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java issues

Scott Cain
Hi All,

I'm trying to update my instance of Apollo to 2+ and running into issues with Java; specificially, it says this during the attempt to compile:

[javac] javac: invalid target release: 1.7

I assume this is referring to javac version 1.7, but I'm using that:

$ javac -version
javac 1.7.0_79

The other thing I'd point out is that I'm using OpenJDK:

$ sudo update-alternatives --config java
There are 2 choices for the alternative java (providing /usr/bin/java)

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
  1            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
* 2            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode


Can I please get a little guidance?

Thanks much,
Scott



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: java issues

nathandunn

Scott . . how are you compiling / building? 

You should be using:

 “./apollo deploy”

from here (if you are deploying from tomcat):




Nathan

On Oct 23, 2015, at 1:56 PM, Scott Cain <[hidden email]> wrote:

Hi All,

I'm trying to update my instance of Apollo to 2+ and running into issues with Java; specificially, it says this during the attempt to compile:

[javac] javac: invalid target release: 1.7

I assume this is referring to javac version 1.7, but I'm using that:

$ javac -version
javac 1.7.0_79

The other thing I'd point out is that I'm using OpenJDK:

$ sudo update-alternatives --config java
There are 2 choices for the alternative java (providing /usr/bin/java)

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
  1            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
* 2            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode


Can I please get a little guidance?

Thanks much,
Scott



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: java issues

Scott Cain
Yes:

./apollo clean-all
....
./apollo compile  #just to get shorter output, release and deploy end the same

Buildfile: /home/ubuntu/sources/Apollo/build.xml

javac:
    [mkdir] Created dir: /home/ubuntu/sources/Apollo/target/classes/gwt
    [javac] Compiling 62 source files to /home/ubuntu/sources/Apollo/target/classes/gwt
    [javac] javac: invalid target release: 1.7
    [javac] Usage: javac <options> <source files>
    [javac] use -help for a list of possible options

BUILD FAILED

/home/ubuntu/sources/Apollo/build.xml:26: Compile failed; see the compiler error output for details.


On Fri, Oct 23, 2015 at 5:09 PM, Nathan Dunn <[hidden email]> wrote:

>
>
> Scott . . how are you compiling / building?
>
> You should be using:
>
>  “./apollo deploy”
>
> from here (if you are deploying from tomcat):
>
> https://github.com/GMOD/Apollo/blob/master/docs/Apollo2Build.md
>
>
>
> Nathan
>
> On Oct 23, 2015, at 1:56 PM, Scott Cain <[hidden email]> wrote:
>
> Hi All,
>
> I'm trying to update my instance of Apollo to 2+ and running into issues with Java; specificially, it says this during the attempt to compile:
>
> [javac] javac: invalid target release: 1.7
>
> I assume this is referring to javac version 1.7, but I'm using that:
>
> $ javac -version
> javac 1.7.0_79
>
> The other thing I'd point out is that I'm using OpenJDK:
>
> $ sudo update-alternatives --config java
> There are 2 choices for the alternative java (providing /usr/bin/java)
>
>   Selection    Path                                            Priority   Status
> ------------------------------------------------------------
>   0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
>   1            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
> * 2            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode
>
> Can I please get a little guidance?
>
> Thanks much,
> Scott
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: java issues

nathandunn

This is very weird.   I just ran this on my linux machine (in VirtualBox) (you’re in linux, right . . if on a mac I have some other suggestions) as I have an identical configuration (openjdk java 7) without a hitch. 

In the build.xml file try removing the source and target lines (maybe its inadvertently calling the wrong one?).  Another possibility is make sure that “ant" is up to date (I’m using 1.9, not sure what the minimum is):

<javac srcdir="src/gwt" includes="**" encoding="utf-8"
destdir="target/classes/gwt"
includeantruntime="false"
source="1.7" target="1.7" nowarn="true"
debug="true" debuglevel="lines,vars,source">
<classpath refid="project.class.path"/>
If for some reason this STILL doesn’t work . . try to download and build this (if its easy).    



Nathan

On Oct 23, 2015, at 2:21 PM, Scott Cain <[hidden email]> wrote:

Yes:

./apollo clean-all
....
./apollo compile  #just to get shorter output, release and deploy end the same

Buildfile: /home/ubuntu/sources/Apollo/build.xml

javac:
    [mkdir] Created dir: /home/ubuntu/sources/Apollo/target/classes/gwt
    [javac] Compiling 62 source files to /home/ubuntu/sources/Apollo/target/classes/gwt
    [javac] javac: invalid target release: 1.7
    [javac] Usage: javac <options> <source files>
    [javac] use -help for a list of possible options

BUILD FAILED

/home/ubuntu/sources/Apollo/build.xml:26: Compile failed; see the compiler error output for details.


On Fri, Oct 23, 2015 at 5:09 PM, Nathan Dunn <[hidden email]> wrote:

>
>
> Scott . . how are you compiling / building?
>
> You should be using:
>
>  “./apollo deploy”
>
> from here (if you are deploying from tomcat):
>
> https://github.com/GMOD/Apollo/blob/master/docs/Apollo2Build.md
>
>
>
> Nathan
>
> On Oct 23, 2015, at 1:56 PM, Scott Cain <[hidden email]> wrote:
>
> Hi All,
>
> I'm trying to update my instance of Apollo to 2+ and running into issues with Java; specificially, it says this during the attempt to compile:
>
> [javac] javac: invalid target release: 1.7
>
> I assume this is referring to javac version 1.7, but I'm using that:
>
> $ javac -version
> javac 1.7.0_79
>
> The other thing I'd point out is that I'm using OpenJDK:
>
> $ sudo update-alternatives --config java
> There are 2 choices for the alternative java (providing /usr/bin/java)
>
>   Selection    Path                                            Priority   Status
> ------------------------------------------------------------
>   0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
>   1            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
> * 2            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode
>
> Can I please get a little guidance?
>
> Thanks much,
> Scott
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: java issues

Scott Cain
I'm guessing this was the problem:

$ echo $JAVA_HOME
/usr/lib/jvm/java-6-openjdk-amd64


Building seems to be going as it should now.



On Fri, Oct 23, 2015 at 5:42 PM, Nathan Dunn <[hidden email]> wrote:

>
>
> This is very weird.   I just ran this on my linux machine (in VirtualBox) (you’re in linux, right . . if on a mac I have some other suggestions) as I have an identical configuration (openjdk java 7) without a hitch.
>
> In the build.xml file try removing the source and target lines (maybe its inadvertently calling the wrong one?).  Another possibility is make sure that “ant" is up to date (I’m using 1.9, not sure what the minimum is):
>
> <javac srcdir="src/gwt" includes="**" encoding="utf-8"
>        destdir="target/classes/gwt"
>        includeantruntime="false"
>        source="1.7" target="1.7" nowarn="true"
>        debug="true" debuglevel="lines,vars,source">
>     <classpath refid="project.class.path"/>
>
> If for some reason this STILL doesn’t work . . try to download and build this (if its easy).    
>
> http://www.gwtproject.org/download.html
>
>
> Nathan
>
> On Oct 23, 2015, at 2:21 PM, Scott Cain <[hidden email]> wrote:
>
> Yes:
>
> ./apollo clean-all
> ....
> ./apollo compile  #just to get shorter output, release and deploy end the same
>
> Buildfile: /home/ubuntu/sources/Apollo/build.xml
>
> javac:
>     [mkdir] Created dir: /home/ubuntu/sources/Apollo/target/classes/gwt
>     [javac] Compiling 62 source files to /home/ubuntu/sources/Apollo/target/classes/gwt
>     [javac] javac: invalid target release: 1.7
>     [javac] Usage: javac <options> <source files>
>     [javac] use -help for a list of possible options
>
> BUILD FAILED
>
> /home/ubuntu/sources/Apollo/build.xml:26: Compile failed; see the compiler error output for details.
>
>
> On Fri, Oct 23, 2015 at 5:09 PM, Nathan Dunn <[hidden email]> wrote:
> >
> >
> > Scott . . how are you compiling / building?
> >
> > You should be using:
> >
> >  “./apollo deploy”
> >
> > from here (if you are deploying from tomcat):
> >
> > https://github.com/GMOD/Apollo/blob/master/docs/Apollo2Build.md
> >
> >
> >
> > Nathan
> >
> > On Oct 23, 2015, at 1:56 PM, Scott Cain <[hidden email]> wrote:
> >
> > Hi All,
> >
> > I'm trying to update my instance of Apollo to 2+ and running into issues with Java; specificially, it says this during the attempt to compile:
> >
> > [javac] javac: invalid target release: 1.7
> >
> > I assume this is referring to javac version 1.7, but I'm using that:
> >
> > $ javac -version
> > javac 1.7.0_79
> >
> > The other thing I'd point out is that I'm using OpenJDK:
> >
> > $ sudo update-alternatives --config java
> > There are 2 choices for the alternative java (providing /usr/bin/java)
> >
> >   Selection    Path                                            Priority   Status
> > ------------------------------------------------------------
> >   0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
> >   1            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
> > * 2            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode
> >
> > Can I please get a little guidance?
> >
> > Thanks much,
> > Scott
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain dot net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> >
> >
> >
> > This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> > If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
> >
> >
> >
> >
> >
> >
> > This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> > If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: java issues

nathandunn
That would do it.  Thanks for the update. 

Nathan

On Oct 23, 2015, at 2:59 PM, Scott Cain <[hidden email]> wrote:

I'm guessing this was the problem:

$ echo $JAVA_HOME
/usr/lib/jvm/java-6-openjdk-amd64


Building seems to be going as it should now.



On Fri, Oct 23, 2015 at 5:42 PM, Nathan Dunn <[hidden email]> wrote:

>
>
> This is very weird.   I just ran this on my linux machine (in VirtualBox) (you’re in linux, right . . if on a mac I have some other suggestions) as I have an identical configuration (openjdk java 7) without a hitch.
>
> In the build.xml file try removing the source and target lines (maybe its inadvertently calling the wrong one?).  Another possibility is make sure that “ant" is up to date (I’m using 1.9, not sure what the minimum is):
>
> <javac srcdir="src/gwt" includes="**" encoding="utf-8"
>        destdir="target/classes/gwt"
>        includeantruntime="false"
>        source="1.7" target="1.7" nowarn="true"
>        debug="true" debuglevel="lines,vars,source">
>     <classpath refid="project.class.path"/>
>
> If for some reason this STILL doesn’t work . . try to download and build this (if its easy).    
>
> http://www.gwtproject.org/download.html
>
>
> Nathan
>
> On Oct 23, 2015, at 2:21 PM, Scott Cain <[hidden email]> wrote:
>
> Yes:
>
> ./apollo clean-all
> ....
> ./apollo compile  #just to get shorter output, release and deploy end the same
>
> Buildfile: /home/ubuntu/sources/Apollo/build.xml
>
> javac:
>     [mkdir] Created dir: /home/ubuntu/sources/Apollo/target/classes/gwt
>     [javac] Compiling 62 source files to /home/ubuntu/sources/Apollo/target/classes/gwt
>     [javac] javac: invalid target release: 1.7
>     [javac] Usage: javac <options> <source files>
>     [javac] use -help for a list of possible options
>
> BUILD FAILED
>
> /home/ubuntu/sources/Apollo/build.xml:26: Compile failed; see the compiler error output for details.
>
>
> On Fri, Oct 23, 2015 at 5:09 PM, Nathan Dunn <[hidden email]> wrote:
> >
> >
> > Scott . . how are you compiling / building?
> >
> > You should be using:
> >
> >  “./apollo deploy”
> >
> > from here (if you are deploying from tomcat):
> >
> > https://github.com/GMOD/Apollo/blob/master/docs/Apollo2Build.md
> >
> >
> >
> > Nathan
> >
> > On Oct 23, 2015, at 1:56 PM, Scott Cain <[hidden email]> wrote:
> >
> > Hi All,
> >
> > I'm trying to update my instance of Apollo to 2+ and running into issues with Java; specificially, it says this during the attempt to compile:
> >
> > [javac] javac: invalid target release: 1.7
> >
> > I assume this is referring to javac version 1.7, but I'm using that:
> >
> > $ javac -version
> > javac 1.7.0_79
> >
> > The other thing I'd point out is that I'm using OpenJDK:
> >
> > $ sudo update-alternatives --config java
> > There are 2 choices for the alternative java (providing /usr/bin/java)
> >
> >   Selection    Path                                            Priority   Status
> > ------------------------------------------------------------
> >   0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
> >   1            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
> > * 2            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode
> >
> > Can I please get a little guidance?
> >
> > Thanks much,
> > Scott
> >
> >
> >
> > --
> > ------------------------------------------------------------------------
> > Scott Cain, Ph. D.                                   scott at scottcain dot net
> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
> > Ontario Institute for Cancer Research
> >
> >
> >
> > This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> > If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
> >
> >
> >
> >
> >
> >
> > This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> > If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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