[Bioc-devel] portable make syntax

On Fri, Jan 23, 2015 at 5:18 PM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:

----- Original Message -----

From: "Kevin Ushey" <kevinushey at gmail.com>
To: "Laurent Gatto" <lg390 at cam.ac.uk>
Cc: "bioc-devel" <bioc-devel at stat.math.ethz.ch>
Sent: Friday, January 23, 2015 4:58:40 PM
Subject: Re: [Bioc-devel] portable make syntax

If I understand correctly, all versions of `make` on the BioC build
systems will support GNU extensions to Makefiles, and so it's
probably
not worth your time to make this 'portable' -- just add the
SystemRequirements bit.

BTW, the warning was added in recent versions of R-devel and I don't know why it was added.
It could be that GNU extensions may not be supported in future versions of Rtools (the windows
toolchain maintained by Duncan Murdoch). I really have no idea. But since a warning was added, it's probably a good idea to find out why rather than to ignore it. So it might be worth a note to R-devel asking about the intention of that warning.

Dan

Very unlikely -- I am really not sure of what the motivation is,
beyond R wanting to support platforms with versions of make that do
not support GNU extensions (whichever those might be... BSD make? AT&T
make on Solaris? See:
http://cran.r-project.org/doc/manuals/r-release/R-exts.html#FOOT51)

I am guessing that the Windows toolchain will continue to be based off
of MinGW + GCC for the foreseeable future, and hence will continue to
allow GNU extensions. In fact, R-exts specifically prescribes GNU
extensions for Windows makefiles -- from R-exts,

    Since the only viable make for Windows is GNU make, it is
permissible to use GNU extensions in files Makevars.win or
Makefile.win.

so I really doubt Windows would ever foresake GNU extensions.

Kevin

However, you could work around this by (following R-exts at
http://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-portable-packages)
wrapping your shell command in backticks, e.g.

    R_HOME=`if test -z ${R_HOME}; then ...; else ...; fi`

or something to that effect.

On Fri, Jan 23, 2015 at 4:05 PM, Laurent Gatto <lg390 at cam.ac.uk>
wrote:

Dear all,

I have been using the following in various vignettes/Makefile

ifeq (${R_HOME},)
R_HOME= $(shell R RHOME)
endif

This syntax is GNU specific and now results in warnings when
checking
the package:

* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  vignettes/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=,
$(shell),
$(wildcard), ifeq ... endif. See section ?Writing portable
packages? in
the ?Writing R Extensions? manual.

I couldn't find anything in R-exts; does anyone know a more
portable
syntax?

Alternatively, I could add

SystemRequirements: GNU make

to my DESCRIPTION file, which however does not seem ideal.

Any suggestions?

Thank you very much in advance.

Laurent