ERROR:Deprecated function: Call-time pass-by-reference has been deprecated in menu_execute_active_handler() line 515....

I have the same problem here, I don't know what causes it.

I've just installed a fresh install with report_builder, ctools, views, entity, and chart. I wasn't able to reproduce this error. Can you do one or both of these:

1) Post a full module listing so we can see what the conflict is?

2) Install the devel module and put

ddebug_backtrace();

Just before line 515 of menu.inc and post the results.

I'm getting the same thing.
I'm attaching a screen shot.

First time for me trying the devel module - so if i did something wrong let me know - but this is what I got

! ) Parse error: syntax error, unexpected '<' in C:\wamp\www\demo\includes\menu.inc on line 514
Call Stack
# Time Memory Function Location
1 0.0010 368824 {main}( ) ..\index.php:0
2 0.0171 980248 drupal_bootstrap( ) ..\index.php:20
3 0.0996 6371192 _drupal_bootstrap_full( ) ..\bootstrap.inc:2186

this is what the code looks like that I pasted in

if ($router_item['include_file']) {

ddebug_backtrace();

require_once DRUPAL_ROOT . '/' . $router_item['include_file'];
}

Don't know if this helps - but according to another module that was having a similiar issue

"this is caused by passing arguments by reference in function calls"

http://drupal.org/node/1332294

Yeah, I understood what the error was for, but I didn't know what lines of code were causing it. I did a sweep through report builder for usage of the & operator and removed any call-time pass-by-references. I've updated the DEV version only, and it should take about 12 hours for the new package to be downloadable on drupal.org. Can you please try the latest dev release tomorrow evening and see if this error has disappeared?

If you want to try it right away, a patch is attached.

After install of the dev I got this on the confirm page

Fatal error: Call to undefined method stdClass::save() in C:\wamp\www\demo\sites\all\modules\report_builder\report_builder.module on line 170

Call Stack
# Time Memory Function Location
1 0.0006 416208 {main}( ) ..\index.php:0
2 0.4471 33140976 menu_execute_active_handler( ) ..\index.php:21
3 0.4546 34110576 call_user_func_array ( ) ..\menu.inc:516
4 0.4546 34110760 drupal_get_form( ) ..\menu.inc:516
5 0.4546 34111232 drupal_build_form( ) ..\form.inc:131
6 8.1168 40849720 drupal_process_form( ) ..\form.inc:374
7 8.4527 44167264 form_execute_handlers( ) ..\form.inc:854
8 8.4527 44169240 system_modules_submit( ) ..\form.inc:1443
9 8.4659 44304216 module_enable( ) ..\system.admin.inc:1208
10 9.7510 46974920 module_invoke( ) ..\module.inc:450
11 9.7510 46975136 call_user_func_array ( ) ..\module.inc:799
12 9.7510 46975272 report_builder_install( ) ..\module.inc:799
13 26.0080 80799904 report_builder_save( ) ..\report_builder.install:110

After trying to build a sample report I get the following

( ! ) Fatal error: Call to undefined method stdClass::save() in C:\wamp\www\demo\sites\all\modules\report_builder\report_builder.module on line 170
Call Stack
# Time Memory Function Location
1 0.0014 372720 {main}( ) ..\index.php:0
2 0.5320 32717152 menu_execute_active_handler( ) ..\index.php:21
3 0.5339 32824664 call_user_func_array ( ) ..\menu.inc:516
4 0.5339 32824848 drupal_get_form( ) ..\menu.inc:516
5 0.5339 32825312 drupal_build_form( ) ..\form.inc:131
6 0.7256 43351688 drupal_process_form( ) ..\form.inc:374
7 0.7303 43394328 form_execute_handlers( ) ..\form.inc:854
8 0.7303 43396776 report_builder_configure_report_form_submit( ) ..\form.inc:1443
9 0.8405 47804424 report_builder_save( ) ..\report_builder.admin.inc:231

These errors on save were tied to another issue that has been resolved. I think we're good here.