errors build-db-userprofile in malariamine

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errors build-db-userprofile in malariamine

Sofia Robb
When I `ant build-db-userprofile` I get the following errors. I am trying to do this with the malariamine example. I am also having the same errors when i try this with my own mine.

do-compile-without-gen-src:
    [javac] Compiling 1 source file to /var/lib/pgsql/other_data/intermine/bio/webapp/build/classes
[dependencies] warning: [options] bootstrap class path not set in conjunction with -source 1.6
[dependencies] /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java:113: error: method getSFPathQuery in class Engine cannot be applied to given types;
[dependencies]         return getSFPathQuery(command, command.getSegment());
[dependencies]                ^
[dependencies]   required: Command
[dependencies]   found: Command,Segment
[dependencies]   reason: actual and formal argument lists differ in length
[dependencies] Note: /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java uses unchecked or unsafe operations.
[dependencies] Note: Recompile with -Xlint:unchecked for details.
[dependencies] 1 error
[dependencies] 1 warning

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/library.xml:117: The following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/library.xml:257: Compile failed; see the compiler error output for details.

Total time: 37 seconds

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Re: errors build-db-userprofile in malariamine

Sofia Robb
Hi,

I switched my github branch from dev to master and this error was resolved. I was able to launch my own webapp! Oh my Goodness! 

It isn't quite working, but I will play around with it and send some messages once I have a chance to try to figure some of it out.

Thanks,
Sofia


On Sat, Nov 14, 2015 at 2:23 PM, Sofia Robb <[hidden email]> wrote:
When I `ant build-db-userprofile` I get the following errors. I am trying to do this with the malariamine example. I am also having the same errors when i try this with my own mine.

do-compile-without-gen-src:
    [javac] Compiling 1 source file to /var/lib/pgsql/other_data/intermine/bio/webapp/build/classes
[dependencies] warning: [options] bootstrap class path not set in conjunction with -source 1.6
[dependencies] /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java:113: error: method getSFPathQuery in class Engine cannot be applied to given types;
[dependencies]         return getSFPathQuery(command, command.getSegment());
[dependencies]                ^
[dependencies]   required: Command
[dependencies]   found: Command,Segment
[dependencies]   reason: actual and formal argument lists differ in length
[dependencies] Note: /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java uses unchecked or unsafe operations.
[dependencies] Note: Recompile with -Xlint:unchecked for details.
[dependencies] 1 error
[dependencies] 1 warning

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/library.xml:117: The following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/library.xml:257: Compile failed; see the compiler error output for details.

Total time: 37 seconds


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Re: errors build-db-userprofile in malariamine

Julie Sullivan
Hi Sofia!

I am glad you got it working! :) Let us know how we can help resolve the
webapp problems.

You can usually find the relevant error messages in

        $TOMCAT/logs/catalina.out
        $TOMCAT/logs/localhost$DATE.log
        $TOMCAT/*mine.log

See intermine.readthedocs.org/en/latest/support/troubleshooting-tips/

If you send me those I can try to figure out what's wrong. It's possibly
InterMine's fault. We make a lot of assumptions that might not be true
for you, e.g. every gene has an organism name, etc.

See http://intermine.readthedocs.org/en/latest/data-model/overview/

Julie

On 19/11/15 03:02, Sofia Robb wrote:

> Hi,
>
> I switched my github branch from dev to master and this error was
> resolved. I was able to launch my own webapp! Oh my Goodness!
>
> It isn't quite working, but I will play around with it and send some
> messages once I have a chance to try to figure some of it out.
>
> Thanks,
> Sofia
>
>
> On Sat, Nov 14, 2015 at 2:23 PM, Sofia Robb <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     When I `ant build-db-userprofile` I get the following errors. I am
>     trying to do this with the malariamine example. I am also having the
>     same errors when i try this with my own mine.
>
>     do-compile-without-gen-src:
>          [javac] Compiling 1 source file to
>     /var/lib/pgsql/other_data/intermine/bio/webapp/build/classes
>     [dependencies] warning: [options] bootstrap class path not set in
>     conjunction with -source 1.6
>     [dependencies]
>     /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java:113:
>     error: method getSFPathQuery in class Engine cannot be applied to
>     given types;
>     [dependencies]         return getSFPathQuery(command,
>     command.getSegment());
>     [dependencies]                ^
>     [dependencies]   required: Command
>     [dependencies]   found: Command,Segment
>     [dependencies]   reason: actual and formal argument lists differ in
>     length
>     [dependencies] Note:
>     /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java
>     uses unchecked or unsafe operations.
>     [dependencies] Note: Recompile with -Xlint:unchecked for details.
>     [dependencies] 1 error
>     [dependencies] 1 warning
>
>     BUILD FAILED
>     /var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The
>     following error occurred while executing this line:
>     /var/lib/pgsql/other_data/intermine/imbuild/library.xml:117: The
>     following error occurred while executing this line:
>     /var/lib/pgsql/other_data/intermine/imbuild/library.xml:257: Compile
>     failed; see the compiler error output for details.
>
>     Total time: 37 seconds
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: errors build-db-userprofile in malariamine

Sofia Robb
Hi Julie,

Ok. changed back to the dev branch and tried the `ant build-db-userprofile` and received the same errors as before, but nothing was written to my tomcat error directory. 

I am attaching the complete output when I run the command. I hope it is helpful. You are likely correct, I am likely missing something in my data that I loaded and that is causing the problem. I am getting there!!

Sofia



On Thu, Nov 19, 2015 at 3:42 AM, Julie Sullivan <[hidden email]> wrote:
Hi Sofia!

I am glad you got it working! :) Let us know how we can help resolve the webapp problems.

You can usually find the relevant error messages in

        $TOMCAT/logs/catalina.out
        $TOMCAT/logs/localhost$DATE.log
        $TOMCAT/*mine.log

See intermine.readthedocs.org/en/latest/support/troubleshooting-tips/

If you send me those I can try to figure out what's wrong. It's possibly InterMine's fault. We make a lot of assumptions that might not be true for you, e.g. every gene has an organism name, etc.

See http://intermine.readthedocs.org/en/latest/data-model/overview/

Julie

On 19/11/15 03:02, Sofia Robb wrote:
Hi,

I switched my github branch from dev to master and this error was
resolved. I was able to launch my own webapp! Oh my Goodness!

It isn't quite working, but I will play around with it and send some
messages once I have a chance to try to figure some of it out.

Thanks,
Sofia


On Sat, Nov 14, 2015 at 2:23 PM, Sofia Robb <[hidden email]
<mailto:[hidden email]>> wrote:

    When I `ant build-db-userprofile` I get the following errors. I am
    trying to do this with the malariamine example. I am also having the
    same errors when i try this with my own mine.

    do-compile-without-gen-src:
         [javac] Compiling 1 source file to
    /var/lib/pgsql/other_data/intermine/bio/webapp/build/classes
    [dependencies] warning: [options] bootstrap class path not set in
    conjunction with -source 1.6
    [dependencies]
    /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java:113:
    error: method getSFPathQuery in class Engine cannot be applied to
    given types;
    [dependencies]         return getSFPathQuery(command,
    command.getSegment());
    [dependencies]                ^
    [dependencies]   required: Command
    [dependencies]   found: Command,Segment
    [dependencies]   reason: actual and formal argument lists differ in
    length
    [dependencies] Note:
    /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java
    uses unchecked or unsafe operations.
    [dependencies] Note: Recompile with -Xlint:unchecked for details.
    [dependencies] 1 error
    [dependencies] 1 warning

    BUILD FAILED
    /var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The
    following error occurred while executing this line:
    /var/lib/pgsql/other_data/intermine/imbuild/library.xml:117: The
    following error occurred while executing this line:
    /var/lib/pgsql/other_data/intermine/imbuild/library.xml:257: Compile
    failed; see the compiler error output for details.

    Total time: 37 seconds




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sofia-errs.txt (121K) Download Attachment
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Re: errors build-db-userprofile in malariamine

Julie Sullivan
Which version of InterMine are you using?

Because your error message had different line numbers than is in the dev
branch. (btw you should only use the master branch)

Your error message says this is on line 113:

        return getSFPathQuery(command, command.getSegment());

when it's on line 289 for me:

https://github.com/intermine/intermine/blob/dev/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java#L289

So maybe you should do an update?

        git pull origin dev

There is a danger that other things will have updated though.

Maybe switching branches caused this? Or merging issues?

The other option would be to remove that Java file, if you aren't using
JBrowse. Just to get things working again!


On 20/11/15 00:03, Sofia Robb wrote:

> Hi Julie,
>
> Ok. changed back to the dev branch and tried the `ant
> build-db-userprofile` and received the same errors as before, but
> nothing was written to my tomcat error directory.
>
> I am attaching the complete output when I run the command. I hope it is
> helpful. You are likely correct, I am likely missing something in my
> data that I loaded and that is causing the problem. I am getting there!!
>
> Sofia
>
>
>
> On Thu, Nov 19, 2015 at 3:42 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Sofia!
>
>     I am glad you got it working! :) Let us know how we can help resolve
>     the webapp problems.
>
>     You can usually find the relevant error messages in
>
>              $TOMCAT/logs/catalina.out
>              $TOMCAT/logs/localhost$DATE.log
>              $TOMCAT/*mine.log
>
>     See
>     intermine.readthedocs.org/en/latest/support/troubleshooting-tips/
>     <http://intermine.readthedocs.org/en/latest/support/troubleshooting-tips/>
>
>     If you send me those I can try to figure out what's wrong. It's
>     possibly InterMine's fault. We make a lot of assumptions that might
>     not be true for you, e.g. every gene has an organism name, etc.
>
>     See http://intermine.readthedocs.org/en/latest/data-model/overview/
>
>     Julie
>
>     On 19/11/15 03:02, Sofia Robb wrote:
>
>         Hi,
>
>         I switched my github branch from dev to master and this error was
>         resolved. I was able to launch my own webapp! Oh my Goodness!
>
>         It isn't quite working, but I will play around with it and send some
>         messages once I have a chance to try to figure some of it out.
>
>         Thanks,
>         Sofia
>
>
>         On Sat, Nov 14, 2015 at 2:23 PM, Sofia Robb <[hidden email]
>         <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>              When I `ant build-db-userprofile` I get the following
>         errors. I am
>              trying to do this with the malariamine example. I am also
>         having the
>              same errors when i try this with my own mine.
>
>              do-compile-without-gen-src:
>                   [javac] Compiling 1 source file to
>              /var/lib/pgsql/other_data/intermine/bio/webapp/build/classes
>              [dependencies] warning: [options] bootstrap class path not
>         set in
>              conjunction with -source 1.6
>              [dependencies]
>
>         /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java:113:
>              error: method getSFPathQuery in class Engine cannot be
>         applied to
>              given types;
>              [dependencies]         return getSFPathQuery(command,
>              command.getSegment());
>              [dependencies]                ^
>              [dependencies]   required: Command
>              [dependencies]   found: Command,Segment
>              [dependencies]   reason: actual and formal argument lists
>         differ in
>              length
>              [dependencies] Note:
>
>         /var/lib/pgsql/other_data/intermine/bio/webapp/src/org/intermine/webservice/server/jbrowse/genomic/Engine.java
>              uses unchecked or unsafe operations.
>              [dependencies] Note: Recompile with -Xlint:unchecked for
>         details.
>              [dependencies] 1 error
>              [dependencies] 1 warning
>
>              BUILD FAILED
>              /var/lib/pgsql/other_data/intermine/imbuild/library.xml:78: The
>              following error occurred while executing this line:
>
>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:117: The
>              following error occurred while executing this line:
>
>         /var/lib/pgsql/other_data/intermine/imbuild/library.xml:257: Compile
>              failed; see the compiler error output for details.
>
>              Total time: 37 seconds
>
>
>
>
>         _______________________________________________
>         dev mailing list
>         [hidden email] <mailto:[hidden email]>
>         http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>

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