Re: How can I change the Makeconf file of R to not use hardcoded, wrong include paths when compiling a package with Rcpp

[zimoun]

Hi Moritz,

On Thu, 16 Jan 2020 at 01:35, Moritz Lell <address@hidden> wrote:

> While you're right that a manifest of R and all packages is the best
> way, I will still need R to compile something from time to time, for
> example C++ code from within my project.

What do you mean by "still need R to compile something from time to time"?

I am a Bioconductor user and my workflow is:

 1. "guix search <r-pkg>" and if <r-pkg> is there, go to 5.
 2. Else, try to package. If the package is on the CRAN or the
Bioconductor archive, then I use "guix import cran -r". If not, e.g.,
on GitHub, then I write down the package definition reading the doc
and the requirements.
 3. Build the package "guix build -L /path/to/my/definition <r-pkg>".
Ask here or on IRC if I am not able to fix it.
 4. If the package fits the GNU compliance, send the patch. Else push
the package definition to my repo/channel.
 5. Create a profile using a manifest (storing the Guix commit and the
channel). And time to time, I build Docker images to release the
package to my colleagues.


For example, give a look to the package 'r-umap' with "guix edit r-umap".
Then try: guix build r-umap --no-grafts --check -K
You will see that C++ code is compiled.

If the package is correctly done by the R packagers, then the Guix
'r-build-system' does the correct thing. :-)

With this discipline, you keep your project reproducible.


However, sometimes I need to do quick and dirty hack by compiling
stuff with R (often directly in RStudio). But I am not targeting
reproducibility but experimentations that will go to trash at the end
of the day. And I never had issues, if I remember well.


> I have already found out some knobs in the R installation but I'm not
> done yet. I need someone with more experience with C++ linking and
> including flags to help me for this to work.

Some years back, I was tweaking flags etc. and it was often a mess and
spending some time to fix stuff that broke, etc.
Now, I prefer to write a clean R package, then use it to have a Guix
package. Everything stays clean. :-)


> I tried to translate this into R with a patch versus the guix git repo,
> commit 40b1cee620a55bf1fc5d8d897ed1ec147b2535c8 that I have attached to
> this mail. However, I think I got some include paths wrong because I get
> errors when starting R:

Hum? I am not convinced that it comes from the R package definition.
And there you are modifying the version 3.6.2. Which version do you
want to use? 3.6.2 or 3.4.3? I am lost.

> Are the paths that I set in the attached commit correct?

I do not know, I am a bit lost on what you want to achieve.

I thought you want to use R@3.4.3 with Rcpp@1.0.3.

Because the current default R which is R@3.6.2 works nicely with
Rcpp@1.0.3. The '-l/usr/local/lib' is not an issue, AKAICT.


All the best,
simon