Re: Help with building BioJava using Maven?
Jose Duarte <[email protected]> Wed, 23 May 2018 13:36:42 -0700
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CAHhO=JFEC2_4MrFaX00KVudGfBECJatMWCEZjjbiqZf495DuyQ@mail.gmail.com> |
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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 <[email protected]> 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 - [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>
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<div dir=3D"ltr">If what you want is to use biojava in your project, then y=
ou don't need to clone biojava at all.=C2=A0<div><br></div><div>Instead=
you simply make your project a maven project (have a look at a tutorial, t=
here's plenty around) and add the latest biojava release as a dependenc=
y with this:</div><div><br></div><div><pre style=3D"box-sizing:border-box;f=
ont-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,Courie=
r,monospace;font-size:13.6px;margin-top:0px;margin-bottom:0px;word-wrap:nor=
mal;padding:16px;overflow:auto;line-height:1.45;background-color:rgb(246,24=
8,250);border-radius:3px;word-break:normal;color:rgb(36,41,46);font-style:n=
ormal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:40=
0;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:non=
e;word-spacing:0px;text-decoration-style:initial;text-decoration-color:init=
ial"> <<span class=3D"gmail-pl-ent" style=3D"box-sizing:border-box;co=
lor:rgb(34,134,58)">dependencies</span>>
<<span class=3D"gmail-pl-ent" style=3D"box-sizing:border-box;color=
:rgb(34,134,58)">dependency</span>>
<<span class=3D"gmail-pl-ent" style=3D"box-sizing:border-box;col=
or:rgb(34,134,58)">groupId</span>>org.biojava</<span class=3D"gmail-p=
l-ent" style=3D"box-sizing:border-box;color:rgb(34,134,58)">groupId</span>&=
gt;
<<span class=3D"gmail-pl-ent" style=3D"box-sizing:border-box;col=
or:rgb(34,134,58)">artifactId</span>>biojava-core</<span class=3D"gma=
il-pl-ent" style=3D"box-sizing:border-box;color:rgb(34,134,58)">artifactId<=
/span>>
<<span class=3D"gmail-pl-ent" style=3D"box-sizing:border-box;col=
or:rgb(34,134,58)">version</span>>5.0.2</<span class=3D"gmail-pl-ent"=
style=3D"box-sizing:border-box;color:rgb(34,134,58)">version</span>>
</<span class=3D"gmail-pl-ent" style=3D"box-sizing:border-box;colo=
r:rgb(34,134,58)">dependency</span>>
<span class=3D"gmail-pl-c" style=3D"box-sizing:border-box;color:rgb(1=
06,115,125)"><span class=3D"gmail-pl-c" style=3D"box-sizing:border-box;colo=
r:rgb(106,115,125)"><!--</span> other biojava dependencies as needed <sp=
an class=3D"gmail-pl-c" style=3D"box-sizing:border-box;color:rgb(106,115,12=
5)">--></span></span>
</<span class=3D"gmail-pl-ent" style=3D"box-sizing:border-box;color:=
rgb(34,134,58)">dependencies</span>></pre><br></div><div>Once you have t=
he dependency you can then use biojava classes within your project. Maven w=
ill pick everything up automatically.</div><div><br></div><div>Jose</div><d=
iv><br></div></div><div class=3D"gmail_extra"><br><div class=3D"gmail_quote=
">On Wed, May 23, 2018 at 12:26 PM, Caitlin <span dir=3D"ltr"><<a href=
=3D"mailto:[email protected]" target=3D"_blank">[email protected]=
om</a>></span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"marg=
in:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"=
><div>Hi all.</div><div><br></div><div>I am completely inexperienced with r=
espect to using Maven and I am encountering immense difficulty in building =
the latest version that I have cloned from GitHub.</div><div><br></div><div=
>After entering the BioJava folder, edited my pom.xml file to include the f=
ollowing dependencies:</div><div><br></div><div>=C2=A0=C2=A0=C2=A0 <depe=
ndencyManagement><br><dependencies><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0 <dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <gr=
oupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0 <artifactId>biojava-core</<wbr>artifactId><br>=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br>=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <br><dependency><br>=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0 <groupId>org.biojava</groupId><br>=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <artifactId>biojava-aa-prop&l=
t;/<wbr>artifactId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <ve=
rsion>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <gro=
upId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0 <artifactId>biojava-alignment<<wbr>/artifactId><br>=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT </version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </depe=
ndency><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0 <groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0 <artifactId>biojava-genome</<wbr>artifact=
Id><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <gro=
upId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0 <artifactId>biojava-<wbr>integrationtest</artifactId><br=
>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <=
;groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0 <artifactId>biojava-modfinder<<wbr>/artifactId><br=
>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <=
;groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0 <artifactId>biojava-ontology</<wbr>artifactId><br>=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
<groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 <artifactId>biojava-protein-<wbr>disorder</artifac=
tId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
<groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 <artifactId>biojava-structure-<wbr>gui</artifactId=
><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
<groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0=C2=A0 <artifactId>biojava-structure<<wbr>/artifactId>=
<br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br><=
br><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <=
;groupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=
=C2=A0=C2=A0 <artifactId>biojava-survival</<wbr>artifactId><br>=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>5.1.0-SNAPSHOT<=
;/<wbr>version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency><br=
><br><dependency><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <g=
roupId>org.biojava</groupId><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=
=A0=C2=A0 <artifactId>biojava-ws</<wbr>artifactId><br>=C2=A0=C2=
=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 <version>
5.1.0-SNAPSHOT
</version><br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 </dependency></div=
><div><br></div><div>I then issued the command "mvn clean" which =
displayed the message "Build Success". I then issued "mvn in=
stall" which failed with:</div><div><br></div><div>[INFO] Tests run: 1=
, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.377 s - in org.biojav=
a.nbio.core.<wbr>TestAmbiguityCompoundSet<br>[INFO] Running org.biojava.nbi=
o.core.util.<wbr>TestUncompressInputStream<br>[ERROR] Tests run: 1, Failure=
s: 1, Errors: 0, Skipped: 0, Time elapsed: 0.35 s <<< FAILURE! - i=
n org.biojava.nbio.core.util.<wbr>TestUncompressInputStream<br>[ERROR] test=
Uncompression(org.biojava.<wbr>nbio.core.util.<wbr>TestUncompressInputStrea=
m)=C2=A0 Time elapsed: 0.31 s=C2=A0 <<< FAILURE!<br>java.lang.Asse=
rtionError: array lengths differed, expected.length=3D9068 actual.length=3D=
9257<br>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 at org.biojava.nbio.core=
.util.<wbr>TestUncompressInputStream.<wbr>testUncompression(<wbr>TestUncomp=
ressInputStream.<wbr>java:70)<br><br>[INFO]<br>[INFO] Results:<br>[INFO]<br=
>[ERROR] Failures:<br>[ERROR]=C2=A0=C2=A0 TestUncompressInputStream.<wbr>te=
stUncompression:70 array lengths differed, expected.length=3D9068 actual.le=
ngth=3D9257<br>[INFO]<br>[ERROR] Tests run: 244, Failures: 1, Errors: 0, Sk=
ipped: 6<br>[INFO]<br>[INFO] ------------------------------<wbr>-----------=
-------------------<wbr>------------<br>[INFO] Reactor Summary:<br>[INFO]<b=
r>[INFO] biojava-core 5.1.0-SNAPSHOT ........................ FAILURE [01:3=
5 min]<br>[INFO] biojava-alignment 5.1.0-SNAPSHOT ................... SKIPP=
ED<br>[INFO] biojava-structure 5.1.0-SNAPSHOT ................... SKIPPED<b=
r>[INFO] biojava-structure-gui 5.1.0-SNAPSHOT ............... SKIPPED<br>[I=
NFO] biojava-genome 5.1.0-SNAPSHOT ...................... SKIPPED<br>[INFO]=
biojava-modfinder 5.1.0-SNAPSHOT ................... SKIPPED<br>[INFO] bio=
java-ws 5.1.0-SNAPSHOT .......................... SKIPPED<br>[INFO] biojava=
-protein-disorder 5.1.0-SNAPSHOT ............ SKIPPED<br>[INFO] biojava-aa-=
prop 5.1.0-SNAPSHOT ..................... SKIPPED<br>[INFO] biojava-surviva=
l 5.1.0-SNAPSHOT .................... SKIPPED<br>[INFO] biojava-ontology 5.=
1.0-SNAPSHOT .................... SKIPPED<br>[INFO] biojava-integrationtest=
5.1.0-SNAPSHOT ............. SKIPPED<br>[INFO] biojava 4.2.2 .............=
.................<wbr>........ SKIPPED<br>[INFO] --------------------------=
----<wbr>------------------------------<wbr>------------<br>[INFO] BUILD FA=
ILURE<br>[INFO] ------------------------------<wbr>------------------------=
------<wbr>------------<br>[INFO] Total time: 01:36 min<br>[INFO] Finished =
at: 2018-05-23T12:26:00-07:00<br>[INFO] ------------------------------<wbr>=
------------------------------<wbr>------------<br>[ERROR] Failed to execut=
e goal org.apache.maven.plugins:<wbr>maven-surefire-plugin:2.21.0:<wbr>test=
(default-test) on project biojava-core: There are test failures.<br>[ERROR=
]<br>[ERROR] Please refer to C:\Users\CaitlinG\biojava\<wbr>biojava-core\ta=
rget\surefire-<wbr>reports for the individual test results.<br>[ERROR] Plea=
se refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstr=
eam and [date]-jvmRun[N].dumpstream.<br>[ERROR] -> [Help 1]<br>[ERROR]<b=
r>[ERROR] To see the full stack trace of the errors, re-run Maven with the =
-e switch.<br>[ERROR] Re-run Maven using the -X switch to enable full debug=
logging.<br>[ERROR]<br>[ERROR] For more information about the errors and p=
ossible solutions, please read the following articles:<br>[ERROR] [Help 1] =
<a href=3D"http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureExce=
ption" target=3D"_blank">http://cwiki.apache.org/<wbr>confluence/display/MA=
VEN/<wbr>MojoFailureException</a><br><br>C:\Users\CaitlinG\biojava></div=
><div><br></div><div>Thank you for any help you can offer.</div><span class=
=3D"HOEnZb"><font color=3D"#888888"><div><br></div><div>~Caitlin</div><div>=
<br></div><div><br></div><div><br></div></font></span></div>
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