[Bioc-devel] portable make syntax

Hi, Martin et al,

At the risk of revealing myself to be an idiot in public... I just cannot get
back ticks to work on an "include" line in a "Makevars" file.

The file contains these lines:
-----------------------------------------
SAMVARS = `echo 'cat(system.file("usretc", .Platform[["r_arch"]],"Rsamtools.mk",
package="Rsamtools", mustWork=TRUE))' | "$(R_HOME)/bin/R" --vanilla --slave`
include $(SAMVARS)
-----------------------------------------
as shown in the Rsamtools "Using samtools C libraries with Rsamtools" document.
  But the "include" line is parsed by make, which ignores the back ticks, not by
the shell, as seen in the following snippet:

-----------------------------------------------------------------
uk-cri-lsrv10 ~/packages $ R CMD build DiffBind
* checking for file 'DiffBind/DESCRIPTION' ... OK
* preparing 'DiffBind':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
       -----------------------------------
* installing *source* package 'DiffBind' ...
** libs
Makevars:2: `echo: No such file or directory
Makevars:2: 'cat(system.file("usretc",: No such file or directory
Makevars:2: .Platform[["r_arch"]],"Rsamtools.mk",: No such file or directory
Makevars:2: package="Rsamtools",: No such file or directory
Makevars:2: mustWork=TRUE))': No such file or directory
Makevars:2: |: No such file or directory
Makevars:2: "/usr/local/lib64/R/bin/R": No such file or directory
Makevars:2: --vanilla: No such file or directory
Makevars:2: --slave`: No such file or directory
make: *** No rule to make target `--slave`'.  Stop.
ERROR: compilation failed for package 'DiffBind'
* removing '/tmp/RtmpJaAJ8I/Rinst297e5010e355/DiffBind'
       -----------------------------------
ERROR: package installation failed
-----------------------------------------------------------------
Reading through the make source code, there doesn't seem to be any attempt to
evaluate the back tick-ed expression after macro expansion but before splitting
into filenames, as seems clear from the errors above.  Nor can I see any
POSIX-compatible way to force evaluation of the expression (reading from this
page: http://pubs.opengroup.org/onlinepubs/9699919799/utilities/make.html ).  I
see the same behaviour if I use an actual Makefile as opposed to Makevars.

As you noted, I was indeed following the instructions in the Samtools docs... I
must be doing something simple wrong, but just can't see it.  Can you give me a
hint as to what I should be doing differently?

Thanks in advance,

  - Gord Brown

Details:
R v3.1.2, and also the latest devel version
gnu make 3.81, 3.82, 4.1
centos linux 6.6

*
*


    Message: 3
    Date: Fri, 23 Jan 2015 19:36:46 -0800
    From: Martin Morgan <mtmorgan at fredhutch.org <mailto:mtmorgan at fredhutch.org>>
    To: Michael Lawrence <lawrence.michael at gene.com
    <mailto:lawrence.michael at gene.com>>, Kevin Ushey
    <kevinushey at gmail.com <mailto:kevinushey at gmail.com>>
    Cc: bioc-devel <bioc-devel at stat.math.ethz.ch
    <mailto:bioc-devel at stat.math.ethz.ch>>
    Subject: Re: [Bioc-devel] portable make syntax
    Message-ID: <54C3134E.8080604 at fredhutch.org
    <mailto:54C3134E.8080604 at fredhutch.org>>
    Content-Type: text/plain; charset="utf-8"; format=flowed

    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
        <mailto:kevinushey at gmail.com>> wrote:

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



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

                    From: "Kevin Ushey" <kevinushey at gmail.com
                    <mailto:kevinushey at gmail.com>>
                    To: "Laurent Gatto" <lg390 at cam.ac.uk <mailto:lg390 at cam.ac.uk>>
                    Cc: "bioc-devel" <bioc-devel at stat.math.ethz.ch
                    <mailto: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 <mailto: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