bugGNU Octave - Bugs: bug #44859, octave forge NAN 2.7.4 install...

 
 

bug #44859: octave forge NAN 2.7.4 install fails in window

Submitter:  John Donoghue <lostbard>
Submitted:  Thu 16 Apr 2015 06:59:36 PM UTC
   
 
Category:  Octave Package Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Build Failure
Status:  Fixed Assigned to:  None
Originator Name:  JohnD Open/Closed:  * Closed
Release:  * dev Operating System:  * Microsoft Windows
Fixed Release:  None Planned Release:  None
* Mandatory Fields

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Tue 29 Mar 2016 05:27:44 PM UTC, comment #8: 

I think the issues here have been resolved in the NaN package, closing as fixed.

There is another issue with CC, see bug #47559.

Mike Miller <mtmiller>
Group Member
Wed 24 Jun 2015 10:03:29 AM UTC, comment #7: 

Marking as duplicate of bug #45363 . THat bug as a fix attached.

Carnë Draug <carandraug>
Group Member
Wed 17 Jun 2015 03:31:47 PM UTC, comment #6: 

Hi Marco

I have set a DL_LDFLAGS environment variable on my system (I am using windows 7), and still getting the same error.

I have also downloaded the latest revision, but not sure what to do with it. I have placed it under the packages folder of my Octave installation, but how can I make the pkg install command use this revision?

Thanks in advance! :-)

Jakob Abermann <jogglabe>
Wed 17 Jun 2015 01:23:52 PM UTC, comment #5: 

sorry Jakob,
I was not clear enough

1)   export DL_LDFLAGS="-shared -fopenmp"
is a bash command executed before running octave.

2) I used latest revision of the code
http://sourceforge.net/p/octave/code/HEAD/tree/trunk/octave-forge/extra/NaN/

marco atzeri <matzeri>
Wed 17 Jun 2015 12:34:00 PM UTC, comment #4: 

having the same problem and Marco's workaround doesnt work for me.

************
pkg install -forge nan
ls: /usr/local/: No such file or directory
tron.cpp:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
linear.cpp:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
svm.cpp:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
svm_model_matlab.c:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
svm_model_matlab.c:64:17: fatal error: mex.h: No such file or directory
 #include "mex.h"
                 ^
compilation terminated.
make: * [svm_model_octave.o] Error 1
make: Entering directory `/tmp/oct-wQC9V9/NaN/src'
mkoctfile --mex "histo_mex.cpp"
mkoctfile --mex "covm_mex.cpp"
mkoctfile --mex "kth_element.cpp"
mkoctfile --mex "sumskipnan_mex.cpp"
mkoctfile --mex "str2array.cpp"
g++ -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -c tron.cpp
g++ -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -c linear.cpp
env CC=g++ mkoctfile --mex -lblas train.c tron.o linear.o linear_model_matlab.c
gcc -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -c svm.cpp
gcc  -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -IC:\Octave\Octave-4.0.0\include\octave
-4.0.0\octave\.. -IC:\Octave\Octave-4.0.0\include\octave-4.0.0\octave -IC:\Octave\Octave-4.0.0\includ
e -o "svm_model_octave.o" -c "svm_model_matlab.c"
make: Leaving directory `/tmp/oct-wQC9V9/NaN/src'

pkg: error running `make' for the nan package.
error: called from 'configure_make' in file C:\Octave\Octave-4.0.0\share\octave\4.0.0\m\pkg\private\c
onfigure_make.m near line 96, column 9


*************
and
export DL_LDFLAGS="-shared -fopenmp"
warning: the 'export' function belongs to the statistics package from Octave
Forge but has not yet been implemented.

Please read `http://www.octave.org/missing.html' to learn how you can
contribute missing functionality.

error: 'export' undefined near line 1 column 1

Jakob Abermann <jogglabe>
Mon 15 Jun 2015 09:11:42 AM UTC, comment #3: 

I wrote too early:

It seems that error: ‘__isnan’ was already tackled

http://sourceforge.net/p/octave/code/12790/

The undefined reference to `GOMP_loop_ull_dynamic_start'
seems a duplicate of
https://savannah.gnu.org/bugs/?45280

using
export DL_LDFLAGS="-shared -fopenmp"

before calling octave solves this issue.

sorry for the noise

marco atzeri <matzeri>
Sat 13 Jun 2015 02:19:38 PM UTC, comment #2: 

the build fails also on cygwin for different reasons:

untar (/pub/devel/octave-forge/32bit/new/octave-nan-2.7.4-1.i686/src/nan-2.7.4/nan-2.7.4.tar.gz, /tmp/oct-PHvCCy)
make: Entering directory '/tmp/oct-PHvCCy/NaN/src'
mkoctfile --mex "histo_mex.cpp"
mkoctfile --mex "covm_mex.cpp"
mkoctfile --mex "kth_element.cpp"
mkoctfile --mex "sumskipnan_mex.cpp"
histo_mex.cpp: In function ‘int compare(const void*, const void*)’:
histo_mex.cpp:124:18: error: ‘__isnan’ was not declared in this scope
    z = __isnan(f1) - __isnan(f2);
                  ^
Makefile:113: recipe for target 'histo_mex.mex' failed
make: * [histo_mex.mex] Error 1
make: * Waiting for unfinished jobs....
covm_mex.o: In function `mexFunction._omp_fn.0':
/tmp/oct-PHvCCy/NaN/src/covm_mex.cpp:274: undefined reference to `GOMP_loop_ull_dynamic_start'

marco atzeri <matzeri>
Thu 16 Apr 2015 08:48:27 PM UTC, comment #1: 

Adding maintainer of the NaN to the CC list.

Carnë Draug <carandraug>
Group Member
Thu 16 Apr 2015 06:59:36 PM UTC, original submission:  



>> pkg install -forge -verbose nan
mkdir (C:\Users\JOHN\AppData\Local\Temp\oct-rlcsAW)
untar (C:\Users\JOHN\nan-2.7.4.tar.gz, C:\Users\JOHN\AppData\Local\Temp\oct-rlcsAW)
ls: /usr/local/: No such file or directory
make: Entering directory `/tmp/oct-rlcsAW/NaN/src'
mkoctfile --mex "histo_mex.cpp"
mkoctfile --mex "covm_mex.cpp"
mkoctfile --mex "kth_element.cpp"
mkoctfile --mex "sumskipnan_mex.cpp"
mkoctfile --mex "str2array.cpp"
g++ -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -c tron.cpp
tron.cpp:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
g++ -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -c linear.cpp
linear.cpp:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
env CC=g++ mkoctfile --mex -lblas train.c tron.o linear.o linear_model_matlab.c
gcc -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -c svm.cpp
svm.cpp:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
gcc  -fopenmp -Wall -Wextra -Wconversion -O2 -fPIC  -fopenmp  -IC:\Octave\Octave-4.0.0-rc3\include\octave-4.0.0-rc3\octave\.. -IC:\Octave
\Octave-4.0.0-rc3\include\octave-4.0.0-rc3\octave -IC:\Octave\Octave-4.0.0-rc3\include -o "svm_model_octave.o" -c "svm_model_matlab.c"
svm_model_matlab.c:1:0: warning: -fPIC ignored for target (all code is position independent)
 /*
 ^
svm_model_matlab.c:64:17: fatal error: mex.h: No such file or directory
 #include "mex.h"
                 ^
compilation terminated.
make: *** [svm_model_octave.o] Error 1


John Donoghue <lostbard>
Group Member

 

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    Follow 7 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2016-03-29 mtmiller StatusConfirmed Fixed
        Open/ClosedOpen Closed
    2015-06-24 carandraug Dependencies- Depends on bugs #45363
    2015-06-03 mtmiller Dependencies- bugs #45250 is dependent
    2015-04-23 lostbard StatusFixed Confirmed
    2015-04-16 carandraug StatusNone Fixed
        Carbon-Copy- Added -email is unavailable-

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