[Biojava-dev] compilation of 1.8.2

Wed May 23 16:14:27 UTC 2012

Hi Oliver,

couple of things:

- the structure dependency is the correct one for the 1.8 series,
however it is named in a misleading way.  It is really still the 1.8
version.

- not sure why you want to do this via ant, that sounds like you are
up for a lot of extra work... Aren't there any other Maven based
projects in Debian? The Maven packaging is fairly standardised, so
there might be some scripts that manage to convert from one packaging
to another... In fact, not sure how your requirements are but it might
be entirely sufficient to just copy and paste the jars from our Maven
repository, we provide source, binary and javadoc jars. Going back to
an ant build sounds like going one step back.

- If you go through all the trouble why don't you do this update for
the 3.X series?

Andreas

On Wed, May 23, 2012 at 5:58 AM, Olivier Sallou <olivier.sallou at irisa.fr> wrote:
> As additional info,
> I tried to build with maven, to see what could going on....
> and for DAS compile, here is maven extract:
>
> I am afraid of this 'cause DAS seems to download lots of biojava3
> dependencies (in which he  founds my missing Atom class source).
>
> DAS downloads:
> http://www.biojava.org/download/maven/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.jar
> which contains:
> org/biojava/bio/structure/io/SeqRes2AtomAligner.class
> org/biojava/bio/structure/io/mmcif/model/AtomSite.class
> org/biojava/bio/structure/AtomImpl.class
> org/biojava/bio/structure/Atom.class    <----------------- My missing
> source files in 1.8.2
> org/biojava/bio/structure/align/util/AtomCache.class
> org/biojava/bio/structure/AtomIterator.class
>
> This is not really consistent and does not help me to compile v1.8.2.
>
> So, sources located at http://www.biojava.org/download/bj1.8.2/ seem to
> have missing files (structure), and maven build is wrong, using v3
> package....
>
> Maven logs:
>
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Building das 1.8.2
> [INFO]
> ------------------------------------------------------------------------
> Downloading:
> http://repo1.maven.org/maven2/xerces/xercesImpl/2.4.0/xercesImpl-2.4.0.pom
> Downloaded:
> http://repo1.maven.org/maven2/xerces/xercesImpl/2.4.0/xercesImpl-2.4.0.pom
> (150 B at 0.3 KB/sec)
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.pom
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.pom
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.pom
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.pom
> (2 KB at 2.1 KB/sec)
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava/3.0-alpha2-SNAPSHOT/maven-metadata.xml
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava/3.0-alpha2-SNAPSHOT/maven-metadata.xml
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava/3.0-alpha2-SNAPSHOT/maven-metadata.xml
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava/3.0-alpha2-SNAPSHOT/maven-metadata.xml
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava/3.0-alpha2-SNAPSHOT/maven-metadata.xml
> (315 B at 1.3 KB/sec)
> [WARNING] Could not transfer metadata
> org.biojava:biojava:3.0-alpha2-SNAPSHOT/maven-metadata.xml from/to
> maven-repository.dev.java.net (http://download.java.net/maven/1): No
> connector available to access repository maven-repository.dev.java.net
> (http://download.java.net/maven/1) of type legacy using the available
> factories WagonRepositoryConnectorFactory
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava/3.0-alpha2-SNAPSHOT/biojava-3.0-alpha2-SNAPSHOT.pom
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava/3.0-alpha2-SNAPSHOT/biojava-3.0-alpha2-SNAPSHOT.pom
> (8 KB at 18.2 KB/sec)
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.pom
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.pom
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.pom
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.pom
> (2 KB at 8.6 KB/sec)
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.pom
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.pom
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.pom
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.pom
> (2 KB at 8.7 KB/sec)
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.pom
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.pom
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.pom
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.pom
> (3 KB at 8.8 KB/sec)
> Downloading:
> http://repo1.maven.org/maven2/org/forester/0.955/forester-0.955.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/forester/0.955/forester-0.955.pom
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/forester/0.955/forester-0.955.pom
> Downloading:
> http://download.java.net/maven/2/org/forester/0.955/forester-0.955.pom
> Downloading:
> http://www.biojava.org/download/maven/org/forester/0.955/forester-0.955.pom
> Downloaded:
> http://www.biojava.org/download/maven/org/forester/0.955/forester-0.955.pom
> (421 B at 1.9 KB/sec)
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.jar
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.jar
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.jar
> Downloading:
> http://repo1.maven.org/maven2/org/forester/0.955/forester-0.955.jar
> Downloading:
> http://repo1.maven.org/maven2/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/forester/0.955/forester-0.955.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-release/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/forester/0.955/forester-0.955.jar
> Downloading:
> http://maven.irisa.fr/artifactory/genouest-public-snapshot/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.jar
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.jar
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.jar
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.jar
> Downloading:
> http://download.java.net/maven/2/org/forester/0.955/forester-0.955.jar
> Downloading:
> http://download.java.net/maven/2/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.jar
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.jar
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.jar
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.jar
> Downloading:
> http://www.biojava.org/download/maven/org/forester/0.955/forester-0.955.jar
> Downloading:
> http://www.biojava.org/download/maven/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.jar
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-phylo/3.0-alpha1/biojava3-phylo-3.0-alpha1.jar
> (58 KB at 68.2 KB/sec)
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-alignment/3.0-alpha1/biojava3-alignment-3.0-alpha1.jar
> (102 KB at 101.8 KB/sec)
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-core/3.0-alpha1/biojava3-core-3.0-alpha1.jar
> (238 KB at 189.0 KB/sec)
> Downloaded:
> http://www.biojava.org/download/maven/org/biojava/biojava3-structure/3.0-alpha1/biojava3-structure-3.0-alpha1.jar
> (501 KB at 312.7 KB/sec)
> Downloaded:
> http://www.biojava.org/download/maven/org/forester/0.955/forester-0.955.jar
> (2394 KB at 505.3 KB/sec)
> [INFO]
> [INFO] --- maven-resources-plugin:2.4.3:resources (default-resources) @
> das ---
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] skip non existing resourceDirectory
> /Users/osallou/Downloads/biojava-legacy-1.8.2-src/das/src/main/resources
> [INFO]
> [INFO] --- maven-compiler-plugin:2.0.2:compile (default-compile) @ das ---
> [INFO] Compiling 91 source files to
> /Users/osallou/Downloads/biojava-legacy-1.8.2-src/das/target/classes
>
>
> Le 5/23/12 1:12 PM, Olivier Sallou a écrit :
>> Hi,
>> I am trying to compile biojava 1.8.2 from source but I have an issue.
>>
>> I do not use Maven, and created an ant build file, for Debian packaging
>> reasons.
>>
>> I failed at compile time in DAS library, not finding
>> org.biojava.bio.structure.Atom
>>
>> Indeed, nor core or das define this interface:
>> osallou at debiansid:$ ls core/src/main/resources/org/biojava/bio/structure
>> blosum62.mat  standardaminos.pdb
>> osallou at debiansid:$ ls das/src/main/java/org/biojava/bio/structure
>> io
>>
>>
>>     [mkdir] Created dir:
>> /home/osallou/DEBIAN-MED/biojava/biojava-live-1.8.2.orig/build/biojava-das/classes
>>     [javac]
>> /home/osallou/DEBIAN-MED/biojava/biojava-live-1.8.2.orig/das/build.xml:56:
>> warning: 'includeantruntime' was not set, defaulting to
>> build.sysclasspath=last; set to false for repeatable builds
>>     [javac] Compiling 100 source files to
>> /home/osallou/DEBIAN-MED/biojava/biojava-live-1.8.2.orig/build/biojava-das/classes
>>     [javac] Alignment.java:33: cannot find symbol
>>     [javac] symbol  : class Atom
>>     [javac] location: package org.biojava.bio.structure
>>     [javac] import org.biojava.bio.structure.Atom;
>>
>> Has anyone an idea of why it is missing or what I should get to find it?
>>
>
> --
> Olivier Sallou
> IRISA / University of Rennes 1
> Campus de Beaulieu, 35000 RENNES - FRANCE
> Tel: 02.99.84.71.95
>
> gpg key id: 4096R/326D8438  (keyring.debian.org)
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>
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