From bioprogrammer at gmail.com  Wed May 23 19:26:39 2018
From: bioprogrammer at gmail.com (Caitlin)
Date: Wed, 23 May 2018 12:26:39 -0700
Subject: [Biojava-l] Help with building BioJava using Maven?
Message-ID: <CABDKo+wpwU3hasDokm1sCuvXKwfJ8EQnze=bpnM2=i9=T-uz-g@mail.gmail.com>

Hi all.

I am completely inexperienced with respect to using Maven and I am
encountering immense difficulty in building the latest version that I have
cloned from GitHub.

After entering the BioJava folder, edited my pom.xml file to include the
following dependencies:

    <dependencyManagement>
<dependencies>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-core</artifactId>
        <version>5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-aa-prop</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-alignment</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-genome</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-integrationtest</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>


<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-modfinder</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>


<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-ontology</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>



<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-protein-disorder</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>



<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-structure-gui</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>



<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-structure</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>


<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-survival</artifactId>
        <version>5.1.0-SNAPSHOT</version>
      </dependency>

<dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-ws</artifactId>
        <version> 5.1.0-SNAPSHOT </version>
      </dependency>

I then issued the command "mvn clean" which displayed the message "Build
Success". I then issued "mvn install" which failed with:

[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
0.377 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
[INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
[ERROR] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed:
0.35 s <<< FAILURE! - in
org.biojava.nbio.core.util.TestUncompressInputStream
[ERROR]
testUncompression(org.biojava.nbio.core.util.TestUncompressInputStream)
Time elapsed: 0.31 s  <<< FAILURE!
java.lang.AssertionError: array lengths differed, expected.length=9068
actual.length=9257
        at
org.biojava.nbio.core.util.TestUncompressInputStream.testUncompression(TestUncompressInputStream.java:70)

[INFO]
[INFO] Results:
[INFO]
[ERROR] Failures:
[ERROR]   TestUncompressInputStream.testUncompression:70 array lengths
differed, expected.length=9068 actual.length=9257
[INFO]
[ERROR] Tests run: 244, Failures: 1, Errors: 0, Skipped: 6
[INFO]
[INFO]
------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] biojava-core 5.1.0-SNAPSHOT ........................ FAILURE [01:35
min]
[INFO] biojava-alignment 5.1.0-SNAPSHOT ................... SKIPPED
[INFO] biojava-structure 5.1.0-SNAPSHOT ................... SKIPPED
[INFO] biojava-structure-gui 5.1.0-SNAPSHOT ............... SKIPPED
[INFO] biojava-genome 5.1.0-SNAPSHOT ...................... SKIPPED
[INFO] biojava-modfinder 5.1.0-SNAPSHOT ................... SKIPPED
[INFO] biojava-ws 5.1.0-SNAPSHOT .......................... SKIPPED
[INFO] biojava-protein-disorder 5.1.0-SNAPSHOT ............ SKIPPED
[INFO] biojava-aa-prop 5.1.0-SNAPSHOT ..................... SKIPPED
[INFO] biojava-survival 5.1.0-SNAPSHOT .................... SKIPPED
[INFO] biojava-ontology 5.1.0-SNAPSHOT .................... SKIPPED
[INFO] biojava-integrationtest 5.1.0-SNAPSHOT ............. SKIPPED
[INFO] biojava 4.2.2 ...................................... SKIPPED
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 01:36 min
[INFO] Finished at: 2018-05-23T12:26:00-07:00
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.21.0:test (default-test)
on project biojava-core: There are test failures.
[ERROR]
[ERROR] Please refer to
C:\Users\CaitlinG\biojava\biojava-core\target\surefire-reports for the
individual test results.
[ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump,
[date].dumpstream and [date]-jvmRun[N].dumpstream.
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

C:\Users\CaitlinG\biojava>

Thank you for any help you can offer.

~Caitlin
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From jose.duarte at rcsb.org  Wed May 23 20:36:42 2018
From: jose.duarte at rcsb.org (Jose Duarte)
Date: Wed, 23 May 2018 13:36:42 -0700
Subject: [Biojava-l] Help with building BioJava using Maven?
In-Reply-To: <CABDKo+wpwU3hasDokm1sCuvXKwfJ8EQnze=bpnM2=i9=T-uz-g@mail.gmail.com>
References: <CABDKo+wpwU3hasDokm1sCuvXKwfJ8EQnze=bpnM2=i9=T-uz-g@mail.gmail.com>
Message-ID: <CAHhO=JFEC2_4MrFaX00KVudGfBECJatMWCEZjjbiqZf495DuyQ@mail.gmail.com>

If what you want is to use biojava in your project, then you don't need to
clone biojava at all.

Instead you simply make your project a maven project (have a look at a
tutorial, there's plenty around) and add the latest biojava release as a
dependency with this:

    <dependencies>
      <dependency>
        <groupId>org.biojava</groupId>
        <artifactId>biojava-core</artifactId>
        <version>5.0.2</version>
      </dependency>
      <!-- other biojava dependencies as needed -->
    </dependencies>


Once you have the dependency you can then use biojava classes within your
project. Maven will pick everything up automatically.

Jose


On Wed, May 23, 2018 at 12:26 PM, Caitlin <bioprogrammer at gmail.com> wrote:

> Hi all.
>
> I am completely inexperienced with respect to using Maven and I am
> encountering immense difficulty in building the latest version that I have
> cloned from GitHub.
>
> After entering the BioJava folder, edited my pom.xml file to include the
> following dependencies:
>
>     <dependencyManagement>
> <dependencies>
>       <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-core</artifactId>
>         <version>5.1.0-SNAPSHOT </version>
>       </dependency>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-aa-prop</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-alignment</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-genome</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-integrationtest</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-modfinder</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-ontology</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-protein-disorder</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-structure-gui</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-structure</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-survival</artifactId>
>         <version>5.1.0-SNAPSHOT</version>
>       </dependency>
>
> <dependency>
>         <groupId>org.biojava</groupId>
>         <artifactId>biojava-ws</artifactId>
>         <version> 5.1.0-SNAPSHOT </version>
>       </dependency>
>
> I then issued the command "mvn clean" which displayed the message "Build
> Success". I then issued "mvn install" which failed with:
>
> [INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed:
> 0.377 s - in org.biojava.nbio.core.TestAmbiguityCompoundSet
> [INFO] Running org.biojava.nbio.core.util.TestUncompressInputStream
> [ERROR] Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed:
> 0.35 s <<< FAILURE! - in org.biojava.nbio.core.util.
> TestUncompressInputStream
> [ERROR] testUncompression(org.biojava.nbio.core.util.TestUncompressInputStream)
> Time elapsed: 0.31 s  <<< FAILURE!
> java.lang.AssertionError: array lengths differed, expected.length=9068
> actual.length=9257
>         at org.biojava.nbio.core.util.TestUncompressInputStream.
> testUncompression(TestUncompressInputStream.java:70)
>
> [INFO]
> [INFO] Results:
> [INFO]
> [ERROR] Failures:
> [ERROR]   TestUncompressInputStream.testUncompression:70 array lengths
> differed, expected.length=9068 actual.length=9257
> [INFO]
> [ERROR] Tests run: 244, Failures: 1, Errors: 0, Skipped: 6
> [INFO]
> [INFO] ------------------------------------------------------------
> ------------
> [INFO] Reactor Summary:
> [INFO]
> [INFO] biojava-core 5.1.0-SNAPSHOT ........................ FAILURE [01:35
> min]
> [INFO] biojava-alignment 5.1.0-SNAPSHOT ................... SKIPPED
> [INFO] biojava-structure 5.1.0-SNAPSHOT ................... SKIPPED
> [INFO] biojava-structure-gui 5.1.0-SNAPSHOT ............... SKIPPED
> [INFO] biojava-genome 5.1.0-SNAPSHOT ...................... SKIPPED
> [INFO] biojava-modfinder 5.1.0-SNAPSHOT ................... SKIPPED
> [INFO] biojava-ws 5.1.0-SNAPSHOT .......................... SKIPPED
> [INFO] biojava-protein-disorder 5.1.0-SNAPSHOT ............ SKIPPED
> [INFO] biojava-aa-prop 5.1.0-SNAPSHOT ..................... SKIPPED
> [INFO] biojava-survival 5.1.0-SNAPSHOT .................... SKIPPED
> [INFO] biojava-ontology 5.1.0-SNAPSHOT .................... SKIPPED
> [INFO] biojava-integrationtest 5.1.0-SNAPSHOT ............. SKIPPED
> [INFO] biojava 4.2.2 ...................................... SKIPPED
> [INFO] ------------------------------------------------------------
> ------------
> [INFO] BUILD FAILURE
> [INFO] ------------------------------------------------------------
> ------------
> [INFO] Total time: 01:36 min
> [INFO] Finished at: 2018-05-23T12:26:00-07:00
> [INFO] ------------------------------------------------------------
> ------------
> [ERROR] Failed to execute goal org.apache.maven.plugins:
> maven-surefire-plugin:2.21.0:test (default-test) on project biojava-core:
> There are test failures.
> [ERROR]
> [ERROR] Please refer to C:\Users\CaitlinG\biojava\
> biojava-core\target\surefire-reports for the individual test results.
> [ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump,
> [date].dumpstream and [date]-jvmRun[N].dumpstream.
> [ERROR] -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the
> -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/
> MojoFailureException
>
> C:\Users\CaitlinG\biojava>
>
> Thank you for any help you can offer.
>
> ~Caitlin
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>
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From cmmo at infomed.sld.cu  Fri May 25 16:40:11 2018
From: cmmo at infomed.sld.cu (=?iso-8859-1?Q?Carlos_M._Mart=EDnez_Ortiz?=)
Date: Fri, 25 May 2018 12:40:11 -0400
Subject: [Biojava-l] blast parser
Message-ID: <000001d3f447$0ddf7500$299e5f00$@infomed.sld.cu>

Hi, I have implemented a code using the recipe of BiojavaHowTo to parse a
BLAST output in xml. I?m using netbean IDE and biojava-1.7.jar library.
This is the error:

org.xml.sax.SAXException: Could not recognise the format of this file as one
supported by the framework.

                At
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java
:185)

                at javaapplication1.BlastParser.main(BlastParser.java:41)

 

the line 41 is:

parser.parse(new InputSource(is));

 

Any help? Thanks you 



--
Este mensaje le ha llegado mediante el servicio de correo electronico que ofrece Infomed para respaldar el cumplimiento de las misiones del Sistema Nacional de Salud. La persona que envia este correo asume el compromiso de usar el servicio a tales fines y cumplir con las regulaciones establecidas

Infomed: http://www.sld.cu/


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From jose.duarte at rcsb.org  Fri May 25 18:00:21 2018
From: jose.duarte at rcsb.org (Jose Duarte)
Date: Fri, 25 May 2018 11:00:21 -0700
Subject: [Biojava-l] blast parser
In-Reply-To: <000001d3f447$0ddf7500$299e5f00$@infomed.sld.cu>
References: <000001d3f447$0ddf7500$299e5f00$@infomed.sld.cu>
Message-ID: <CAHhO=JE+e89hmFm-Y5xYkzRL6JrJnA+eCg8nh4ghk4Mg9f-_rQ@mail.gmail.com>

Biojava 1.7 seems like an ancient version. Did you try 1.9.3 from the
biojava-legacy project? Or even better 5.0.2, the latest current release?

Jose

On Fri, May 25, 2018 at 9:40 AM, Carlos M. Mart?nez Ortiz <
cmmo at infomed.sld.cu> wrote:

> Hi, I have implemented a code using the recipe of BiojavaHowTo to parse a
> BLAST output in xml. I?m using netbean IDE and biojava-1.7.jar library.
> This is the error:
>
> org.xml.sax.SAXException: Could not recognise the format of this file as
> one supported by the framework.
>
>                 At org.biojava.bio.program.sax.BlastLikeSAXParser.parse(
> BlastLikeSAXParser.java:185)
>
>                 at javaapplication1.BlastParser.main(BlastParser.java:41)
>
>
>
> the line 41 is:
>
> parser.parse(new InputSource(is));
>
>
>
> Any help? Thanks you
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>
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