[Biojava-dev] [Biojava-l] BioJava 3.0.8 released
Michael Heuer
heuermh at gmail.com
Wed Apr 2 01:04:45 UTC 2014
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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