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....

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

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