As Martin says, it looks like the difference between GNU makefiles and portable makefiles are very minor for most usages. What we just need is some easy accessible comments on how to do it portable, perhaps on the HOWTOs. I see no need to sacrifice portability when the fixes are so easy.
Best, Kasper On Fri, Jan 23, 2015 at 10:36 PM, Martin Morgan <mtmor...@fredhutch.org> wrote: > 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 >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>>>> >>>>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
