Does not compile (javac problem ubuntu)

[nibortolum]

Hello,

i run on ubuntu 16.04 LTS and openjdk 9-internal.

RDPtool compilation fails with this error:

-do-compile:
[javac] Compiling 73 source files to /home/mulot/repo/RDPTools/ReadSeq/build/classes
[javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5
[javac] error: Source option 1.5 is no longer supported. Use 1.6 or later.
[javac] error: Target option 1.5 is no longer supported. Use 1.6 or later.

BUILD FAILED
/home/mulot/repo/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/home/mulot/repo/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

I got stuck on this for hal a day and couldn't find any workaround. Maybe you have an idea ?

Cheers,

Matthieu

[rdpstaffmsu]

Hi, Mattieu, Would you tell us the procedure you used in cloning RDPTools? Thank you. Benli Chai RDP Staff

…

On Wed, Jun 7, 2017 at 8:48 AM, nibortolum ***@***.***> wrote: Hello, i run on ubuntu 16.04 LTS and openjdk 9-internal. RDPtool compilation fails with this error: -do-compile: [javac] Compiling 73 source files to /home/mulot/repo/RDPTools/ ReadSeq/build/classes [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] error: Source option 1.5 is no longer supported. Use 1.6 or later. [javac] error: Target option 1.5 is no longer supported. Use 1.6 or later. BUILD FAILED /home/mulot/repo/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line: /home/mulot/repo/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line: /home/mulot/repo/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line: /home/mulot/repo/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line: /home/mulot/repo/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line: /home/mulot/repo/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details. I got stuck on this for hal a day and couldn't find any workaround. Maybe you have an idea ? Cheers, Matthieu — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKlEVtC7jWTZcobTiNIIxzcmzkXuiWuPks5sBpw2gaJpZM4Nyp5E> .

-- RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

[nibortolum]

So, I striclty followed the README :
git clone https://github.com/rdpstaff/RDPTools.git
git submodule init
git submodule update

and then make.

Thank you,

Matthieu

[gunturus]

can you try using jdk8
Also what version of ant do you have

[nibortolum]

it actually did work, thanks a lot ! <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Garanti sans virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> 2017-06-07 15:43 GMT+02:00 Santosh Kumar G <notifications@github.com>:

…

can i try using jdk8 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGnHlkVFxNA5X1wWJcavzYxZLhC-jRvXks5sBqjwgaJpZM4Nyp5E> .

[Toliman06]

I have the same problem when I try to make:

-do-compile:
    [javac] Compiling 73 source files to /home/dunoyerd/bin/RDPTools/ReadSeq/build/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 5
    [javac] error: Source option 5 is no longer supported. Use 6 or later.
    [javac] error: Target option 1.5 is no longer supported. Use 1.6 or later.

BUILD FAILED
/home/dunoyerd/bin/RDPTools/Clustering/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/dunoyerd/bin/RDPTools/Clustering/nbproject/build-impl.xml:1470: The following error occurred while executing this line:
/home/dunoyerd/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:896: The following error occurred while executing this line:
/home/dunoyerd/bin/RDPTools/AlignmentTools/nbproject/build-impl.xml:1414: The following error occurred while executing this line:
/home/dunoyerd/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:920: The following error occurred while executing this line:
/home/dunoyerd/bin/RDPTools/ReadSeq/nbproject/build-impl.xml:300: Compile failed; see the compiler error output for details.

Here are my java and javac:

~/bin/RDPTools$ update-alternatives --config java
Il existe 3 choix pour l'alternative java (qui fournit /usr/bin/java).

  Sélection   Chemin                                          Priorité  État
------------------------------------------------------------
  0            /usr/lib/jvm/java-10-oracle/bin/java             1091      mode automatique
  1            /usr/lib/jvm/java-10-oracle/bin/java             1091      mode manuel
  2            /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java   1081      mode manuel
* 3            /usr/lib/jvm/java-8-oracle/jre/bin/java          1081      mode manuel

~/bin/RDPTools$ update-alternatives --config javac
Il existe 2 choix pour l'alternative javac (qui fournit /usr/bin/javac).

  Sélection   Chemin                                 Priorité  État
------------------------------------------------------------
  0            /usr/lib/jvm/java-10-oracle/bin/javac   1091      mode automatique
  1            /usr/lib/jvm/java-10-oracle/bin/javac   1091      mode manuel
* 2            /usr/lib/jvm/java-8-oracle/bin/javac    1081      mode manuel

Anf here the command lines before the make:

git clone https://github.com/rdpstaff/RDPTools.git
cd RDPTools
git checkout 2.0.2
git submodule init
git submodule update
make

I am following the FROGS install commands... (https://github.com/geraldinepascal/FROGS/blob/master/INSTALL_from_source.md)

Can anybody help me?