Re: [DIYbio] Protein Shop Help!

> I'm working on this too, will try updating Geometry, where did you get
> it? I didn't find it in apt-cache search....
http://idav.ucdavis.edu/~okreylos/ResDev/Geometry/Download.html

Literally deleted the "Geometry" folder in the src directory and
replaced with the one from this archive.

On Thu, 19 Sep 2013 16:09:39 -0700
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
> >> > >
> >> >
> >> >
> >>
> >
>
>
>

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