build errors for Mattorch

Tlacael Esparza

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Feb 9, 2014, 3:17:13 PM2/9/14

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Hi Everyone,

I'm having trouble installing mattorch on osx Mavericks and I haven't been able to find a solution.

Any help is appreciated.

This is my call:

MATLAB_ROOT=/Applications/MATLAB_R2012a_Student.app luarocks install mattorch

It seems to be finding my Matlab installation fine:

-- The C compiler identification is Clang 5.0.0
-- The CXX compiler identification is Clang 5.0.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found Torch7 in /usr/local
-- Using Matlab in: /Applications/MATLAB_R2012a_Student.app
-- Found Matlab: /Applications/MATLAB_R2012a_Student.app/bin/maci64/libmex.dylib
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/luarocks_mattorch-1.0-0-7693/lua---mattorch/build

But then there are a bunch of deprecation warnings:

13 warnings generated.
Linking C shared module libmattorch.so
[ 50%] Built target mattorch
Scanning dependencies of target mattorchlive
[100%] Building C object CMakeFiles/mattorchlive.dir/mattorchlive.c.o
/tmp/luarocks_mattorch-1.0-0-7693/lua---mattorch/mattorchlive.c:74:3: warning: implicit declaration of function 'lua_executable_dir' is
invalid in C99 [-Wimplicit-function-declaration]
lua_executable_dir("./lua");
^
/tmp/luarocks_mattorch-1.0-0-7693/lua---mattorch/mattorchlive.c:158:33: warning: 'luaT_checktypename2id' is deprecated
[-Wdeprecated-declarations]
luaT_pushudata(L, tensor, luaT_checktypename2id(L, "torch.DoubleTensor"));
^
/usr/local/include/luaT.h:106:38: note: 'luaT_checktypename2id' declared here
LUAT_API LUAT_DEPRECATED const char* luaT_checktypename2id(lua_State *L, const char *tname); /* same as luaT_typenameid */
^

...

And then the build fails:

Linking C shared library libmattorchlive.dylib

Undefined symbols for architecture x86_64:

"_luaL_error", referenced from:

_lstop in mattorchlive.c.o

"_luaL_loadbuffer", referenced from:

_mattorch_dostring in mattorchlive.c.o

"_luaL_loadfile", referenced from:

_mattorch_dofile in mattorchlive.c.o

"_luaL_newstate", referenced from:

_mattorch_init in mattorchlive.c.o

"_luaL_openlibs", referenced from:

_mattorch_init in mattorchlive.c.o

"_lua_call", referenced from:

_mattorch_callfunc in mattorchlive.c.o

_traceback in mattorchlive.c.o

"_lua_close", referenced from:

_mattorch_close in mattorchlive.c.o

"_lua_executable_dir", referenced from:

_mattorch_init in mattorchlive.c.o

"_lua_gc", referenced from:

_mattorch_init in mattorchlive.c.o

_docall in mattorchlive.c.o

"_lua_getfield", referenced from:

_mattorch_dorequire in mattorchlive.c.o

_mattorch_callfunc in mattorchlive.c.o

_traceback in mattorchlive.c.o

"_lua_gettop", referenced from:

_docall in mattorchlive.c.o

"_lua_insert", referenced from:

_docall in mattorchlive.c.o

"_lua_isstring", referenced from:

_traceback in mattorchlive.c.o

"_lua_pcall", referenced from:

_docall in mattorchlive.c.o

"_lua_pushcclosure", referenced from:

_docall in mattorchlive.c.o

"_lua_pushinteger", referenced from:

_traceback in mattorchlive.c.o

"_lua_pushstring", referenced from:

_mattorch_dorequire in mattorchlive.c.o

"_lua_pushvalue", referenced from:

_traceback in mattorchlive.c.o

"_lua_remove", referenced from:

_docall in mattorchlive.c.o

"_lua_sethook", referenced from:

_laction in mattorchlive.c.o

_lstop in mattorchlive.c.o

"_lua_settop", referenced from:

_report in mattorchlive.c.o

_mattorch_callfunc in mattorchlive.c.o

_traceback in mattorchlive.c.o

"_lua_tolstring", referenced from:

_report in mattorchlive.c.o

"_lua_type", referenced from:

_report in mattorchlive.c.o

_traceback in mattorchlive.c.o

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)

make[2]: *** [libmattorchlive.dylib] Error 1

make[1]: *** [CMakeFiles/mattorchlive.dir/all] Error 2

make: *** [all] Error 2

Error: Build error: Failed building.

Full log attached.

mattorch_fail.txt

Olivier Henaff

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May 1, 2014, 10:15:25 PM5/1/14

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I am having the same problem. I'm installing mattorch on OSX with the following call

olivierhenaff$ MATLAB_ROOT=/Users/olivierhenaff/Applications/MATLAB.app/bin/ luarocks install mattorch

Installing https://raw.github.com/torch/rocks/master/mattorch-1.0-0.rockspec...

Using https://raw.github.com/torch/rocks/master/mattorch-1.0-0.rockspec... switching to 'build' mode

Cloning into 'lua---mattorch'...

remote: Counting objects: 19, done.

remote: Compressing objects: 100% (16/16), done.

remote: Total 19 (delta 0), reused 8 (delta 0)

Receiving objects: 100% (19/19), 11.32 KiB | 0 bytes/s, done.

Checking connectivity... done.

Note: checking out 'c3640f86dc23c9cac836752576f6a3594d9fc4e3'.

**stuff**

cmake -E make_directory build;

cd build;

cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="/usr/local/bin/.." -DCMAKE_INSTALL_PREFIX="/usr/local/lib/luarocks/rocks/mattorch/1.0-0";

make

-- The C compiler identification is Clang 5.1.0

-- The CXX compiler identification is Clang 5.1.0

-- Check for working C compiler: /usr/bin/cc

-- Check for working C compiler: /usr/bin/cc -- works

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working CXX compiler: /usr/bin/c++

-- Check for working CXX compiler: /usr/bin/c++ -- works

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Found Torch7 in /usr/local

-- Using Matlab in: /Users/olivierhenaff/Applications/MATLAB.app/bin/

CMake Error at /usr/local/Cellar/cmake/2.8.12.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:108 (message):

MATLAB_INCLUDE_DIR (missing: MATLAB_MEX_LIBRARY MATLAB_MAT_LIBRARY

MATLAB_ENG_LIBRARY MATLAB_MX_LIBRARY)

Call Stack (most recent call first):

/usr/local/Cellar/cmake/2.8.12.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:315 (_FPHSA_FAILURE_MESSAGE)

FindMatlab.cmake:123 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)

CMakeLists.txt:11 (FIND_PACKAGE)

-- Configuring incomplete, errors occurred!

See also "/tmp/luarocks_mattorch-1.0-0-3562/lua---mattorch/build/CMakeFiles/CMakeOutput.log".

make: *** No targets specified and no makefile found. Stop.

Any ideas?

thanks!

Olivier

soumith

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May 2, 2014, 12:31:31 AM5/2/14

to torch7 on behalf of Olivier Henaff

Alternatively, you can try this package:

https://github.com/soumith/matio-ffi.torch

it will load variables from matlab .mat files as tensors.

It doesn't require matlab installed on your system, but you have to install libmatio (brew install libmatio)

I just created it, so haven't tested it extensively.

Seems to work for the matlab matrices I threw at it for my work.

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Zhang Chenyang

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Aug 19, 2014, 10:01:36 PM8/19/14

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Hi I use 'brew install libmatio' and 'luarocks install matio' and then I can load matio but cannot use it:

>>require 'matio'

{

load : function: 0x0b30a1d0

ffi :

{

T_UINT32 : 6

F_DONT_COPY_DATA : 1

T_COMPRESSED : 15

C_EMPTY : 0

T_INT16 : 3

logInit : cdata<int ()>: 0x0b321f4b

varGetStructFieldByName : cdata<struct matvar_t *()>: 0x0b34346f

C_UINT32 : 13

calcSingleSubscript : cdata<int ()>: 0x0b34201d

COMPRESSION_NONE : 0

varWriteInfo : cdata<int ()>: 0x0b342be2

varRead : cdata<struct matvar_t *()>: 0x0b342b6d

BY_INDEX : 2

varCreate : cdata<struct matvar_t *()>: 0x0b3414e0

calcSubscripts : cdata<int *()>: 0x0b34207b

help : cdata<void ()>: 0x0b321f08

setVerbose : cdata<int ()>: 0x0b321af1

logClose : cdata<int ()>: 0x0b321f35

varWriteData : cdata<int ()>: 0x0b342c13

varWrite : cdata<int ()>: 0x0b341bd7

varSetStructFieldByName : cdata<struct matvar_t *()>: 0x0b343c62

COMPRESSION_ZLIB : 1

sizeOf : cdata<uint64_t ()>: 0x0b3221a4

varSetStructFieldByIndex : cdata<struct matvar_t *()>: 0x0b343bb1

varGetNumberOfFields : cdata<unsigned int ()>: 0x0b34339d

C_CELL : 1

varReadNextInfo : cdata<struct matvar_t *()>: 0x0b342a23

C_CHAR : 4

varGetStructsLinear : cdata<struct matvar_t *()>: 0x0b343a25

T_UINT16 : 4

varReadNext : cdata<struct matvar_t *()>: 0x0b341b5e

T_INT8 : 1

varReadInfo : cdata<struct matvar_t *()>: 0x0b342a4b

message : cdata<int ()>: 0x0b321b13

varReadDataLinear : cdata<int ()>: 0x0b3429de

close : cdata<int ()>: 0x0b34113f

varGetCell : cdata<struct matvar_t *()>: 0x0b342d80

C_OBJECT : 3

varDuplicate : cdata<struct matvar_t *()>: 0x0b341c05

T_INT32 : 5

C_INT64 : 14

F_COMPLEX : 2048

T_UNKNOWN : 0

rewind : cdata<int ()>: 0x0b3410ef

C_UINT16 : 11

varPrint : cdata<void ()>: 0x0b3421e4

varGetStructs : cdata<struct matvar_t *()>: 0x0b3435da

C_SINGLE : 7

F_GLOBAL : 1024

getVersion : cdata<enum mat_ft ()>: 0x0b3413e1

varGetStructFieldnames : cdata<char *const *()>: 0x0b3433bc

T_MATRIX : 14

varGetStructField : cdata<struct matvar_t *()>: 0x0b34355f

T_INT64 : 12

C : userdata: 0x0b2fdac0

C_SPARSE : 5

varSetCell : cdata<struct matvar_t *()>: 0x0b3430c8

C_INT8 : 8

T_UTF8 : 16

FT_MAT5 : 256

FT_MAT4 : 16

varGetCells : cdata<struct matvar_t **()>: 0x0b342dc7

setDebug : cdata<int ()>: 0x0b321b05

varReadDataAll : cdata<int ()>: 0x0b342991

varDelete : cdata<int ()>: 0x0b3419c0

debugMessage : cdata<int ()>: 0x0b321c20

varFree : cdata<void ()>: 0x0b341195

warning : cdata<void ()>: 0x0b3220ed

varCreateStruct : cdata<struct matvar_t *()>: 0x0b343110

T_DOUBLE : 9

T_UINT8 : 2

varCalloc : cdata<struct matvar_t *()>: 0x0b341411

T_FUNCTION : 24

varAddStructField : cdata<int ()>: 0x0b343270

BY_NAME : 1

T_UTF32 : 18

varGetCellsLinear : cdata<struct matvar_t **()>: 0x0b34305e

sizeOfClass : cdata<uint64_t ()>: 0x0b3413f1

getFilename : cdata<const char *()>: 0x0b3413d0

createVer : cdata<struct _mat_t *()>: 0x0b340e03

T_SINGLE : 7

varGetSize : cdata<uint64_t ()>: 0x0b342119

open : cdata<struct _mat_t *()>: 0x0b340e19

error : cdata<void ()>: 0x0b321e51

F_LOGICAL : 512

C_INT16 : 10

T_UTF16 : 17

varReadData : cdata<int ()>: 0x0b34294c

C_STRUCT : 2

T_STRUCT : 22

verbMessage : cdata<int ()>: 0x0b321cdd

T_STRING : 20

T_CELL : 21

logInitFunc : cdata<int ()>: 0x0b3220c3

FT_MAT73 : 512

C_INT32 : 12

C_FUNCTION : 16

C_UINT8 : 9

critical : cdata<void ()>: 0x0b321d9a

ACC_RDONLY : 0

T_UINT64 : 13

varGetStructFieldByIndex : cdata<struct matvar_t *()>: 0x0b3433e0

C_UINT64 : 15

T_ARRAY : 23

getLibraryVersion : cdata<void ()>: 0x0b340ddc

C_DOUBLE : 6

ACC_RDWR : 1

}

>>type(matio)

nil

On Friday, May 2, 2014 12:31:31 AM UTC-4, smth chntla wrote:

Alternatively, you can try this package:
https://github.com/soumith/matio-ffi.torch

it will load variables from matlab .mat files as tensors.

It doesn't require matlab installed on your system, but you have to install libmatio (brew install libmatio)

I just created it, so haven't tested it extensively.

Seems to work for the matlab matrices I threw at it for my work.

soumith

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Aug 19, 2014, 11:10:54 PM8/19/14

to torch7 on behalf of abes

Mario follows lua52 package convention. So do

matio = require 'matio';

Zhang Chenyang

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Aug 25, 2014, 6:02:57 PM8/25/14

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Hi,

For Mac it works fine but under ubuntu, it cannot find 'libmatio.so'

and I checked /usr/local/share/lua/5.1/ and there is not a libmatio.so there, where it suppose to be?

Thanks

On Tuesday, August 19, 2014 11:10:54 PM UTC-4, smth chntla wrote:

Mario follows lua52 package convention. So do

matio = require 'matio';

soumith

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Aug 26, 2014, 12:31:06 PM8/26/14

to torch7 on behalf of Zhang Chenyang

did you install libmatio before-hand? sudo apt-get install libmatio2

Message has been deleted

Zhang Chenyang

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Aug 31, 2014, 4:20:27 PM8/31/14

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Hi,

Yes I have installed libmatio2:

~$ sudo apt-get install libmatio2
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
libhdf5-7
The following NEW packages will be installed:
libhdf5-7 libmatio2
0 upgraded, 2 newly installed, 0 to remove and 146 not upgraded.
Need to get 1,282 kB of archives.
After this operation, 4,142 kB of additional disk space will be used.
Do you want to continue? [Y/n]
Get:1 http://us.archive.ubuntu.com/ubuntu/ trusty/universe libhdf5-7 amd64 1.8.11-5ubuntu7 [1,205 kB]
Get:2 http://us.archive.ubuntu.com/ubuntu/ trusty/universe libmatio2 amd64 1.5.2-1ubuntu1 [76.8 kB]
Fetched 1,282 kB in 1s (896 kB/s)
Selecting previously unselected package libhdf5-7:amd64.
(Reading database ... 179105 files and directories currently installed.)
Preparing to unpack .../libhdf5-7_1.8.11-5ubuntu7_amd64.deb ...
Unpacking libhdf5-7:amd64 (1.8.11-5ubuntu7) ...
Selecting previously unselected package libmatio2:amd64.
Preparing to unpack .../libmatio2_1.5.2-1ubuntu1_amd64.deb ...
Unpacking libmatio2:amd64 (1.5.2-1ubuntu1) ...
Setting up libhdf5-7:amd64 (1.8.11-5ubuntu7) ...
Setting up libmatio2:amd64 (1.5.2-1ubuntu1) ...
Processing triggers for libc-bin (2.19-0ubuntu6) ...

and then :

~$ sudo luarocks install matio
Installing https://raw.githubusercontent.com/torch/rocks/master/matio-scm-1.rockspec...
Using https://raw.githubusercontent.com/torch/rocks/master/matio-scm-1.rockspec... switching to 'build' mode
Cloning into 'matio-ffi.torch'...
remote: Counting objects: 14, done.
remote: Compressing objects: 100% (13/13), done.
remote: Total 14 (delta 0), reused 11 (delta 0)
Receiving objects: 100% (14/14), 7.41 KiB | 0 bytes/s, done.
Checking connectivity... done.
Warning: Directory 'doc' not found
Updating manifest for /usr/local/lib/luarocks/rocks
matio scm-1 is now built and installed in /usr/local/ (license: BSD)

but in th, I use matio = require 'matio', it shows:

/usr/local/share/lua/5.1/matio/ffi.lua:5: libmatio.so: cannot open shared object file: No such file or directory
stack traceback:
[C]: in function 'load'
/usr/local/share/lua/5.1/matio/ffi.lua:5: in main chunk
[C]: in function 'require'
/usr/local/share/lua/5.1/matio/init.lua:3: in main chunk
[C]: in function 'require'
[string "local matio = require 'matio'..."]:1: in main chunk
[C]: in function 'xpcall'
/usr/local/share/lua/5.1/trepl/init.lua:588: in function </usr/local/share/lua/5.1/trepl/init.lua:489>
[0.0011s]

On Tuesday, August 26, 2014 12:31:06 PM UTC-4, smth chntla wrote:

did you install libmatio before-hand? sudo apt-get install libmatio2

Sourabh Kulhare

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Jul 1, 2015, 3:27:56 PM7/1/15

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Hey there,

I am having the same problem, has anyone solved the problem???

Julie Dequaire

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Nov 24, 2015, 5:55:15 AM11/24/15

to torch7

I am getting the same linker errors - have you found a solution to this ?

Thanks

Julie

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