[Biojava-dev] [Biojava-l] BioJava 3.0.8 released
Michael Heuer
heuermh at gmail.com
Tue Apr 1 02:02:54 UTC 2014
Hello Andreas, Bruno
Thanks for the help. I have added debug output and additional
information to the JIRA issue linked below.
At this point I'm not sure I want to do a release:rollback since the
prepare step worked fine and the 1.8.5 git tags look correct.
michael
On Mon, Mar 31, 2014 at 11:12 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> Hi Michael,
>
> At first glimpse I suspect some ssh/key issue...
>
> - can you try a mvn release:rollback ?
> - what is the output of mvn release:prepare ?
>
> finally, as Bruno says, try to use -X for more verbose output.
>
> Thanks,
>
> Andreas
>
>
> On Mon, Mar 31, 2014 at 8:12 AM, Bruno P. Kinoshita
> <brunodepaulak at yahoo.com.br> wrote:
>>
>> Hi Michael,
>>
>> Maybe you could try mvn release -e -X too. It gives more verbose output,
>> you may be able to find something there.
>>
>> Hope that helps
>>
>> Bruno P. Kinoshita
>> http://kinoshita.eti.br
>> http://tupilabs.com
>>
>>
>> ----- Original Message -----
>> > From: Michael Heuer <heuermh at gmail.com>
>> > To: Andreas Prlic <andreas at sdsc.edu>
>> > Cc: biojava-dev <biojava-dev at lists.open-bio.org>
>> > Sent: Monday, March 31, 2014 11:14 AM
>> > Subject: Re: [Biojava-dev] [Biojava-l] BioJava 3.0.8 released
>> >
>> > 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
>> >>>
>> >>> -----------------------------------------------------------------------
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> >
>
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
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