Installing Openslide with Matlab toolbox

[Jocelyn Barker]

Hello,

I have installed openslide-tools and libopenslide dev on Ubuntu I believe
successfully, but when I try to use it with the Matlab toolbox found here:

http://www.medicalimagecomputing.net/software/openslide-matlab-toolbox-reading-whole-slide-images/

I get a series of errors that prevents anything from working.  I try to
load the library with openslide_load_library and get the error at the
bottom of this email.  I think the top bit is just warnings having to do
with loading the libraries in Matlab, but I believe the bottom errors are
actually related to the base openslide package.

I am not sure if the problem is with openslide or the Matlab toolbox, but
any help would be greatly appreciated.

Thank you,

Jocelyn

Error loading library intermediate output follows.
The actual error is at the end of this output.
*********

Type '' was not found.  Defaulting to type error.

Found on line 103 of input from line 67 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) _Bool openslide_can_open
( char * filename' original input '( visibility (" default "))) _Bool
openslide_can_open ( const char * filename '
Found on line 103 of input from line 67 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 106 of input from line 81 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) openslide_t *
openslide_open ( char * filename' original input '( visibility (" default
"))) openslide_t * openslide_open ( const char * filename '
Found on line 106 of input from line 81 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 109 of input from line 92 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) int32_t
openslide_get_level_count ( openslide_t * osr' original input '( visibility
(" default "))) int32_t openslide_get_level_count ( openslide_t * osr '
Found on line 109 of input from line 92 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 133 of input from line 182 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) void openslide_close (
openslide_t * osr' original input '( visibility (" default "))) void
openslide_close ( openslide_t * osr '
Found on line 133 of input from line 182 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 136 of input from line 227 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) char *
openslide_get_error ( openslide_t * osr' original input '( visibility ("
default "))) const char * openslide_get_error ( openslide_t * osr '
Found on line 136 of input from line 227 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 139 of input from line 302 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) char * *
openslide_get_property_names ( openslide_t * osr' original input '(
visibility (" default "))) const char * const *
openslide_get_property_names ( openslide_t * osr '
Found on line 139 of input from line 302 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 145 of input from line 345 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) char * *
openslide_get_associated_image_names ( openslide_t * osr' original input '(
visibility (" default "))) const char * const *
openslide_get_associated_image_names ( openslide_t * osr '
Found on line 145 of input from line 345 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 158 of input from line 400 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) char *
openslide_get_version ( void' original input '( visibility (" default ")))
const char * openslide_get_version ( void '
Found on line 158 of input from line 400 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.

Type '' was not found.  Defaulting to type error.

Found on line 162 of input from line 422 of file
/usr/include/openslide/openslide.h

Failed to parse type '( visibility (" default "))) __attribute__ ((
deprecated (" Use " " openslide_get_level_count " " instead "))) int32_t
openslide_get_layer_count ( openslide_t * osr' original input '( visibility
(" default "))) __attribute__ (( deprecated (" Use " "
openslide_get_level_count " " instead "))) int32_t
openslide_get_layer_count ( openslide_t * osr '
Found on line 162 of input from line 422 of file
/usr/include/openslide/openslide.h
Error parsing argument for function __attribute__ function may be invalid.
*********
Error using loadlibrary (line 419)
Building openslidelib_thunk_glnxa64 failed.  Compiler output is:
gcc -I"/usr/local/MATLAB/R2012b/extern/include"  -D_GNU_SOURCE
-fexceptions -fPIC
-fno-omit-frame-pointer -pthread -I"/usr/local/MATLAB/R2012b/bin"
-I"/usr/include/openslide"
"openslidelib_thunk_glnxa64.c" -o "openslidelib_thunk_glnxa64.so" -Wl,-E
-shared
openslidelib_thunk_glnxa64.c:25:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
(visibility("default")))_Boolopenslide_can_open(char*filenameThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:34:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
(visibility("default")))openslide_t*openslide_open(char*filenameThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:43:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
 (visibility("default")))int32_topenslide_get_level_count(openslide_t*osrThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:52:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
(visibility("default")))voidopenslide_close(openslide_t*osrThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:61:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
(visibility("default")))char*openslide_get_error(openslide_t*osrThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:70:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
 (visibility("default")))char*const*openslide_get_property_names(openslide_t*osrThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:79:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
 (visibility("default")))char*const*openslide_get_associated_image_names(openslide_t*osrThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:88:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
(visibility("default")))char*openslide_get_version(voidThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^
openslidelib_thunk_glnxa64.c:97:30: error: expected declaration specifiers
or ‘...’ before
string constant
 EXPORT_EXTERN_C
 (visibility("default")))__attribute__((deprecated("Use""openslide_get_level_count""instead")))int32_topenslide_get_layer_count(openslide_t*osrThunk(void
 fcn(),const char *callstack,int stacksize)
                              ^


Error in openslide_load_library (line 40)
loadlibrary('libopenslide-0.dll','openslide.h','alias','openslidelib')
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