[Biojava-dev] [Biojava-l] BioJava 3.0.8 released
Andreas Prlic
andreas at sdsc.edu
Mon Mar 31 16:12:24 UTC 2014
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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