[Biojava-dev] compilation of 1.8.2

Wed May 23 16:31:26 UTC 2012

Le 5/23/12 6:14 PM, Andreas Prlic a écrit :
> 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.
As it is for Debian packaging, I need to go from sources for compilation
to reproduce the jars.
I cannot get any jar. Maven, in Debian build mechanism is quite complex
as we cannot use any external jar (and this is waht maven does...).

Creating an ant build file is fine, it works for all the libraries but DAS.

My issue is, if I look in jars, I indeed find the files:

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

But if I look in the source archive located at:
http://www.biojava.org/download/bj1.8.2/biojava-legacy-1.8.2-src.tar.gz

I cannot find any file corresponding to this jar (Atom, AtomImpl,
SeqRes2AtomAligner...)

So, in my compilation, it fails....

In maven compilation, I see that it tries to compile:
[INFO] bytecode
[INFO] core
[INFO] alignment
[INFO] biosql
[INFO] blast
[INFO] das
[INFO] sequencing
[INFO] gui
[INFO] phylo

das has the dependency biojava3-structure in pom.xml, which is not
generated with the biojava sources.

>
> - If you go through all the trouble why don't you do this update for
> the 3.X series?
I am packaging biojava for Debian, we plan to package v1.8 and v3.
>
> 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)
>> Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev

-- 
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)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438