[WIP] [R-package] R-package installation with CRAN toolchain

[jameslamb]

In this PR, I'm testing a CRAN-compliant installation setup for the R package. We can't assume the presence of cmake and hopefully don't need it.

Relevant links:

• https://unconj.ca/blog/an-autoconf-primer-for-r-package-authors.html
• https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Configure-and-cleanup
• https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Initializing-configure.html
• https://github.com/dmlc/xgboost/blob/master/Makefile#L218
• https://stackoverflow.com/questions/11647208/where-to-add-a-cflag-such-as-std-gnu99-into-an-autotools-project
• substitution with AC_SUBST

[jameslamb]

From RcppArmadillo docs (http://dirk.eddelbuettel.com/blog/2017/06/04/):

Here, we once again rely on the build infrastructure automagically provided by R itself: if and when OpenMP is available, R will use it via $(SHLIB_OPENMP_CXXFLAGS) etc

[jameslamb]

Some possible models from Makevars.win and configure.win

• https://github.com/cran/pbdZMQ/blob/8c2c54eb1eb12759a0b1ca5f83ebd1a4e63a8ab9/src/Makevars.win
• https://github.com/cran/cxxPack/blob/956af335f418a489f226555c550359c7b887d577/configure.win

[jameslamb]

found the use of Biarch field in DESCRIPTION, that one was new to me.

https://github.com/kthohr/BMR/pull/43/files

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file

[jameslamb]

dealing with this issue:

* checking top-level files ... WARNING
  Output from running autoreconf:
  Can't exec "aclocal": No such file or directory at /usr/local/Cellar/autoconf/2.69/share/autoconf/Autom4te/FileUtils.pm line 326.
  autoreconf: failed to run aclocal: No such file or directory

buffer/pylibemu#24

[jameslamb]

nice example of a configure.win finding Rscript in the right place: https://github.com/stewid/SimInf/blob/master/configure.win

Per "Writing R Extensions"

provide a configure.win script to be used on that platform. (Optionally, there can be a cleanup.win script. Both should be shell scripts to be executed by ash, which is a minimal version of Bourne-style sh.) When configure.win is run the environment variables R_HOME (which uses ‘/’ as the file separator), R_ARCH and Use R_ARCH_BIN will be set. Use R_ARCH to decide if this is a 64-bit build (its value there is ‘/x64’) and to install DLLs to the correct place (${R_HOME}/libs${R_ARCH}). Use R_ARCH_BIN to find the correct place under the bin directory, e.g. ${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe.

[jameslamb]

other configure.win examples:

• rJava: https://github.com/cran/rJava/blob/master/configure.win
• nimble: https://github.com/cran/nimble/blob/master/configure.win
• cxxPack: https://github.com/cran/cxxPack/blob/master/configure.win
• rGraphviz: https://github.com/cran/Rgraphviz/blob/master/configure.win
• covafillr: https://github.com/cran/covafillr/blob/master/configure.win
• SnakeCharmR: https://github.com/cran/SnakeCharmR/blob/master/configure.win
• rPython: https://github.com/cran/rPython/blob/master/configure.win
• C50: https://github.com/cran/C50/blob/master/configure.win
• RBrownie: https://github.com/cran/RBrownie/blob/master/configure.win
• RSiena: https://github.com/cran/RSiena/blob/master/configure.win
• Cubist: https://github.com/cran/Cubist/blob/master/configure.win
• bigtabulate: https://github.com/cran/bigtabulate/blob/master/configure.win
• Rssa: https://github.com/cran/Rssa/blob/master/configure.win

really big configure example, maybe there are things we can steal from there

• https://github.com/ecrc/exageostatR/blob/master/configure

configure example setting linker flags

• https://github.com/sgaure/lfe/blob/master/configure.ac

[jameslamb]

After banging my head against it for a while, I found that it is not possible to pass --configure-args to configure.win for Windows packages. This means we cannot pass --enable-gpu.

https://community.rstudio.com/t/configure-args-option-on-windows/20320/4

That isn't documented anywhere that I have found, but Jim Hester is an expert and also you can see it in the R source code: https://github.com/wch/r-source/blob/8bc3a6f4b0c2fca3195cac427e9ad8b4448eaa73/src/library/tools/R/install.R#L670-L697

I think the only way we can get around it might be with environment variables. I'm testing that now.

[jameslamb]

Notes on non-portable flags:

• -O3 is not portable
• -funroll-loops is not portable
• -Wno-unknown-pragmas is not portable and is not allowed because it suppresses warnings

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