[Biojava-dev] [Biojava-l] BioJava 3.0.8 released
Andreas Prlic
andreas at sdsc.edu
Wed Apr 2 03:45:14 UTC 2014
Hi Michael,
My build server is still on maven 3.0.4...
Andreas
On Tue, Apr 1, 2014 at 6:04 PM, Michael Heuer <heuermh at gmail.com> wrote:
> Hello Andreas,
>
> Did you use maven version 3.2.1 to perform the biojava 3.0.8 release
> or an earlier version?
>
> I'm still struggling to find a cause for or a solution to this problem.
>
> Thanks,
>
> michael
>
>
> On Mon, Mar 31, 2014 at 9:02 PM, Michael Heuer <heuermh at gmail.com> wrote:
> > 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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