[Biojava-dev] [Biojava-l] BioJava 3.0.8 released

Mon Mar 31 03:26:05 UTC 2014

F@#$ me, what is it with the maven release plugin?

The release:perform step is getting stuck, possibly because of
something wrong with maven-metadata.xml (notice 711/710 B were
received, see below).

Could it be that Travis CI is interfering?  I'm not seeing any other
network problems.

   michael

$ mvn release:perform
...
[INFO] [INFO] --- maven-deploy-plugin:2.8.1:deploy (default-deploy) @
biojava-legacy ---
[INFO] Uploading:
scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/org/biojava/biojava-legacy/1.8.5/biojava-legacy-1.8.5.pom
[INFO] 4/9 KB
[INFO] 8/9 KB
[INFO] 9/9 KB
[INFO]
[INFO] Uploaded:
scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/org/biojava/biojava-legacy/1.8.5/biojava-legacy-1.8.5.pom
(9 KB at 3.1 KB/sec)
[INFO] Downloading:
scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/org/biojava/biojava-legacy/maven-metadata.xml
[INFO] 710/710 B
[INFO] 711/710 B

^C~/working/biojava-legacy
$ mvn release:perform
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO]
[INFO] biojava-legacy
[INFO] bytecode
[INFO] core
[INFO] alignment
[INFO] biosql
[INFO] blast
[INFO] das
[INFO] sequencing
[INFO] gui
[INFO] phylo
[INFO]
[INFO] Using the builder
org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder
with a thread count of 1
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building biojava-legacy 1.8.6-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-release-plugin:2.5:perform (default-cli) @ biojava-legacy ---
[INFO] Checking out the project to perform the release ...
[INFO] Executing: /bin/sh -c cd
/Users/heuermh/working/biojava-legacy/target && git clone --branch
biojava-legacy-1.8.5 git at github.com:biojava/biojava-legacy.git
/Users/heuermh/working/biojava-legacy/target/checkout
[INFO] Working directory: /Users/heuermh/working/biojava-legacy/target
[INFO] Executing: /bin/sh -c cd
/var/folders/cr/hxqk0k7n3kd3mk6phfjqfp5h0000gn/T/ && git ls-remote
git at github.com:biojava/biojava-legacy.git
[INFO] Working directory: /var/folders/cr/hxqk0k7n3kd3mk6phfjqfp5h0000gn/T
[INFO] Executing: /bin/sh -c cd
/Users/heuermh/working/biojava-legacy/target/checkout && git fetch
git at github.com:biojava/biojava-legacy.git
[INFO] Working directory: /Users/heuermh/working/biojava-legacy/target/checkout
[INFO] Executing: /bin/sh -c cd
/Users/heuermh/working/biojava-legacy/target/checkout && git checkout
biojava-legacy-1.8.5
[INFO] Working directory: /Users/heuermh/working/biojava-legacy/target/checkout
[INFO] Executing: /bin/sh -c cd
/Users/heuermh/working/biojava-legacy/target/checkout && git ls-files
[INFO] Working directory: /Users/heuermh/working/biojava-legacy/target/checkout
[INFO] Invoking perform goals in directory
/Users/heuermh/working/biojava-legacy/target/checkout
[INFO] Executing goals 'deploy'...
[WARNING] Maven will be executed in interactive mode, but no input
stream has been configured for this MavenInvoker instance.
[INFO] [INFO] Scanning for projects...
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Reactor Build Order:
[INFO] [INFO]
[INFO] [INFO] biojava-legacy
[INFO] [INFO] bytecode
[INFO] [INFO] core
[INFO] [INFO] alignment
[INFO] [INFO] biosql
[INFO] [INFO] blast
[INFO] [INFO] das
[INFO] [INFO] sequencing
[INFO] [INFO] gui
[INFO] [INFO] phylo
[INFO] [INFO]
[INFO] [INFO] Using the builder
org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder
with a thread count of 1
[INFO] [INFO]
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO] Building biojava-legacy 1.8.5
[INFO] [INFO] ------------------------------------------------------------------------
[INFO] [INFO]
[INFO] [INFO] >>> maven-source-plugin:2.2.1:jar (attach-sources) @
biojava-legacy >>>
[INFO] [INFO]
[INFO] [INFO] <<< maven-source-plugin:2.2.1:jar (attach-sources) @
biojava-legacy <<<
[INFO] [INFO]
[INFO] [INFO] --- maven-source-plugin:2.2.1:jar (attach-sources) @
biojava-legacy ---
[INFO] [INFO]
[INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @
biojava-legacy ---
[INFO] [INFO] Not executing Javadoc as the project is not a Java
classpath-capable package
[INFO] [INFO]
[INFO] [INFO] --- maven-install-plugin:2.4:install (default-install) @
biojava-legacy ---
[INFO] [INFO] Installing
/Users/heuermh/working/biojava-legacy/target/checkout/pom.xml to
/Users/heuermh/.m2/repository/org/biojava/biojava-legacy/1.8.5/biojava-legacy-1.8.5.pom
[INFO] [INFO]
[INFO] [INFO] --- maven-deploy-plugin:2.8.1:deploy (default-deploy) @
biojava-legacy ---
[INFO] Uploading:
scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/org/biojava/biojava-legacy/1.8.5/biojava-legacy-1.8.5.pom
[INFO] 4/9 KB
[INFO] 8/9 KB
[INFO] 9/9 KB
[INFO]
[INFO] Uploaded:
scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/org/biojava/biojava-legacy/1.8.5/biojava-legacy-1.8.5.pom
(9 KB at 3.2 KB/sec)
[INFO] Downloading:
scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/org/biojava/biojava-legacy/maven-metadata.xml
[INFO] 710/710 B
[INFO] 711/710 B

On Tue, Mar 25, 2014 at 5:42 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> that would be great. after all there were some bug fixes...
>
> Thanks,
>
> Andreas
>
>
> On Tue, Mar 25, 2014 at 3:41 PM, Michael Heuer <heuermh at gmail.com> wrote:
>>
>> Nice work, Andreas.
>>
>> Should I cut a new biojava-legacy release as well?  There aren't as many
>> changes
>>
>>
>> https://github.com/biojava/biojava-legacy/compare/biojava-legacy-1.8.4...master
>>
>>    michael
>>
>>
>> On Tue, Mar 25, 2014 at 5:34 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>> > == BioJava 3.0.8 released ==
>> >
>> > BioJava 3.0.8 was released on March 25th 2014 and is available from
>> > http://biojava.org/wiki/BioJava:Download as well as from the
>> > BioJava maven repository at http://www.biojava.org/download/maven/
>> >
>> > This release would not have been possible without contributions from
>> > 13 developers, thanks to all for their support!
>> >
>> > BioJava 3.0.8 includes a lot of new features as well as numerous bug
>> > fixes
>> > and improvements.
>> >
>> > New Features:
>> >
>> >  - new Genbank writer
>> >  - new parser for Karyotype file from UCSC
>> >  - new parser for Gene locations from UCSC
>> >  - new parser for Gene names file from genenames.org
>> >  - new module for Cox regression code for survival analysis
>> >  - new calculation of accessible surface area (ASA)
>> >  - new module for parsing .OBO files (ontologies)
>> >  - improved representation of SCOP and Berkeley-SCOP classifications
>> >
>> > For a detailed comparison see here:
>> > https://github.com/biojava/biojava/compare/biojava-3.0.7...biojava-3.0.8
>> >
>> > For the next release we are planning some refactoring and removal of
>> > code
>> > that has been deprecated for a long time. As such the next release will
>> > be
>> > named 3.1.0.
>> >
>> > About BioJava:
>> >
>> > BioJava is a mature open-source project that provides a framework for
>> > processing of biological data. BioJava contains powerful analysis and
>> > statistical routines, tools for parsing common file formats, and
>> > packages for manipulating sequences and 3D structures. It enables
>> > rapid bioinformatics application development in the Java programming
>> > language.
>> >
>> > Happy BioJava-ing,
>> >
>> > Andreas
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------