DICOM package installation problem

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DICOM package installation problem

adama
Hi,
 
I've been having trouble installing the DICOM toolbox, which fails with the following error message:
 
octave:2> pkg install dicom-0.1.1.tar.gz
/usr/bin/ld: /usr/local/lib/libgdcmDSED.a(gdcmReader.cxx.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libgdcmDSED.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [dicominfo.oct] Error 1
'make' returned the following error: make: Entering directory `/tmp/oct-iaKJnH/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 dicominfo.o dicomdict.o -o dicominfo.oct
make: Leaving directory `/tmp/oct-iaKJnH/dicom/src'
error: called from `pkg>configure_make' in file /usr/local/share/octave/3.6.3/m/pkg/pkg.m near line 1385, column 9
error: called from:
error:   /usr/local/share/octave/3.6.3/m/pkg/pkg.m at line 827, column 5
error:   /usr/local/share/octave/3.6.3/m/pkg/pkg.m at line 383, column 9
 
This is on a 64-bit Scientific Linux 5.7 system, with gdcm-2.0.19.  I've tried recompiling gdcm with -fPIC and -64 with no success.
 
I've previously installed it on a different system (64-bit Scientific Linux 6.2 with gdcm-2.0.19 compiled with the default settings) without any problems.
 
Any ideas what the problem might be?
 
Thanks,
Adam
 
 

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Re: DICOM package installation problem

andy buckle
On 1 October 2012 12:51, adam aitkenhead <[hidden email]> wrote:

> Hi,
>
> I've been having trouble installing the DICOM toolbox, which fails with the
> following error message:
>
> octave:2> pkg install dicom-0.1.1.tar.gz
> /usr/bin/ld: /usr/local/lib/libgdcmDSED.a(gdcmReader.cxx.o): relocation
> R_X86_64_32 against `a local symbol' can not be used when making a shared
> object; recompile with -fPIC
> /usr/local/lib/libgdcmDSED.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make: *** [dicominfo.oct] Error 1
> 'make' returned the following error: make: Entering directory
> `/tmp/oct-iaKJnH/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
> dicominfo.o dicomdict.o -o dicominfo.oct
> make: Leaving directory `/tmp/oct-iaKJnH/dicom/src'
> error: called from `pkg>configure_make' in file
> /usr/local/share/octave/3.6.3/m/pkg/pkg.m near line 1385, column 9
> error: called from:
> error:   /usr/local/share/octave/3.6.3/m/pkg/pkg.m at line 827, column 5
> error:   /usr/local/share/octave/3.6.3/m/pkg/pkg.m at line 383, column 9
>
> This is on a 64-bit Scientific Linux 5.7 system, with gdcm-2.0.19.  I've
> tried recompiling gdcm with -fPIC and -64 with no success.
>
> I've previously installed it on a different system (64-bit Scientific Linux
> 6.2 with gdcm-2.0.19 compiled with the default settings) without any
> problems.

I have not tried against Octave 3.6.3. I also don't think I have got
it to work against a static gdcm. Could you try a dynamically linked
gdcm?

(I will own up in advance - I struggle with this kind of thing too).

--
/* andy buckle */

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Re: DICOM package installation problem

adama
> Date: Mon, 1 Oct 2012 13:01:36 +0100

> Subject: Re: [OctDev] DICOM package installation problem
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> On 1 October 2012 12:51, adam aitkenhead <[hidden email]> wrote:
> > Hi,
> >
> > I've been having trouble installing the DICOM toolbox, which fails with the
> > following error message:
> >
> > octave:2> pkg install dicom-0.1.1.tar.gz
> > /usr/bin/ld: /usr/local/lib/libgdcmDSED.a(gdcmReader.cxx.o): relocation
> > R_X86_64_32 against `a local symbol' can not be used when making a shared
> > object; recompile with -fPIC
> > /usr/local/lib/libgdcmDSED.a: could not read symbols: Bad value
> > collect2: ld returned 1 exit status
> > make: *** [dicominfo.oct] Error 1
> > 'make' returned the following error: make: Entering directory
> > `/tmp/oct-iaKJnH/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
> > dicominfo.o dicomdict.o -o dicominfo.oct
> > make: Leaving directory `/tmp/oct-iaKJnH/dicom/src'
> > error: called from `pkg>configure_make' in file
> > /usr/local/share/octave/3.6.3/m/pkg/pkg.m near line 1385, column 9
> > error: called from:
> > error: /usr/local/share/octave/3.6.3/m/pkg/pkg.m at line 827, column 5
> > error: /usr/local/share/octave/3.6.3/m/pkg/pkg.m at line 383, column 9
> >
> > This is on a 64-bit Scientific Linux 5.7 system, with gdcm-2.0.19. I've
> > tried recompiling gdcm with -fPIC and -64 with no success.
> >
> > I've previously installed it on a different system (64-bit Scientific Linux
> > 6.2 with gdcm-2.0.19 compiled with the default settings) without any
> > problems.
>
> I have not tried against Octave 3.6.3. I also don't think I have got
> it to work against a static gdcm. Could you try a dynamically linked
> gdcm?
>
> (I will own up in advance - I struggle with this kind of thing too).
>
> --
> /* andy buckle */

Thanks for the help, it's working now.  It was a simple thing in the end - compile gdcm as a shared library (the default settings), and then add the following line to ~/.bashrc
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

(The .bashrc bit was what I'd forgotten...)





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