This is similar to this question and answer, except specialized to R packages. Since R uses its own custom build process, what is the correct way to force a rebuild using Rcpp?
(For reasons that I won't go into here, all of my C++ code is located outside /pkg/src, and is called via a simple wrapper function that never changes. For this reason, when the important code changes, R thinks nothing has changed and declares the dreaded make: Nothing to be done for 'all'.)
The simplest solution is to add the flag --preclean to R CMD INSTALL. In Rstudio, this flag can be added under Project Options -> Build Tools -> Build and reload - R CMD INSTALL additonal options.
Regarding
what is the correct way to force a rebuild using Rcpp
the obvious answer is to rebuild from source
R CMD INSTALL sourceTarballOfPackage_0.1.2.tar.gz
The question then becomes where to get the source: CRAN, GitHub, GitLab, BitBucket, ... but we have helpers for that.
If your code is internal, then you just need to rebuild the wrapper calling it, and that is still in src/ in the package. That is no different then another R(cpp) package linking against external resources.
Related
How I can build local sources and dependancies with flatpak-builder?
I can build local sources
flatpak build ../dictionary ./configure --prefix=/app
I can extract and build application with dependancies with a .json
flatpak-builder --repo=repo dictionary2 org.gnome.Dictionary.json
But no way to build dependancies and local sources? I don't find sources type
like dir or other, only archive, git (no hg?) ...
flatpak-builder is meant to automate the whole build process, with a single entry-point: the JSON manifest.
Everything else it obtains from Git, Bazaar or tarballs. Note that for these the "url" property may be a local URL starting with file://.
(There is indeed no support for Hg. If that's important for you, feel free to request it.)
In addition to that, there are a few more source types (see the flatpak-manifest(5) manpage), which can be used to modify the extracted sources:
file which point to a local file to copy somewhere in the extracted sources;
patch which point to a local patch file to apply to the extracted sources;
script which creates a script in the extracted sources, from an array of commands;
shell which modifies the extracted sources by running an array of commands;
Adding a dir source type might be useful.
However (and I only flatpaked a few apps, and contributed 2 or 3 patches to the code, so I might be completely wrong) care must be taken as this would easily make builds completely unreproducible, which is one thing flatpak-builder tries very hard to enable.
For example, when using a local file source, flatpak-builder will base64-econde the content of that file and use it as a data:text/plain;charset=utf8;base64,<content> URL for the file which it stores in the manifest included inside the final build.
Something similar might be needed for a dir source (tar the folder then base64-encode the content of the tar?), otherwise it would be impossible to reproduce the build. I've just been told (after submitting this answer) that this changed in Git master, in favour of a new flatpak-builder --bundle-sources option. This would probably make it easier to support reproducible builds with a dir source type.
In any case, feel free to start the conversation around a new dir source type in the upstream bug tracker. :)
There's a expermental cli tool if you want to use it https://gitlab.com/csoriano/flatpak-dev-cli
You can read the docs
http://docs.flatpak.org/en/latest/building-simple-apps.html
http://docs.flatpak.org/en/latest/flatpak-builder.html
In a nutshell this is what you need to use flatpak as develop workbench
https://github.com/albfan/gnome-builder/wiki/flatpak
I currently have a .cpp file that I can compile using sourceCpp(). As expected the corresponding R function is created and the code works as expected.
Here it is:
#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericVector exampleOne(NumericVector vectorOne, NumericVector vectorTwo){
NumericVector outputVector = vectorOne + vectorTwo;
return outputVector;
}
I am now converting my project over to a package using Rcpp. So I created the skeleton with rStudio and started looking at how to convert things over.
In Hadley's excellent primer on Cpp, he says in section "Using Rcpp in a Package":
If your packages uses the Rcpp::export attribute then one additional step in the package build process is requried. The compileAttributes function scans the source files within a package for Rcpp::export attributes and generates the code required to export the functions to R.
You should re-run compileAttributes whenever functions are added, removed, or have their signatures changed. Note that if you build your package using RStudio or devtools then this step occurs automatically.
So it looks like the code that compiled with sourceCpp() should work pretty much as is in a package.
I created the corresponding R file.
exampleOne <- function(vectorOne, vectorTwo){
outToR <- .Call("exampleOne", vectorOne, vectorTwo, PACKAGE ="testPackage")
outToR
}
Then I (re)built the package and I get this error:
Error in .Call("exampleOne", vectorOne, vectorTwo, PACKAGE = "voteR") :
C symbol name "exampleOne" not in DLL for package "testPackage"
Does anyone have an idea as to what else I need to do when taking code that compiles with sourceCpp() and then using it in a package?
I should note that I have read: "Writing a package that uses Rcpp" http://cran.rstudio.com/web/packages/Rcpp/vignettes/Rcpp-package.pdf and understand the basic structure presented there. However, after looking at the RcppExamples source code, it appears that the structure in the vignettes is not exactly the same as that used in the example package. For example there are no .h files used. Also neither the vignette nor the source code use the [[Rcpp::export]] attribute. This all makes it difficult to track down exactly where my error is.
Here is my "walk through" of how to go from using sourceCpp() to a package that uses Rcpp. If there is an error please feel free to edit this or let me know and I will edit it.
[NOTE: I HIGHLY recommend using RStudio for this process.]
So you have the sourceCpp() thing down pat and now you need to build a package. This is not hard, but can be a bit tricky, because the information out there about building packages with Rcpp ranges from the exhaustive thorough documentation you want with any R package (but that is above your head as a newbie), and the newbie sensitive introductions (that may leave out a detail you happen to need).
Here I use oneCpp.cpp and twoCpp.cpp as the names of two .cpp files you will use in your package.
Here is what I suggest:
A. First I assume you have a version of theCppFile.cpp that compiles with sourceCpp() and works as you expect it to. This is not a must, but if you are new to Rcpp OR packages, it is nice to make sure your code works in this simple situation before you move to the more complicated case below.
B. Now build your package using Rcpp.package.skeleton() or use the Project>Create Project>Package w/Rcpp wizard in RStudio (HIGHLY recommended). You can find details about using Rcpp.package.skeleton() in hadley/devtools or Rcpp Attributes Vignette. The full documentation for writing packages with Rcpp is in Writing a package that uses Rcpp, however this one assumes you know your way around C++ fairly well, and does not use the new "Attributes" way of doing Rcpp. It will be invaluable though if you move toward making more complex packages.
You should now have a directory structure for your package that looks something like this:
yourPackageName
- DESCRIPTION
- NAMESPACE
- \R\
- RcppExports.R
- Read-and-delete-me
- \man\
- yourPackageName-package.Rd
- \src\
- Makevars
- Makevars.win
- oneCpp.cpp
- twoCpp.cpp
- RcppExports.cpp
Once everything is set up, do a "Build & Reload" if using RStudio, or compileAttributes() if you are not in RStudio.
C. You should now see in your \R directory a file called RcppExports.R. Open it and check it out. In RcppExports.R you should see the R wrapper functions for all the .cpp files you have in your \src directory. Pretty sweet, eh?.
D) Try out the R function that corresponds to the function you wrote in theCppFile.cpp. Does it work? If so move on.
E) You can now just add new .cpp files like otherCpp.cpp to the \src directory as you create them. Then you just have to rebuild the package, and the R wrappers will be generated and added to RcppExports.R for you. In RStudio this is just "Build & Reload" in the Build menu. If you are not using RStudio you should run compileAttributes()
In short, the trick is to call compileAttributes() from within the root of the package. So for instance for package foo
$ cd /path/to/foo
$ ls
DESCRIPTION man NAMESPACE R src
$ R
R> compileAttributes()
This command will generate the RcppExports.cpp and RcppExports.R that were missing.
You are missing the forest for the trees.
sourceCpp() is a recent function; it is part of what we call "Rcpp attributes" which has its own vignette (with the same title, in the package, on my website, and on CRAN) which you may want to read. It among other things details how to turn something you compiled and run using sourceCpp() into a package. Which is what you want.
Randomly jumping between documentation won't help you, and at the end of the genuine source documentation by package authors may be preferable. Or to put a different spin on it: you are using a new feature but old documentation that doesn't reflect it. Try to write a basic package with Rcpp, ie come to it from the other end as well.
Lastly, there is a mailing list...
I'm using Autoconf to build my c++ project. It uses third party code which is also built with the help of Autoconf/Automake. So in my configure.ac I've got the following line:
AC_CONFIG_SUBDIRS([subdirectoryname])
Everything works fine, but I also use the feature to let tests be automatically made if make check is executed - which is done by the third party code as well. Because these tests take a while it's annoying to execute them each time I want to test my own code. So is there any way to avoid that the check option is passed to the subdirectory's Makefile?
Update: Overriding check-recursive does not seem to be an option, as my top-level Makefile.am looks (more or less) like this:
SUBDIRS=library src
So disabling checking on this level would also disable the checking inside my src folder. And that's not what I want to achieve. I just want to disable the checking in the library directory.
Overriding check-recursive in your Makefile.am should work:
check-recursive:
#true
or, if you only wanted to check in a specific directory:
check-recursive:
$(MAKE) -C src check
according to the autoconf manual, it will execute a configure.gnu script in the subdirectory if it finds one. Theoretically that could be a script which adds a --disable-tests or similar option to a call to ./configure
That said, I've yet to get this to work on a project of my own. :-/
Context
I am working on a klee (http://klee.llvm.org) fork and want to clean up our repository to separate our stuff from the "canonical" klee code. Anyway, I'm having trouble understanding/extending the build system.
Problem
The directory structure in /lib/ looks like this
Basic/
Core/
Support/
Expr/
Solver/
Module/
Mine/
Mine was just added by me, so far we threw everything in Core and I am moving it to Mine. How do I tell the build system to do this properly?
My attempt
Being unable to figure this out on my own, I edited /lib/Makefile:
LEVEL=..
PARALLEL_DIRS=Basic Support Expr Solver Module Core Mine
include $(LEVEL)/Makefile.common
and copied the /lib/Core/Makefile to /lib/Mine/Makefile while changing LIBRARYNAME=kleeCore to LIBRARYNAME=kleeMine.
Caveat
I have a feeling that this is not the proper way to do it, and I should rather modify some configure script or something. Also it does not link (it compiles, though).
A colleague just told me how to get it to link, which is by modifying /tools/klee/Makefile
USEDLIBS = kleeCore.a kleeModule.a kleaverSolver.a kleaverExpr.a kleeSupport.a kleeBasic.a kleeMine.a
I want to apply a patch to this bug (http://code.djangoproject.com/ticket/13095) but I have never done it before and I have no idea where to begin. Can anyone point me to a tutorial?
On Linux/UNIX, you can use the patch command for this.
It works in the following way:
cd /usr/lib.../site-packages/django/
patch --dry-run -p1 < ~/downloads/somefix.patch
The patch command looks in the file to find the proper files it needs to update.
The -p1 tells patch to ignore the first level of the folder mentioned in the patch file. Often this is the project name itself. The --dry-run option prevents actual execution, so you can experiment with it.
When everything is allright, you can remove the --dry-run option, and the actual patch will be applied.
On Windows, several tools (e.g. WinMerge / TortoiseMerge) have a "Apply patch" option in the menu, which will allow you to do the same thing.
Try 'patch' if you are using a linux based server.
http://en.wikipedia.org/wiki/Patch_%28Unix%29
Windows appears do have a utility written for it although I havent used one
http://gnuwin32.sourceforge.net/packages/patch.htm
remember to make backups of the directory if you are unsure of its outcome