Re: [DIYbio] Protein Shop Help!

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Hi Tim,
Those errors are what I got prior to replacing the Geometry toolkit
with a more up-to-date version. That's the biggest change in the zipped
codebase I linked to in my prior mail.

On Thu, 19 Sep 2013 13:35:24 -1000
William Heath <wgheath@gmail.com> wrote:

> Hi All,
>
> Can anyone interested in helping me to understand compilation issues
> on linux join me in #diybio on irc.freenode.net. My current error is:
>
> centos@143 src]$ make
> g++ -c -o TCPSocket2.o -D__LINUX__ -D__LITTLE_ENDIAN=1234
> -D__BIG_ENDIAN=4321 -DFLTK_NEW -DFLTK_DOUBLE -DGL_GLEXT_PROTOTYPES
> -ffriend-injection -I. -g0 -O3 -DNDEBUG -I/usr/local/include
> TCPSocket2.cpp In file included from ./Geometry/Box.h:28,
> from Globals.h:41,
> from TCPSocket2.cpp:27:
> ./Geometry/Point.h:46: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::Point<ScalarParam,
> dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/Point.h:47: error: declaration of 'typedef struct
> Geometry::AffineCombiner<ScalarParam, dimensionParam>
> Geometry::Point<ScalarParam, dimensionParam>::AffineCombiner'
> ./Geometry/Point.h:34: error: changes meaning of 'AffineCombiner' from
> 'struct Geometry::AffineCombiner<ScalarParam, dimensionParam>'
> In file included from ./Geometry/Box.h:30,
> from Globals.h:41,
> from TCPSocket2.cpp:27:
> ./Geometry/Ray.h:38: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::Ray<ScalarParam,
> dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/Ray.h:39: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, dimensionParam>
> Geometry::Ray<ScalarParam,
> dimensionParam>::Point'
> ./Geometry/Point.h:38: error: changes meaning of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> In file included from Globals.h:41,
> from TCPSocket2.cpp:27:
> ./Geometry/Box.h:54: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, dimensionParam>
> Geometry::Box<ScalarParam,
> dimensionParam>::Point'
> ./Geometry/Point.h:38: error: changes meaning of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> ./Geometry/Box.h:55: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::Box<ScalarParam,
> dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/Box.h:57: error: declaration of 'typedef class
> Geometry::Ray<ScalarParam, dimensionParam> Geometry::Box<ScalarParam,
> dimensionParam>::Ray'
> ./Geometry/Ray.h:33: error: changes meaning of 'Ray' from 'class
> Geometry::Ray<ScalarParam, dimensionParam>'
> In file included from ./Geometry/OrthonormalTransformation.h:29,
> from DragBox.h:22,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/HVector.h:44: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::HVector<ScalarParam, dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/HVector.h:45: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, dimensionParam>
> Geometry::HVector<ScalarParam,
> dimensionParam>::Point'
> ./Geometry/Point.h:38: error: changes meaning of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> In file included from ./Geometry/OrthonormalTransformation.h:30,
> from DragBox.h:22,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/Rotation.h:44: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::Rotation<ScalarParam, dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/Rotation.h:45: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, dimensionParam>
> Geometry::Rotation<ScalarParam, dimensionParam>::Point'
> ./Geometry/Point.h:38: error: changes meaning of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> ./Geometry/Rotation.h:46: error: declaration of 'typedef class
> Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::Rotation<ScalarParam, dimensionParam>::HVector'
> ./Geometry/HVector.h:35: error: changes meaning of 'HVector' from
> 'class Geometry::HVector<ScalarParam, dimensionParam>'
> ./Geometry/Rotation.h:74: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, 2> Geometry::Rotation<ScalarParam,
> 2>::Vector' ./Geometry/Vector.h:33: error: changes meaning of
> 2>'Vector' from 'class
> Geometry::Vector<ScalarParam, 2>'
> ./Geometry/Rotation.h:75: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, 2> Geometry::Rotation<ScalarParam,
> 2>::Point' ./Geometry/Point.h:38: error: changes meaning of 'Point'
> 2>from 'class
> Geometry::Point<ScalarParam, 2>'
> ./Geometry/Rotation.h:76: error: declaration of 'typedef class
> Geometry::HVector<ScalarParam, 2> Geometry::Rotation<ScalarParam,
> 2>::HVector'
> ./Geometry/HVector.h:35: error: changes meaning of 'HVector' from
> 'class Geometry::HVector<ScalarParam, 2>'
> ./Geometry/Rotation.h:257: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::Vector' ./Geometry/Vector.h:33: error: changes meaning of
> 3>'Vector' from 'class
> Geometry::Vector<ScalarParam, 3>'
> ./Geometry/Rotation.h:258: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::Point' ./Geometry/Point.h:38: error: changes meaning of 'Point'
> 3>from 'class
> Geometry::Point<ScalarParam, 3>'
> ./Geometry/Rotation.h:259: error: declaration of 'typedef class
> Geometry::HVector<ScalarParam, 3> Geometry::Rotation<ScalarParam,
> 3>::HVector'
> ./Geometry/HVector.h:35: error: changes meaning of 'HVector' from
> 'class Geometry::HVector<ScalarParam, 3>'
> In file included from DragBox.h:22,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/OrthonormalTransformation.h:56: error: declaration of
> 'typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Vector' ./Geometry/Vector.h:33: error: changes
> dimensionParam>meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/OrthonormalTransformation.h:57: error: declaration of
> 'typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Point' ./Geometry/Point.h:38: error: changes meaning
> dimensionParam>of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> ./Geometry/OrthonormalTransformation.h:58: error: declaration of
> 'typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::HVector' ./Geometry/HVector.h:35: error: changes
> dimensionParam>meaning of 'HVector' from 'class
> Geometry::HVector<ScalarParam, dimensionParam>'
> ./Geometry/OrthonormalTransformation.h:59: error: declaration of
> 'typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::OrthonormalTransformation<ScalarParam,
> dimensionParam>::Rotation' ./Geometry/Rotation.h:39: error: changes
> dimensionParam>meaning of 'Rotation' from 'class
> Geometry::Rotation<ScalarParam, dimensionParam>'
> In file included from DragBox.h:23,
> from Globals.h:43,
> from TCPSocket2.cpp:27:
> ./Geometry/ProjectiveTransformation.h:260: error: declaration of
> 'typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Vector' ./Geometry/Vector.h:33: error: changes
> dimensionParam>meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/ProjectiveTransformation.h:261: error: declaration of
> 'typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Point' ./Geometry/Point.h:38: error: changes meaning
> dimensionParam>of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> ./Geometry/ProjectiveTransformation.h:262: error: declaration of
> 'typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::HVector' ./Geometry/HVector.h:35: error: changes
> dimensionParam>meaning of 'HVector' from 'class
> Geometry::HVector<ScalarParam, dimensionParam>'
> ./Geometry/ProjectiveTransformation.h:263: error: declaration of
> 'typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Rotation' ./Geometry/Rotation.h:39: error: changes
> dimensionParam>meaning of 'Rotation' from 'class
> Geometry::Rotation<ScalarParam, dimensionParam>'
> ./Geometry/ProjectiveTransformation.h:265: error: declaration of
> 'typedef class Geometry::Matrix<ScalarParam, (dimensionParam + 1),
> (dimensionParam + 1)> Geometry::ProjectiveTransformation<ScalarParam,
> dimensionParam>::Matrix' ./Geometry/Matrix.h:196: error: changes
> dimensionParam>meaning of 'Matrix' from 'class
> Geometry::Matrix<ScalarParam, (dimensionParam + 1), (dimensionParam +
> 1)>' In file included from ./Geometry/Sphere.h:30,
> from Atom.h:22,
> from Protein.h:28,
> from Globals.h:44,
> from TCPSocket2.cpp:27:
> ./Geometry/OrthogonalTransformation.h:59: error: declaration of
> 'typedef class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Vector' ./Geometry/Vector.h:33: error: changes
> dimensionParam>meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/OrthogonalTransformation.h:60: error: declaration of
> 'typedef class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Point' ./Geometry/Point.h:38: error: changes meaning
> dimensionParam>of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> ./Geometry/OrthogonalTransformation.h:61: error: declaration of
> 'typedef class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::HVector' ./Geometry/HVector.h:35: error: changes
> dimensionParam>meaning of 'HVector' from 'class
> Geometry::HVector<ScalarParam, dimensionParam>'
> ./Geometry/OrthogonalTransformation.h:62: error: declaration of
> 'typedef class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::OrthogonalTransformation<ScalarParam,
> dimensionParam>::Rotation' ./Geometry/Rotation.h:39: error: changes
> dimensionParam>meaning of 'Rotation' from 'class
> Geometry::Rotation<ScalarParam, dimensionParam>'
> In file included from Atom.h:22,
> from Protein.h:28,
> from Globals.h:44,
> from TCPSocket2.cpp:27:
> ./Geometry/Sphere.h:43: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::Sphere<ScalarParam,
> dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/Sphere.h:44: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, dimensionParam>
> Geometry::Sphere<ScalarParam,
> dimensionParam>::Point'
> ./Geometry/Point.h:38: error: changes meaning of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> ./Geometry/Sphere.h:45: error: declaration of 'typedef class
> Geometry::Ray<ScalarParam, dimensionParam>
> Geometry::Sphere<ScalarParam,
> dimensionParam>::Ray'
> ./Geometry/Ray.h:33: error: changes meaning of 'Ray' from 'class
> Geometry::Ray<ScalarParam, dimensionParam>'
> In file included from ProteinRenderer.h:30,
> from ProteinInteractor.h:43,
> from Globals.h:46,
> from TCPSocket2.cpp:27:
> ./Geometry/SplineCurve.h:53: error: declaration of 'typedef class
> Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::SplineCurve<ScalarParam, dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/SplineCurve.h:54: error: declaration of 'typedef class
> Geometry::Point<ScalarParam, dimensionParam>
> Geometry::SplineCurve<ScalarParam, dimensionParam>::Point'
> ./Geometry/Point.h:38: error: changes meaning of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> In file included from IK.h:24,
> from ProteinInteractor.h:45,
> from Globals.h:46,
> from TCPSocket2.cpp:27:
> ./Geometry/AffineTransformation.h:167: error: declaration of 'typedef
> class Geometry::Vector<ScalarParam, dimensionParam>
> Geometry::AffineTransformation<ScalarParam, dimensionParam>::Vector'
> ./Geometry/Vector.h:33: error: changes meaning of 'Vector' from 'class
> Geometry::Vector<ScalarParam, dimensionParam>'
> ./Geometry/AffineTransformation.h:168: error: declaration of 'typedef
> class Geometry::Point<ScalarParam, dimensionParam>
> Geometry::AffineTransformation<ScalarParam, dimensionParam>::Point'
> ./Geometry/Point.h:38: error: changes meaning of 'Point' from 'class
> Geometry::Point<ScalarParam, dimensionParam>'
> ./Geometry/AffineTransformation.h:169: error: declaration of 'typedef
> class Geometry::HVector<ScalarParam, dimensionParam>
> Geometry::AffineTransformation<ScalarParam, dimensionParam>::HVector'
> ./Geometry/HVector.h:35: error: changes meaning of 'HVector' from
> 'class Geometry::HVector<ScalarParam, dimensionParam>'
> ./Geometry/AffineTransformation.h:170: error: declaration of 'typedef
> class Geometry::Rotation<ScalarParam, dimensionParam>
> Geometry::AffineTransformation<ScalarParam, dimensionParam>::Rotation'
> ./Geometry/Rotation.h:39: error: changes meaning of 'Rotation' from
> 'class Geometry::Rotation<ScalarParam, dimensionParam>'
> ./Geometry/AffineTransformation.h:172: error: declaration of 'typedef
> class Geometry::Matrix<ScalarParam, dimensionParam, (dimensionParam +
> 1)> Geometry::AffineTransformation<ScalarParam,
> dimensionParam>::Matrix' ./Geometry/Matrix.h:196: error: changes
> dimensionParam>meaning of 'Matrix' from 'class
> Geometry::Matrix<ScalarParam, dimensionParam, (dimensionParam + 1)>'
> make: *** [TCPSocket2.o] Error 1
>
> -Tim
>
>
> On Thu, Sep 19, 2013 at 1:09 PM, Nathan McCorkle <nmz787@gmail.com>
> wrote:
>
> > I'm working on this too, will try updating Geometry, where did you
> > get it? I didn't find it in apt-cache search....
> >
> > If you're running a 64-bit system, you could try downloading the RPM
> > file and using alien to convert it.... I'm not running 64-bit so I
> > can't confirm it will work:
> > wget sourcefourge.com/path/to/download
> > sudo apt-get install alien
> > sudo alien downloadedFile
> >
> > it warned that I might need to invoke alien with the --script (or
> > was it scripts) option
> >
> > On Thu, Sep 19, 2013 at 3:46 PM, Cathal Garvey
> > <cathalgarvey@cathalgarvey.me> wrote:
> > > Hey Tim!
> > >
> > > Below is my original mail outlining the progress I made before
> > > losing heart. It refers to "attached", but here's a link instead
> > > to the archive, as I can't attach it through google groups:
> > > https://anonfiles.com/file/a4c961f31541d7f38575c534ff20a5d1
> > > (Yes, a zip rather than tar.gz, because bizarrely anonfiles.com
> > > doesn't like gzip?)
> > >
> > > --- Original Message ---
> > > Hey John!
> > > Welcome to Linux! Sorry you're having trouble already, but
> > > looking at Protein Shop, that's not surprising. I tried to come
> > > up with a comprehensive guide to getting it running, considering
> > > that the developers don't offer compiled programs but rather only
> > > the source code. Worse, it's got big dependencies; OpenGL and
> > > FLTK, plus others. That'd be ok if it was pre-built, because you
> > > could just install OpenGL and FLTK afterwards, but you need to
> > > install the "dev" versions of those, and then build this.
> > >
> > > So I tried. I installed all the dependencies and wrote a big email
> > > explaining how, then downloaded the source code, uncompressed it,
> > > and tried to build. Then I found that the source code bundles
> > > "Geometry" and it doesn't compile, so I replaced "Geometry" with
> > > the newest version, and that fixed that. I had to fix a bug where
> > > it was using the "isnan" function as if it was in Math (i.e.
> > > Math::isNan), but I think that must have been deprecated at some
> > > point; changed to read "isnan" because that's now part of C++
> > > standard lib.
> > >
> > > And now I've got this new, exciting, bizzarre bug I don't have the
> > > heart to solve, where it says this of compiling
> > > "EnergyRenderer.cpp":
> > >
> > > g++ -c -o EnergyRenderer.o -D__LINUX__ -D__LITTLE_ENDIAN=1234
> > > -D__BIG_ENDIAN=4321 -DFLTK_NEW -DFLTK_DOUBLE -DGL_GLEXT_PROTOTYPES
> > > -ffriend-injection -I. -g0 -O3 -DNDEBUG -I/usr/include
> > > EnergyRenderer.cpp In file included from EnergyRenderer.cpp:33:0:
> > > ColorFunction.h:70:27: error: expected ';' at end of member
> > > declaration ColorFunction.h:70:37: error: expected ')' before
> > > 'number' ColorFunction.h:86:27: error: expected ';' at end of
> > > member declaration ColorFunction.h:86:40: error: expected ')'
> > > before 'number' EnergyRenderer.cpp: In member function
> > > 'AtomClassifier* EnergyRenderer::getClassifier()':
> > > EnergyRenderer.cpp:639:61: error: 'ColorFunction::get' cannot be
> > > used as a function make: *** [EnergyRenderer.o] Error 1
> > >
> > > ..I don't even know where to start with this crap. I don't code
> > > in C++, I'm barely able to read it! :)
> > >
> > > So, with my condolences, you've picked the most troublesome piece
> > > of software I've seen in ages as your first use-case for Linux,
> > > which is sad. I was sort of hoping this would be a case of "it's
> > > easy, just pop up the software center and click install", as
> > > things usually are for Linux these days.. :P
> > >
> > > I'm attaching the modified source code I have so far that
> > > includes the functioning version of Geometry and the "isnan"
> > > changes, if anyone else who knows more about C++ wants to have a
> > > go at getting this to compile..
> > >
> > > Best,
> > > Cathal
> > >
> > > On Thu, 19 Sep 2013 11:27:04 -1000
> > > William Heath <wgheath@gmail.com> wrote:
> > >
> > >> Hi All,
> > >>
> > >> I used to teach c++ and programmed in it for over 5 years
> > >> etc... I also specialize in linux. I will see what I can do :>
> > >>
> > >> -Tim BCSE, MSCS, MBA
> > >>
> > >>
> > >> On Thu, Sep 19, 2013 at 9:29 AM, Cathal Garvey
> > >> <cathalgarvey@cathalgarvey.me
> > >> > wrote:
> > >>
> > >> > Lol, ignore last message a minute, the preceding message
> > >> > failed to deliver because Google Groups didn't like the
> > >> > attachments. Will post later.
> > >> >
> > >> > I'm afraid it's bad news, John; ProteinShop is either a very
> > >> > buggy or very outdated codebase, and won't compile for me.
> > >> > Perhaps someone with better C++ chops can pick up where I've
> > >> > left off and make it work.
> > >> >
> > >> > On Thu, 19 Sep 2013 05:46:59 -0700 (PDT)
> > >> > John Dohnal <johnhdohnal@aol.com> wrote:
> > >> >
> > >> > > I have never used a Linux OS before, but I downloaded the
> > >> > > latest version of Ubuntu in order to run Protein Shop. I
> > >> > > downloaded the latest version of Protein Shop, but I don't
> > >> > > know how to start it. I know nothing about using Linux, so
> > >> > > any explicit, basic instructions would be most helpful. In
> > >> > > the readme file, it mentions some other files that may need
> > >> > > to be installed, but I don't even know where to begin.
> > >> > > Please help! Thanks,
> > >> > > John
> > >> > >
> > >> >
> > >> >
> > >>
> > >
> >
> >
> >
> > --
> > -Nathan
> >
> > --
> > -- You received this message because you are subscribed to the
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