build-matlab crashes under Linux

[brockho]

Tobias also gets errors when running the build-matlab on his ubuntu linux machine:

twagner@TR30:~/numbbo$ python do.py build-matlab
AML     ['code-experiments/src/coco_generics.c', 'code-experiments/src/coco_random.c', 'code-experiments/src/coco_suite.c', 'code-experiments/src/coco_observer.c', 'code-experiments/src/coco_runtime_c.c'] -> code-experiments/build/matlab/coco.c
COPY    code-experiments/src/coco.h -> code-experiments/build/matlab/coco.h
COPY    code-experiments/src/best_values_hyp.txt -> code-experiments/build/matlab/best_values_hyp.txt
WRITE   code-experiments/build/matlab/REVISION
WRITE   code-experiments/build/matlab/VERSION
RUN     matlab -nodisplay -nosplash -r setup, exit in code-experiments/build/matlab

Here, the system seems to stall. After killing the process:
File "/vol2/twagner/numbbo/code-experiments/tools/cocoutils.py", line 68, in run
    universal_newlines=True)
  File "/usr/local/lib/python2.7/subprocess.py", line 569, in check_output
    output, unused_err = process.communicate()
  File "/usr/local/lib/python2.7/subprocess.py", line 798, in communicate
    stdout = _eintr_retry_call(self.stdout.read)
  File "/usr/local/lib/python2.7/subprocess.py", line 478, in _eintr_retry_call
    return func(*args)
KeyboardInterrupt
The terminal cannot be used any longer (no typed keyboard characters are shown)


When I open MATLAB manually and call setup.m, I get the following warnings and errors:


Warning: You are using gcc version "4.4.3-4ubuntu5.1)".  The earliest gcc version supported
         with mex is "4.1".  The latest version tested for use with mex is "4.2".
         To download a different version of gcc, visit http://gcc.gnu.org

In file included from cocoEvaluateFunction.c:7:
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_openIndexFile’:
code-experiments/src/logger_bbob.c:226: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’

code-experiments/src/logger_bbob.c:227: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:266: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:294: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_initialize’:
code-experiments/src/logger_bbob.c:323: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:343: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
In file included from cocoEvaluateFunction.c:7:
code-experiments/src/observer_biobj.c: In function ‘observer_biobj_get_string_pairs_from_file’:
code-experiments/src/observer_biobj.c:122: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
In file included from cocoEvaluateFunction.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_tree_output’:
code-experiments/src/logger_biobj.c:209: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator’:
code-experiments/src/logger_biobj.c:424: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:425: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:434: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:436: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator_finalize’:
code-experiments/src/logger_biobj.c:455: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_evaluate’:
code-experiments/src/logger_biobj.c:549: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:556: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
In file included from cocoEvaluateFunction.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj’:
code-experiments/src/logger_biobj.c:696: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c:702: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
cocoEvaluateFunction.c: In function ‘mexFunction’:
cocoEvaluateFunction.c:28: warning: cast to pointer from integer of different size


Warning: You are using gcc version "4.4.3-4ubuntu5.1)".  The earliest gcc version supported
         with mex is "4.1".  The latest version tested for use with mex is "4.2".
         To download a different version of gcc, visit http://gcc.gnu.org

In file included from cocoSuite.c:7:
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_openIndexFile’:
code-experiments/src/logger_bbob.c:226: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:227: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:266: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:294: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_initialize’:
code-experiments/src/logger_bbob.c:323: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:343: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
In file included from cocoSuite.c:7:
code-experiments/src/observer_biobj.c: In function ‘observer_biobj_get_string_pairs_from_file’:
code-experiments/src/observer_biobj.c:122: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
In file included from cocoSuite.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_tree_output’:
code-experiments/src/logger_biobj.c:209: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator’:
code-experiments/src/logger_biobj.c:424: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:425: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:434: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:436: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator_finalize’:
code-experiments/src/logger_biobj.c:455: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_evaluate’:
code-experiments/src/logger_biobj.c:549: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:556: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
In file included from cocoSuite.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj’:
code-experiments/src/logger_biobj.c:696: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c:702: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
cocoSuite.c: In function ‘mexFunction’:
cocoSuite.c:35: warning: cast from pointer to integer of different size


Warning: You are using gcc version "4.4.3-4ubuntu5.1)".  The earliest gcc version supported
         with mex is "4.1".  The latest version tested for use with mex is "4.2".
         To download a different version of gcc, visit http://gcc.gnu.org

In file included from cocoSuiteFree.c:7:
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_openIndexFile’:
code-experiments/src/logger_bbob.c:226: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:227: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:266: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:294: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_initialize’:
code-experiments/src/logger_bbob.c:323: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:343: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
In file included from cocoSuiteFree.c:7:
code-experiments/src/observer_biobj.c: In function ‘observer_biobj_get_string_pairs_from_file’:
code-experiments/src/observer_biobj.c:122: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
In file included from cocoSuiteFree.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_tree_output’:
code-experiments/src/logger_biobj.c:209: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator’:
code-experiments/src/logger_biobj.c:424: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:425: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:434: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:436: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator_finalize’:
code-experiments/src/logger_biobj.c:455: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_evaluate’:
code-experiments/src/logger_biobj.c:549: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:556: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
In file included from cocoSuiteFree.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj’:
code-experiments/src/logger_biobj.c:696: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c:702: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
cocoSuiteFree.c: In function ‘mexFunction’:
cocoSuiteFree.c:23: warning: cast to pointer from integer of different size

Warning: You are using gcc version "4.4.3-4ubuntu5.1)".  The earliest gcc version supported
         with mex is "4.1".  The latest version tested for use with mex is "4.2".
         To download a different version of gcc, visit http://gcc.gnu.org
In file included from cocoObserver.c:7:
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_openIndexFile’:
code-experiments/src/logger_bbob.c:226: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:227: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:266: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:294: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_initialize’:
code-experiments/src/logger_bbob.c:323: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:343: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
In file included from cocoObserver.c:7:
code-experiments/src/observer_biobj.c: In function ‘observer_biobj_get_string_pairs_from_file’:
code-experiments/src/observer_biobj.c:122: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
In file included from cocoObserver.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_tree_output’:
code-experiments/src/logger_biobj.c:209: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator’:
code-experiments/src/logger_biobj.c:424: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:425: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:434: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:436: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator_finalize’:
code-experiments/src/logger_biobj.c:455: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_evaluate’:
code-experiments/src/logger_biobj.c:549: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:556: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
In file included from cocoObserver.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj’:
code-experiments/src/logger_biobj.c:696: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c:702: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
cocoObserver.c: In function ‘mexFunction’:
cocoObserver.c:32: warning: cast from pointer to integer of different size

Warning: You are using gcc version "4.4.3-4ubuntu5.1)".  The earliest gcc version supported
         with mex is "4.1".  The latest version tested for use with mex is "4.2".
         To download a different version of gcc, visit http://gcc.gnu.org

In file included from cocoObserverFree.c:7:
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_openIndexFile’:
code-experiments/src/logger_bbob.c:226: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:227: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:266: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:294: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_bbob.c: In function ‘logger_bbob_initialize’:
code-experiments/src/logger_bbob.c:323: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_bbob.c:343: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
In file included from cocoObserverFree.c:7:
code-experiments/src/observer_biobj.c: In function ‘observer_biobj_get_string_pairs_from_file’:
code-experiments/src/observer_biobj.c:122: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
In file included from cocoObserverFree.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_tree_output’:
code-experiments/src/logger_biobj.c:209: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator’:
code-experiments/src/logger_biobj.c:424: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:425: warning: format ‘%2lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:434: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:436: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_indicator_finalize’:
code-experiments/src/logger_biobj.c:455: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:460: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c: In function ‘logger_biobj_evaluate’:
code-experiments/src/logger_biobj.c:549: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:556: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
In file included from cocoObserverFree.c:7:
code-experiments/src/logger_biobj.c: In function ‘logger_biobj’:
code-experiments/src/logger_biobj.c:696: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
code-experiments/src/logger_biobj.c:699: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’
code-experiments/src/logger_biobj.c:702: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘size_t’
cocoObserverFree.c: At top level:
cocoObserverFree.c:10: error: expected identifier or ‘(’ before ‘/’ token
cocoObserverFree.c:10: error: stray ‘#’ in program

    mex: compile of ' "cocoObserverFree.c"' failed.

??? Error using ==> mex at 218

Unable to complete successfully.

Error in ==> setup at 32

mex -Dchar16_t=uint16_t cocoObserverFree.c

[brockho]

The latest changes solved this issue. At least on Tobias' machine both exampleexperiment.m and SMS-EOA example runs again.