[Biojava-dev] compilation of 1.8.2

Wed May 23 16:46:02 UTC 2012

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/

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
>
>
> _______________________________________________
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> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>