[Bioc-devel] portable make syntax

[Martin Morgan]

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 <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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>
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