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Re: Help-octave Digest, Vol 130, Issue 47Re: Can't install dicom package


From: Ericbarnhill
Subject: Re: Help-octave Digest, Vol 130, Issue 47Re: Can't install dicom package (0.1.1 and 0.1.2 (user version)) in octave 4.0.2 and ubuntu 14.0
Date: Sun, 29 Jan 2017 14:19:39 -0500


I reported the same bug a few months back and Carnë did a nice job of fixing it with the release mentioned.

However if you are still having trouble for the CMake reasons, you can easily hack it, just change the include headers to point to your gdcm library (which you identified using locate) rather than the hard-coded path and it will compile.

Eric

----------------------------------------------------------------------

Message: 1
Date: Sat, 28 Jan 2017 17:49:40 +0000
From: Carn? Draug <address@hidden>
To: address@hidden, address@hidden
Cc: Octave Help <address@hidden>
Subject: Re: Can't install dicom package (0.1.1 and 0.1.2 (user
version)) in octave 4.0.2 and ubuntu 14.0
Message-ID:
<CAPOrs_0YKi8Zq+XsYi3zU3WzzxM7AXjkKRVvD=address@hidden>
Content-Type: text/plain; charset=UTF-8

On 28 January 2017 at 11:02:37 +0100, Pablo Fern?ndez Bustamante
<address@hidden> wrote:
>
>
>
> El 28/01/17 a las 07:47, Andy Buckle escribi?:
>>
>>
>> On 27 Jan 2017 11:27 p.m., "Mario Brise?o" <address@hidden
>> <mailto:address@hidden>> wrote:
>>
>>
>> I've been trying a lot of things, even changing from w10 to ubuntu
>> asa virtual
>> machine. So, I'm not a Linux user.
>> NO problem installing octave, but when I try to install dicom at
>> octave CLI i
>> have this errors:
>>
>> pkg install dicom-0.1.1.tar.gz
>> dicominfo.cpp:45:33: fatal error: gdcm-2.0/gdcmReader.h: No such file or
>> directory
>> compilation terminated.
>> make: *** [dicominfo.o] Error 1
>> make: *** Waiting for unfinished jobs....
>> dicomdict.cpp:30:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
>> directory
>> compilation terminated.
>> make: *** [dicomdict.o] Error 1
>> dicomread.cpp:27:38: fatal error: gdcm-2.0/gdcmImageReader.h: No
>> such file or
>> directory
>> compilation terminated.
>> make: *** [dicomread.oct] Error 1
>> make: Entering directory '/tmp/oct-gASVrN/dicom/src'
>> mkoctfile -c -g dicominfo.cpp
>> mkoctfile -c -g dicomdict.cpp
>> mkoctfile -L/usr/local/lib -lgdcmcharls -lgdcmjpeg8 -lgdcmjpeg12
>> -lgdcmjpeg16 -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD
>> -lgdcmMSFF -g
>> dicomread.cpp
>> Makefile:51: recipe for target 'dicominfo.o' failed
>> Makefile:57: recipe for target 'dicomdict.o' failed
>> Makefile:44: recipe for target 'dicomread.oct' failed
>> make: Leaving directory '/tmp/oct-gASVrN/dicom/src'
>>
>> pkg: error running `make' for the dicom package.
>> error: called from 'configure_make' in file
>> /usr/share/octave/4.0.2/m/pkg/private/configure_make.m near line 96,
>> column 9
>>
>> I've installed the latest versions of cmake, installed the gdcm 2.6
>> package
>> and followed this page:
>> http://gdcm.sourceforge.net/wiki/index.php/Compilation
>> <http://gdcm.sourceforge.net/wiki/index.php/Compilation>
>>
>> As I've said, I have just 5 hours using Ubuntu for the first time.
>>
>> I'd appreciate your help!
>>
>> _______________________________________________
>> Help-octave mailing list
>> address@hidden <mailto:address@hidden>
>> https://lists.gnu.org/mailman/listinfo/help-octave
>> <https://lists.gnu.org/mailman/listinfo/help-octave>
>>
>>
>>
>> Find you install the dependency, gdcm?
>>
>>
>> _______________________________________________
>> Help-octave mailing list
>> address@hidden
>> https://lists.gnu.org/mailman/listinfo/help-octave
>
>
> I am not a dicom user but I am trying to help to diagnose the problem.
> I have recently installed ubuntu 16.04 and I have just installed octave
> from the ubuntu repositories:
>
> octave:3> ver
> ----------------------------------------------------------------------
> GNU Octave Version: 4.0.0
> GNU Octave License: GNU General Public License
> Operating System: Linux 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6
> 17:47:47 UTC 2017 x86_64
> ----------------------------------------------------------------------
> no packages installed.
> octave:4> ls
> dicom-0.1.1.tar.gz
> octave:5> pkg install dicom-0.1.1.tar.gz
> dicomlookup.cpp:23:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
> compilation terminated.
> dicominfo.cpp:45:33: fatal error: gdcm-2.0/gdcmReader.h: No such file or
> directory
> compilation terminated.
> dicomdict.cpp:30:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
> compilation terminated.
> dicomread.cpp:27:38: fatal error: gdcm-2.0/gdcmImageReader.h: No such
> file or directory
>
> So, I need gdcm. I search in the ubuntu repositories:
>
> ~$ sudo apt-cache search gdcm
> libgdcm2.6 - Grassroots DICOM runtime libraries
> libvtkgdcm-java - Grassroots DICOM VTK Java bindings
> libvtkgdcm-tools - Utilidades y herramientas Grassroots DICOM VTK
> gdcm-doc - Grassroots DICOM documentation
> libgdcm-cil - Grassroots DICOM CLI bindings
> libgdcm-java - Grassroots DICOM Java bindings
> libgdcm-tools - Grassroots DICOM tools and utilities
> libgdcm2-dev - Grassroots DICOM development libraries and headers
> libgdcm2.6-dbg - Grassroots DICOM runtime libraries, debug version
> libvtkgdcm-cil - Grassroots DICOM VTK CLI bindings
> libvtkgdcm2-dev - Grassroots DICOM VTK development libraries and headers
> libvtkgdcm2.6 - Grassroots DICOM VTK runtime libraries
> python-gdcm - Grassroots DICOM Python bindings
> python-vtkgdcm - Grassroots DICOM VTK/Python bindings
>
>
> I install libgdcm2.6 and libgdcm2-dev:
>
> ~$ sudo apt install libgdcm2.6 libgdcm2-dev
>
> I try again in Octave, same errors:
>
> octave:5> pkg install dicom-0.1.1.tar.gz
> dicominfo.cpp:45:33: fatal error: gdcm-2.0/gdcmReader.h: No such file or
> directory
> compilation terminated.
> dicomlookup.cpp:23:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
> compilation terminated.
> dicomread.cpp:27:38: fatal error: gdcm-2.0/gdcmImageReader.h: No such
> file or directory
> compilation terminated.
> dicomdict.cpp:30:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
>
>
> I try to locate gdcmDict.h and yes, it is in my system
>
> ~$ sudo updatedb
> ~$ locate gdcmDict.h
> /usr/include/gdcm-2.6/gdcmDict.h
>
> So, gdcmDict.h is there, but not under gdcm-2.0 but gdcm-2.6
>

The problem is that the last released version of the dicom package has
a hardcoded dependency on gdcm version 2.0 in specific places. This
has caused Octave bugs #44430 [1], #44624 [2], and #49896 [3] but they
have already been fixed in the dicom repository.

But the fixes also made the package a bit more complicated (uses
autoconf and CMake) and it currently has no maintainer and so there
has not been a release with the fix. You can do it yourself with:

hg clone http://hg.code.sf.net/p/octave/dicom
cd dicom
make install

However, even with the fix it may error. There are certain CMake
versions where it will still fail (CMake bug #15250 [4]). This
impacts users in Debian Jessie (current Debian stable) (Debian bug
#768877 [5]). You may be affected by this bug in CMake if you have
libgdcm2-dev installed and the following still happens:

$ cmake --find-package -DNAME=GDCM -DLANGUAGE=CXX
-DCOMPILER_ID=GNU -DMODE=COMPILE
GDCM not found.
CMake Error: Problem processing arguments. Aborting.

Carn?

[1] https://savannah.gnu.org/bugs/?44430
[2] https://savannah.gnu.org/bugs/?44624
[3] https://savannah.gnu.org/bugs/?49896
[4] https://cmake.org/Bug/view.php?id=15250
[5] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=768877



Sent from ProtonMail, encrypted email based in Switzerland.


----------------------------------------------------------------------

Message: 1
Date: Sat, 28 Jan 2017 17:49:40 +0000
From: Carn? Draug <address@hidden>
To: address@hidden, address@hidden
Cc: Octave Help <address@hidden>
Subject: Re: Can't install dicom package (0.1.1 and 0.1.2 (user
version)) in octave 4.0.2 and ubuntu 14.0
Message-ID:
<address@hidden>
Content-Type: text/plain; charset=UTF-8

On 28 January 2017 at 11:02:37 +0100, Pablo Fern?ndez Bustamante
<address@hidden> wrote:
>
>
>
> El 28/01/17 a las 07:47, Andy Buckle escribi?:
>>
>>
>> On 27 Jan 2017 11:27 p.m., "Mario Brise?o" <address@hidden
>> <mailto:address@hidden>> wrote:
>>
>>
>> I've been trying a lot of things, even changing from w10 to ubuntu
>> asa virtual
>> machine. So, I'm not a Linux user.
>> NO problem installing octave, but when I try to install dicom at
>> octave CLI i
>> have this errors:
>>
>> pkg install dicom-0.1.1.tar.gz
>> dicominfo.cpp:45:33: fatal error: gdcm-2.0/gdcmReader.h: No such file or
>> directory
>> compilation terminated.
>> make: *** [dicominfo.o] Error 1
>> make: *** Waiting for unfinished jobs....
>> dicomdict.cpp:30:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
>> directory
>> compilation terminated.
>> make: *** [dicomdict.o] Error 1
>> dicomread.cpp:27:38: fatal error: gdcm-2.0/gdcmImageReader.h: No
>> such file or
>> directory
>> compilation terminated.
>> make: *** [dicomread.oct] Error 1
>> make: Entering directory '/tmp/oct-gASVrN/dicom/src'
>> mkoctfile -c -g dicominfo.cpp
>> mkoctfile -c -g dicomdict.cpp
>> mkoctfile -L/usr/local/lib -lgdcmcharls -lgdcmjpeg8 -lgdcmjpeg12
>> -lgdcmjpeg16 -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmIOD
>> -lgdcmMSFF -g
>> dicomread.cpp
>> Makefile:51: recipe for target 'dicominfo.o' failed
>> Makefile:57: recipe for target 'dicomdict.o' failed
>> Makefile:44: recipe for target 'dicomread.oct' failed
>> make: Leaving directory '/tmp/oct-gASVrN/dicom/src'
>>
>> pkg: error running `make' for the dicom package.
>> error: called from 'configure_make' in file
>> /usr/share/octave/4.0.2/m/pkg/private/configure_make.m near line 96,
>> column 9
>>
>> I've installed the latest versions of cmake, installed the gdcm 2.6
>> package
>> and followed this page:
>> http://gdcm.sourceforge.net/wiki/index.php/Compilation
>> <http://gdcm.sourceforge.net/wiki/index.php/Compilation>
>>
>> As I've said, I have just 5 hours using Ubuntu for the first time.
>>
>> I'd appreciate your help!
>>
>> _______________________________________________
>> Help-octave mailing list
>> address@hidden <mailto:address@hidden>
>> https://lists.gnu.org/mailman/listinfo/help-octave
>> <https://lists.gnu.org/mailman/listinfo/help-octave>
>>
>>
>>
>> Find you install the dependency, gdcm?
>>
>>
>> _______________________________________________
>> Help-octave mailing list
>> address@hidden
>> https://lists.gnu.org/mailman/listinfo/help-octave
>
>
> I am not a dicom user but I am trying to help to diagnose the problem.
> I have recently installed ubuntu 16.04 and I have just installed octave
> from the ubuntu repositories:
>
> octave:3> ver
> ----------------------------------------------------------------------
> GNU Octave Version: 4.0.0
> GNU Octave License: GNU General Public License
> Operating System: Linux 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6
> 17:47:47 UTC 2017 x86_64
> ----------------------------------------------------------------------
> no packages installed.
> octave:4> ls
> dicom-0.1.1.tar.gz
> octave:5> pkg install dicom-0.1.1.tar.gz
> dicomlookup.cpp:23:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
> compilation terminated.
> dicominfo.cpp:45:33: fatal error: gdcm-2.0/gdcmReader.h: No such file or
> directory
> compilation terminated.
> dicomdict.cpp:30:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
> compilation terminated.
> dicomread.cpp:27:38: fatal error: gdcm-2.0/gdcmImageReader.h: No such
> file or directory
>
> So, I need gdcm. I search in the ubuntu repositories:
>
> ~$ sudo apt-cache search gdcm
> libgdcm2.6 - Grassroots DICOM runtime libraries
> libvtkgdcm-java - Grassroots DICOM VTK Java bindings
> libvtkgdcm-tools - Utilidades y herramientas Grassroots DICOM VTK
> gdcm-doc - Grassroots DICOM documentation
> libgdcm-cil - Grassroots DICOM CLI bindings
> libgdcm-java - Grassroots DICOM Java bindings
> libgdcm-tools - Grassroots DICOM tools and utilities
> libgdcm2-dev - Grassroots DICOM development libraries and headers
> libgdcm2.6-dbg - Grassroots DICOM runtime libraries, debug version
> libvtkgdcm-cil - Grassroots DICOM VTK CLI bindings
> libvtkgdcm2-dev - Grassroots DICOM VTK development libraries and headers
> libvtkgdcm2.6 - Grassroots DICOM VTK runtime libraries
> python-gdcm - Grassroots DICOM Python bindings
> python-vtkgdcm - Grassroots DICOM VTK/Python bindings
>
>
> I install libgdcm2.6 and libgdcm2-dev:
>
> ~$ sudo apt install libgdcm2.6 libgdcm2-dev
>
> I try again in Octave, same errors:
>
> octave:5> pkg install dicom-0.1.1.tar.gz
> dicominfo.cpp:45:33: fatal error: gdcm-2.0/gdcmReader.h: No such file or
> directory
> compilation terminated.
> dicomlookup.cpp:23:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
> compilation terminated.
> dicomread.cpp:27:38: fatal error: gdcm-2.0/gdcmImageReader.h: No such
> file or directory
> compilation terminated.
> dicomdict.cpp:30:31: fatal error: gdcm-2.0/gdcmDict.h: No such file or
> directory
>
>
> I try to locate gdcmDict.h and yes, it is in my system
>
> ~$ sudo updatedb
> ~$ locate gdcmDict.h
> /usr/include/gdcm-2.6/gdcmDict.h
>
> So, gdcmDict.h is there, but not under gdcm-2.0 but gdcm-2.6
>

The problem is that the last released version of the dicom package has
a hardcoded dependency on gdcm version 2.0 in specific places. This
has caused Octave bugs #44430 [1], #44624 [2], and #49896 [3] but they
have already been fixed in the dicom repository.

But the fixes also made the package a bit more complicated (uses
autoconf and CMake) and it currently has no maintainer and so there
has not been a release with the fix. You can do it yourself with:

hg clone http://hg.code.sf.net/p/octave/dicom
cd dicom
make install

However, even with the fix it may error. There are certain CMake
versions where it will still fail (CMake bug #15250 [4]). This
impacts users in Debian Jessie (current Debian stable) (Debian bug
#768877 [5]). You may be affected by this bug in CMake if you have
libgdcm2-dev installed and the following still happens:

$ cmake --find-package -DNAME=GDCM -DLANGUAGE=CXX
-DCOMPILER_ID=GNU -DMODE=COMPILE
GDCM not found.
CMake Error: Problem processing arguments. Aborting.

Carn?

[1] https://savannah.gnu.org/bugs/?44430
[2] https://savannah.gnu.org/bugs/?44624
[3] https://savannah.gnu.org/bugs/?49896
[4] https://cmake.org/Bug/view.php?id=15250
[5] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=768877



------------------------------

Message: 2
Date: Sun, 29 Jan 2017 13:02:48 +0100
From: Adrianna Andrusiewicz <address@hidden>
To: address@hidden
Subject: problem with ode23
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="utf-8"

Hi, I have problem with my code in Octave. I have to solve a differential
equation.
My code is:
%make an m-file for all three, exer442.m
function Yprime3= exer444(t,Y);
x=2, y=5, z=1.5;
Y(1)=x, Y(2)=y, Y(3)=z;
Yprime3(3,1)=2*Y(3)-Y(3).*Y(3)-Y(2).*Y(3);
end
%all three
[t,Y]=ode23(@exer444,[0 200],[2;5;1.5]);
plot(t,Y(:,3),'g') %grass behavior
hold on
plot(t,Y(:,2),'b') %sheep behavior
plot(t,Y(:,1),'r') %wolf behavior


but I have an error:
error: 'ode23' undefined near line 8 column 6.
What is bad with my code?
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