[Bioc-devel] portable make syntax

[Michael Lawrence]

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.

If we absolutely need GNU Make, we can add this to DESCRIPTION:

SystemRequirements: GNU make

On Fri, Jan 23, 2015 at 6:13 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
> 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
>>> >
>>> > _______________________________________________
>>> > Bioc-devel at r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>
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