[Biojava-dev] [Biojava-l] BioJava 3.0.8 released
Michael Heuer
heuermh at gmail.com
Wed Apr 2 06:06:24 UTC 2014
ok, thanks, I may have identified a potential problem, will email you off-list.
michael
On Tue, Apr 1, 2014 at 10:45 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
> 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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