_galaxy_wrapper.sh runTest1.sh /usr/local/bin/
 ---> 1e7e554433ee
Removing intermediate container 1e1744d74d8f
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 ccab062415e6
 ---> 9120cc437848
Removing intermediate container ccab062415e6
Step 17/17 : ENTRYPOINT integrals_galaxy_wrapper.sh
 ---> Running in 08b44561608d
 ---> e595b8f03e1f
Removing intermediate container 08b44561608d
Successfully built e595b8f03e1f
Successfully tagged docker-registry-v2.local:30750/phnmnl/nmr-integrals:dev_v0.1.0_cv0.1.2
[container-nmr-integrals] $ docker tag e595b8f03e1f docker-registry-v2.local:30750/phnmnl/nmr-integrals:latest
[container-nmr-integrals] $ docker inspect e595b8f03e1f
[container-nmr-integrals] $ /bin/bash -xe /tmp/jenkins2524758939011232189.sh
+ wget -O test-built-container https://raw.githubusercontent.com/phnmnl/jenkins-scripts/master/test-built-container
--2018-06-22 16:43:14--  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% 15.5M=0s

2018-06-22 16:43:14 (15.5 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

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

	METABOLITES_TABLE
		Metabolites table in tab-separated format

 	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_cv0.1.2
[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_cv0.1.2
The push refers to a repository [docker-registry-v2.local:30750/phnmnl/nmr-integrals]
eadbdfe9b191: Preparing
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853e0cddde7d: Waiting
4fe15f8d0ae6: Waiting
337d6e9407b6: Pushed
0598c9442f82: Pushed
becc14da172a: Pushed
11faaa953111: Pushed
853e0cddde7d: Layer already exists
eadbdfe9b191: Pushed
4fe15f8d0ae6: Layer already exists
dev_v0.1.0_cv0.1.2: digest: sha256:d4a3936021b6e0baa443d857771ddc581ade81f1d14ca70fa0611a47d37fefbc 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]
eadbdfe9b191: Preparing
0598c9442f82: Preparing
337d6e9407b6: Preparing
11faaa953111: Preparing
becc14da172a: Preparing
853e0cddde7d: Preparing
4fe15f8d0ae6: Preparing
853e0cddde7d: Waiting
4fe15f8d0ae6: Waiting
337d6e9407b6: Layer already exists
eadbdfe9b191: Layer already exists
0598c9442f82: Layer already exists
becc14da172a: Layer already exists
11faaa953111: Layer already exists
853e0cddde7d: Layer already exists
4fe15f8d0ae6: Layer already exists
latest: digest: sha256:d4a3936021b6e0baa443d857771ddc581ade81f1d14ca70fa0611a47d37fefbc size: 1784
Finished: SUCCESS