[Biojava-dev] compilation of 1.8.2

Wed May 23 12:58:12 UTC 2012

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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