I have made some Rcpp functions for some on-going work, but the work may be performed my colleagues who are R beginners. My question is, if my colleagues want to use these function on their machines, do they have to install Rtools and use sourceRcpp() to compile the functions first? Is that any way I can avoid this? For example, use the function just like using require()?
Thanks.
On any OS, R permits you to provide a binary package. On Windows and OS X, this is even common. You did not (explicitly) state what OS your colleagues use; from context (Rtools?) it is presumably Windows. You could even use the win-builder service to compile it.
This is very basic packaging question, which is addressed in the Writing R Extensions manual. There is nothing particular about Rcpp here.
We do however have an entire vignette on packaging which you should read, and the material is also covered in the Rcpp book.
Related
I've spent a couple of days developing a program in Haskell, while learning the language. Now I realize that I'll need to call Arpack (a Fortran library) or Arpack++ (a C++ wrapper to Arpack) -- I can't find a good implementation of Lanczos method with Haskell bindings. Do any more experienced Haskell programers have an opinion of how difficult this would be?
I've been able to get ".so" ("shared object") versions of libarpack and libarpack++ installed through Ubuntu's repository, but I'm not sure that will suffice. I suspect I'm going to ultimately need to build Arpack++ from source code, which is possible, but I'm getting a lot of build errors, so it will take time. Is there any way to use just the ".so" files, without knowing exactly which version of the header files were used to generate them?
I'm considering using GreenCard, because it looks like the most well maintained Haskell/C bridge. I can't find much documentation though, so I'm wondering whether it will support C++ too.
I'm also starting to wonder whether I should rewrite my program in Python, and use scipy to call Arpack, but I've already sunk a couple of days into writing Haskell. I really like Haskell too, so I'm hoping I can make this work. I guess my overall question is this: What would be involved in making this work with Haskell?
Thanks much.
ELF format is standard format of executables and shared libraries, so accessing the code in these compiled modules is only a matter of knowing function names. If I understand correctly, Fortran is interoperable with C. As a consequence, Fortran should be interoperable with any language which can use C bindings, including Haskell. FYI, you can find all names exported by a module (executable or shared object or simple object archive) using nm tool (it is usually available in all linux distros by default). This of course would work if the binary file was not "stripped", but AFAIK it is not common practice.
However, Haskell cannot use C++ bindings in sane way, since C++ polymorphic features require name mangling, and the method of this name transformation is highly compiler-dependent. It is well-known problem which is not specific to Haskell. Of course, you could try to get a list of exported symbols from C++ shared object and then bind them using FFI, but... It isn't worth it.
As dsign said, you can use Foreign Function Interface GHC feature to create bindings to foreign code. All you would require is library headers (and the library itself of course). In case of C language that would be header files (*.h), but since your library is written in Fortran, you have to find header files analogue in library sources, refere to this page to match Fortran and C types, and then use this information to write FFI bindings. It would be helpful first to write C bindings, i.e. write C header. Then you can even use automatic FFI binding programs like c2hs.
It maybe also helpful to look through C++ bindings. It is possible that it has the header file I've described above. If it has one, then writing FFI bindings will be no more difficult than writing them for any other library.
So, it is not entirely impossible, but it may require some thorough work. Writing bindings to scientific/pure computational libraries is way easier than writing them for some system library which does a lot of IO and keeps its own internal state, but since this library is written not in C... Well, it may be advisable to invest your time in easier alternatives. I cannot say anythin about scipy, I've never used it, but since Python as a language is much more simpler than Haskell, it may be good alternative.
I can tell you that using a C/Fortran library from Haskell, with the help of the Foreign Function Interface would be certainly possible and not terribly complicated. Here is an introduction. In my understanding, you should be able to call anything with a C calling convention, and perhaps even Fortran, without need of recompiling the code. The only exception is with things that look like function calls but are indeed macros, in which case you will have to figure out what the macros do and reproduce them in Haskell.
As of greencard, I have never used it, so I can not vouch for it.
Your second idea of using Python could potentially save you more than a couple of days. Sad as it is, I have never managed Haskell code to easily adapt to my changing requirements, while I find that trivial in Python. Of course, that could be a limitation on my skills with Haskell or my thinking process rather that something to blame to the language.
In Ocaml, is there easier ways to write a graphics-based toy programs like deminer (like the one that comes with Windows 95)? I find the only way is to start by scratch using Ocaml's graphics library. There must be better ways around?
There are bindings to the SDL library, that provides more features than Graphics.
There are actually several of them, and I'm not exactly sure which is best:
SdlCaml is a part of the [GLcaml] project
the OcamlSDL library
I think SdlCaml is more bare metal (probably partly automatically generated), and OCamlSDL is an older (but still occasionally updated) library with a larger user base.
Note however that Graphics is simple to use for a start, and you can still move to something more sophisticated later. If you run into speed-of-rendering issues, you have to use double buffering, as explained in the manual.
I'm newbie to haskell.
while wxFreeChart page in wxCode says it supports all wx ports, I have no any idea about how to use it in haskell
It's a C++ library, so you'd have to bind it yourself if you want to use it from Haskell; this is unlikely to be practical, as binding C++ libraries to Haskell is a difficult task. (Indeed, wxHaskell itself is based on a custom "binding" of wxWidgets to pure C.)
You should probably figure out another way to accomplish the same task, or if you really need to use wxFreeChart, write your GUI directly in C++. You could still use Haskell for the core logic using the FFI.
wxWidgets ports aren't relevant here; they're the parts that glue wxWidgets to a windowing system like Windows, GTK+, etc.
If you're not overly tied to wxWidgets, you could check out the Chart library, which can be used with Gtk2Hs. I haven't used it myself, but it seems quite polished.
I'm an author of wxFreeChart. Under "All ports" i meant, Windows, MacOS X, Gtk+, Universal ports.
wxHaskell is not directly supported, and there are no plans to support it. If wxFreeChart will work with wxHaskell, it's great. But, i'm not sure about it.
In Common Lisp, programs are often produced as binaries with a translator bundled inside. StumpWM is a good example.
How would one do the same with Haskell and OCaml?
It is not necessary to provide a debugger as well, as Common Lisp does, the aim is to make extensions while not depending on the whole translator package ( xmonad which requires GHC ).
P.S. I know about ocamlmktop, and it works great, except I don't really get why it requires "pervasives.cmi" and doesn't bundle it with the binary. So, best thing I can do is mycustomtoplevel -I /path/to/dir/with/pervasives.cmi/. Any way to override it?
This isn't really possible for (GHC) Haskell - you would either need to to ship the application binary + GHC so you can extend via GHC-API, or embed an extension language. I don't think there are any "off-the-shelf" extension languages to embed in Haskell at the moment, though HsLua might be close. This is a bridge to the the standard (C source) Lua. There was a thread on Haskell-cafe last month about extension languages written in Haskell, I think the answer was 'there aren't any'.
http://www.haskell.org/pipermail/haskell-cafe/2010-November/085830.html
With GHC, there is GHC-API, which allows you to embed ghci-like interpreters in your program. It's a quite low-level and often changing library, since it simply provides access to GHC internas.
Then, there is Hint, a library which aims to encapsulate ghc-api behind a well designed and more stable interface.
Nevertheless, I've recently switched from using either of these packages to using an external ghci. The external ghci process is controlled via standard input/output pipes. This change made it easy to stay compatible with GHC 6.12.x and 7.0.x, while our ghc-api code broke with GHC 7.x and hint didn't work out of the box either. I don't know whether there is a new version of hint available, which works with GHC 7.
For Ocaml, have you tried using findlib? See the section Custom Toploops.
So, I got this idea that I'd try to prototype an experimental user interface using OpenGL and some physics. I know little about either of the topics, but am pretty experienced with programming languages such as C++, Java and C#. After some initial research, I decided on using Python (with Eclipse/PyDev) and Qt, both new to me, and now have four different topics to learn more or less simultaneously.
I've gotten quite far with both OpenGL and Python, but while Python and its ecosystem initially seemed perfect for the task, I've now discovered some serious drawbacks. Bad API documentation and lacking code completion (due to dynamic typing), having to import every module I use in every other module gets tedious when having one class per module, having to select the correct module to run the program, and having to wait 30 seconds for the program to start and obscure the IDE before being notified of many obvious typos and other mistakes. It gets really annoying really fast. Quite frankly, i don't get what all the fuzz is about. Lambda functions, list comprehensions etc. are nice and all, but there's certainly more important things.
So, unless anyone can resolve at least some of these annoyances, Python is out. C++ is out as well, for obvious reasons, and C# is out, mainly for lack of portability. This leaves Java and JOGL as an attractive option, but I'm also curious about Ruby and Groovy. I'd like your opinion on these and others though, to keep my from making the same mistake again.
The requirements are:
Keeping the hell out of my way.
Good code completion. Complete method signatures, including data types and parameter names.
Good OpenGL support.
Qt support is preferable.
Object Oriented
Suitable for RAD, prototyping
Cross-platform
Preferably Open-Source, but at least free.
It seems you aren't mainly having a problem with Python itself, but instead with the IDE.
"Bad API documentation"
To what API? Python itself, Qt or some other library you are using?
"lacking code completion (due to dynamic typing)"
As long as you are not doing anything magic, I find that PyDev is pretty darn good at figuring these things out. If it gets lost, you can always typehint by doing:
assert isinstance(myObj, MyClass)
Then, PyDev will provide you with code completion even if myObj comes from a dynamic context.
"having to import every module I use in every other module gets tedious when having one class per module"
Install PyDev Extensions, it has auto-import on the fly. Or collect all your imports in a separate module and do:
from mymodulewithallimports import *
"having to select the correct module to run the program"
In Eclipse, you can set up a default startup file, or just check "use last run configuration". Then you never have to select it again.
"before being notified of many obvious typos and other mistakes"
Install PyDev Extensions, it has more advanced syntax checking and will happily notify you about unused imports/variables, uninitialized variables etc.
Looking just at your list I'd recommend C++; especially because Code Completion is so important to you.
About Python: Although I have few experience with OpenGL programming with Python (used C++ for that), the Python community offers a number of interesting modules for OpenGL development: pyopengl, pyglew, pygpu; just to name a few.
BTW, your import issue can be resolved easily by importing the modules in the __init__.py files of the directory the modules are contained in and then just importing the "parent" module. This is not recommended but nonetheless possible.
I don't understand why nobody has heard of the D programing language?
THIS IS THE PERFECT SOLUTION!!!!
The only real alternative if you desire all those things is to use Java, but honestly you're being a bit picky about features. Is code completion really that important a trait? Everything else you've listed is traditionally very well regarded with Python, so I don't see the issue.
The text editor (not even an IDE) which I use lets you import API function definitions. Code completion is not a language feature, especially with OpenGL. Just type gl[Ctrl+I] and you'd get the options.
I tried using Java3D and java once. I realized Java3D is a typical Java API... lots of objects to do simple things, and because it's Java, that translates to a lot of code. I then moved to Jython in Eclipse to which cleaned up the code, leaving me with only the complexity of Java3D.
So in the end, I went in the opposite direction. One advantage this has over pure python is I can use Java with all of Eclipse's benefits like autocomplete and move it over to python when parts get unwieldy in Java.
It seems like Pydev can offer code completion for you in Eclipse.
I started off doing OpenGL programming with GL4Java, which got migrated to JOGL and you should definately give it (JOGL) a try. Java offers most of the features you require (plus Eclipse gives you the code completion) and especially for JOGL there are a lot of tutorials out there to get you started.
Consider Boo -- it has many of Python's advantages while adopting features from elsewhere as well, and its compile-time type inference (when variables are neither explicitly given a specific type or explicitly duck typed) allows the kind of autocompletion support you're asking about.
The Tao.OpenGL library exposes OpenGL to .NET apps (such as those Boo compiles), with explicit support for Mono.
(Personally, I'm mostly a Python developer when not doing C or Java, but couldn't care less about autocompletion... but hey, it's your question; also, the one-class-per-module convention seems like a ridiculous amount of pain you're putting yourself through needlessly).