JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  May 2018

FSL May 2018

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Compile SIENA for OS X Yosemite

From:

Matthew Webster <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 9 May 2018 13:04:06 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (131 lines)

Dear Erika,
		   You will also need to rebuild the core FSL libraries ( as they were build with a different compiler ). To do this you just need to run 

./build utils znzlib niftiio fslio miscmaths newimage 

In $FSLDIR, if this works, then the resulting libraries should be compatible with your system and you can retry the source compilation.

Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

> On 9 May 2018, at 11:27, Erika Molteni <[log in to unmask]> wrote:
> 
> Dear Matthew,
> thank you very much for your support.
> After implementing your suggestion,
> this is (the first and last bits of) what I obtain:
> 
> Undefined symbols for architecture x86_64:
>   "NEWIMAGE::fslbasename(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
>       int NEWIMAGE::save_volume<float>(NEWIMAGE::volume<float> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in gifbased_siena-0410b3.o
>   "int NEWIMAGE::read_volumeROI<float>(NEWIMAGE::volume<float>&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, short&, bool, int, int, int, int, int, int, bool)", referenced from:
>       int NEWIMAGE::read_volume<float>(NEWIMAGE::volume<float>&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, short&, bool) in gifbased_siena-0410b3.o
>   "NEWIMAGE::handle_read_error(int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
>       int NEWIMAGE::read_volume<float>(NEWIMAGE::volume<float>&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in gifbased_siena-0410b3.o
>       int NEWIMAGE::read_volume<float>(NEWIMAGE::volume<float>&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, short&, bool) in gifbased_siena-0410b3.o
>   "int NEWIMAGE::save_basic_volume<float>(NEWIMAGE::volume<float> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, bool)", referenced from:
>       int NEWIMAGE::save_volume<float>(NEWIMAGE::volume<float> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in gifbased_siena-0410b3.o
>   "std::string::compare(char const*) const", referenced from:
>       NEWIMAGE::dimarg(std::string const&) in libnewimage.a(newimage.o)
>       NEWIMAGE::volume<double>::cog(std::string const&) const in libnewimage.a(newimage.o)
>       NEWIMAGE::volume<float>::cog(std::string const&) const in libnewimage.a(newimage.o)
>       NEWIMAGE::volume<int>::cog(std::string const&) const in libnewimage.a(newimage.o)
>       NEWIMAGE::volume<short>::cog(std::string const&) const in libnewimage.a(newimage.o)
>       NEWIMAGE::volume<char>::cog(std::string const&) const in libnewimage.a(newimage.o)
>       MISCMATHS::get_sortindex(NEWMAT::Matrix const&, std::string const&, int) in libmiscmaths.a(miscmaths.o)
>       ...
>   "std::basic_ios<char, std::char_traits<char> >::widen(char) const", referenced from:
>       MISCMATHS::skip_alpha(std::basic_ifstream<char, std::char_traits<char> >&) in libmiscmaths.a(miscmaths.o)
>       MISCMATHS::read_ascii_matrix(std::basic_ifstream<char, std::char_traits<char> >&, int, int) in libmiscmaths.a(miscmaths.o)
>       MISCMATHS::read_ascii_matrix(std::basic_ifstream<char, std::char_traits<char> >&) in libmiscmaths.a(miscmaths.o)
>       std::string MISCMATHS::num2str<int>(int, int) in libmiscmaths.a(miscmaths.o)
>   "std::istream& std::istream::_M_extract<double>(double&)", referenced from:
>       MISCMATHS::read_ascii_matrix(std::basic_ifstream<char, std::char_traits<char> >&, int, int) in libmiscmaths.a(miscmaths.o)
>       MISCMATHS::read_vest(std::string) in libmiscmaths.a(miscmaths.o)
>   "std::istream::read(char*, long)", referenced from:
>       MISCMATHS::read_binary_matrix(NEWMAT::Matrix&, std::basic_ifstream<char, std::char_traits<char> >&) in libmiscmaths.a(miscmaths.o)
>   "std::istream::seekg(std::fpos<__mbstate_t>)", referenced from:
>       MISCMATHS::skip_alpha(std::basic_ifstream<char, std::char_traits<char> >&) in libmiscmaths.a(miscmaths.o)
> 
>       [...MUCH MORE...]
> 
> NOTE: a missing vtable usually means the first non-inline virtual member function has no definition.
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see invocation)
> 
> At the beginning of the C++ code, these two lines are present:
> using namespace MISCMATHS;
> using namespace NEWIMAGE;
> but apparently this was not handled correctly for "round".
> 
> In the case I add "MISCMATHS::round" to single commands, the output becomes much more verbose, as indicated above, but still dealing with MISCMATHS and NEWIMAGE. No executable is generated.
> 
> Kind regards,
> Erika
> 
> 
> On Tue, May 8, 2018 at 4:56 PM, Matthew Webster <[log in to unmask]> wrote:
> Dear Erika,
>                   Can you try replacing all references to “round” in the file with "MISCMATHS::round” and then recompile?
> 
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre 
> John Radcliffe Hospital
> University of Oxford
> 
> > On 8 May 2018, at 14:06, Erika Molteni <[log in to unmask]> wrote:
> > 
> > Thank you, Matthew, for your kind reply.
> > Here is the output:
> > 
> > clang: warning: optimization flag '-fexpensive-optimizations' is not supported
> > 
> > Though, afterwards, I get a long list of errors on the "round" function.
> > Here one example of many (12, all related to "round"):
> > 
> > /Applications/fsl/include/miscmaths/miscmaths.h:143:7: note: candidate function
> >   int round(int x); 
> >       ^
> > gifbased_siena.cc:403:27: error: call to 'round' is ambiguous
> >   d=1; X=round(x+d*ex); Y=round(y+d*ey); Z=round(z+d*ez);
> >                           ^~~~~
> > Kind Regards,
> > Erika
> > 
> > On Tue, May 8, 2018 at 1:39 PM, Matthew Webster <[log in to unmask]> wrote:
> > Hello,
> >        Can you let me know the full output of the c++ command?
> > 
> > Kind Regards
> > Matthew
> > --------------------------------
> > Dr Matthew Webster
> > FMRIB Centre 
> > John Radcliffe Hospital
> > University of Oxford
> > 
> >> On 4 May 2018, at 11:39, Erika Molteni <[log in to unmask]> wrote:
> >> 
> >> Hello,
> >> I need to compile SIENA on a OS X Yosemite version 10.10.5 MacBookPro.
> >> I was given this line of code by a linux user
> >> 
> >> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations -I/Applications/fsl/extras/include/newmat -I/Applications/fsl/extras/include -I. -I/Applications/fsl/include -I/Applications/fsl/include  -L/Applications/fsl/extras/lib -L/Applications/fsl/extras/lib -L. -L/Applications/fsl/lib -L/Applications/fsl/lib -O0 -o gifbased_siena gifbased_siena.cc -lnewimage -lmiscmaths -lfslio -lniftiio -lznz -lnewmat -lutils -lm -lz
> >> 
> >> where the path to fsl is obviously the one set on my Mac.
> >> Unfortunately, though, while compiling I get errors on the "round" command, and the procedure aborts. This seems to be rather "Mac" specific.
> >> 
> >> Any suggestion about how to proceed? I would be grateful for any hint.
> >> Regards,
> >> Erika
> > 
> > 
> 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager