[Biojava-dev] compilation of 1.8.2

Wed May 23 16:52:13 UTC 2012

Le 5/23/12 6:46 PM, Mark Fortner a écrit :
> There are a couple of maven plugins that make it easy to create debs and
> rpms for libraries like biojava.  Here are a couple of links that may help:
>
> http://vafer.org/blog/20070918215154/
> http://mojo.codehaus.org/deb-maven-plugin/
> http://mojo.codehaus.org/rpm-maven-plugin/

Thanks but issue is not maven to deb but missing sources in the source
archive :

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

Olivier
>
> Hope this helps,
>
> Mark
>
>
>
>
> On Wed, May 23, 2012 at 9:31 AM, Olivier Sallou <olivier.sallou at irisa.fr>wrote:
>
>>
>> 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
>>
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
> _______________________________________________
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> 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