On 01/23/2015 06:22 PM, Michael Lawrence wrote:
Here is a quote from Brian's email to CRAN maintainers:
------------
The set of make programs in use for R is shifting (BSD make seems to
be no longer in use by Apple or FreeBSD; dmake and pmake variants are
appearing) and we have taken the POSIX standard as the baseline for
portability.
------------
It sounds like this is a CRAN-specific requirement. Bioc of course is
left to make its own decision on make support.
I think that most make files can be made to conform easily to POSIX standards,
which seems in general like a good idea (Linux flavored packages build from
source, so the compilers on the Bioc build machines are a poor guide to those
encountered in the wild).
If we absolutely need GNU Make, we can add this to DESCRIPTION:
SystemRequirements: GNU make
...remembering that this merely quietens the note, and we would rather address
the issue.
I haven't looked at the build reports, but the it looks like the following
(including several apparently following poorly worded instructions in Rsamtools;
aargh) can be easily brought into conformance through use of ` rather than $(shell).
$ ls */src/Makevars|xargs grep -l shell
ArrayExpressHTS/src/Makevars
ChemmineR/src/Makevars
DiffBind/src/Makevars
eiR/src/Makevars
flipflop/src/Makevars
mosaics/src/Makevars
qrqc/src/Makevars
QuasR/src/Makevars
VariantAnnotation/src/Makevars
Martin
On Fri, Jan 23, 2015 at 6:13 PM, Kevin Ushey <kevinus...@gmail.com> wrote:
On Fri, Jan 23, 2015 at 5:18 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
----- Original Message -----
From: "Kevin Ushey" <kevinus...@gmail.com>
To: "Laurent Gatto" <lg...@cam.ac.uk>
Cc: "bioc-devel" <bioc-de...@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 ${R_HOME}; then ...; else ...; fi`
or something to that effect.
On Fri, Jan 23, 2015 at 4:05 PM, Laurent Gatto <lg...@cam.ac.uk>
wrote:
Dear all,
I have been using the following in various vignettes/Makefile
ifeq (${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
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