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

Mon Mar 31 14:14:17 UTC 2014

Still seeing the same this morning, except now the file sizes are different

$ mvn release:perform
...
[INFO] Downloading:
scp://cloudportal.open-bio.org/home/websites/biojava.org/html/static/download/maven/org/biojava/biojava-legacy/maven-metadata.xml
[INFO] 750/750 B
[INFO] 751/750 B


I created an issue here

http://jira.codehaus.org/browse/MDEPLOY-177

   michael

On Sun, Mar 30, 2014 at 10:26 PM, Michael Heuer <heuermh at gmail.com> wrote:
> 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
>> -----------------------------------------------------------------------