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draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
MIT License
23 stars 7 forks source link

gradle build fails #52

Closed matthiaskoenig closed 5 years ago

matthiaskoenig commented 5 years ago

The gradle build is not working. I am getting

gradle
Setup DB

FAILURE: Build failed with an exception.

* Where:
Build file '/home/mkoenig/git/ModelPolisher/build.gradle' line: 165

* What went wrong:
A problem occurred evaluating root project 'ModelPolisher'.
> .travis.yml (No such file or directory)

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 0s

Tried this on master, develop and docker branch

codekaust commented 5 years ago

@matthiaskoenig This is #36 only. The big is surely present in the master branch, but the develop branch should build fine. I checked that. feat/docker is now updated to build correctly.

matthiaskoenig commented 5 years ago

I see this in all branches, i.e. also in the develop branch. I did a clean clone of the repository, and can reproduce the issue.

codekaust commented 5 years ago

@matthiaskoenig I am not able to reproduce the issue. @mephenor Can you try once? I just made a fresh clone of the repo, but ModelPolisher is building fine. All the below outputs are for branch master. Gradle version:

kaustubh@kaustubh:~/Desktop/ModelPolisher$ gradle -v

------------------------------------------------------------
Gradle 5.5.1
------------------------------------------------------------

Build time:   2019-07-10 20:38:12 UTC
Revision:     3245f748c7061472da4dc184991919810f7935a5

Kotlin:       1.3.31
Groovy:       2.5.4
Ant:          Apache Ant(TM) version 1.9.14 compiled on March 12 2019
JVM:          11.0.1 (Oracle Corporation 11.0.1+13)
OS:           Linux 4.18.0-25-generic amd64

Build lightJar

kaustubh@kaustubh:~/Desktop/ModelPolisher$ gradle lightJar
Starting a Gradle Daemon (subsequent builds will be faster)

> Task :compileJava
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: /home/kaustubh/Desktop/ModelPolisher/src/edu/ucsd/sbrg/cobra/COBRAparser.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

BUILD SUCCESSFUL in 28s
5 actionable tasks: 5 executed

Build fatJar

kaustubh@kaustubh:~/Desktop/ModelPolisher$ gradle

> Task :compileJava
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: /home/kaustubh/Desktop/ModelPolisher/src/edu/ucsd/sbrg/cobra/COBRAparser.java uses unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.

> Task :setupDB
Setup DB
Fetching checksum file
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100    43  100    43    0     0     14      0  0:00:03  0:00:02  0:00:01     0
Fetching bigg.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100   990    0   990    0     0    368      0 --:--:--  0:00:02 --:--:--     0
100  279M  100  279M    0     0  17.0M      0  0:00:16  0:00:16 --:--:-- 26.5M
bigg.zip: OK
Archive:  ../resources/edu/ucsd/sbrg/bigg/bigg.zip
  inflating: ../resources/edu/ucsd/sbrg/bigg/bigg.sqlite  

BUILD SUCCESSFUL in 2m 3s
7 actionable tasks: 7 executed
matthiaskoenig commented 5 years ago

This is fixed by an update of gradle. The default version in ubuntu is gradle 4.4.1 which will fail the build

sudo add-apt-repository ppa:cwchien/gradle
sudo apt-get update
sudo apt-get install gradle
gradle -v

will install gradle version 5.5.1 which builds fine.

codekaust commented 5 years ago

Added Instruction in README. See ff497b218ee3a9987e7a241ddffea20afa8c7f7c