From kasperdanielhansen at gmail.com  Tue Sep 27 16:17:29 2016
From: kasperdanielhansen at gmail.com (Kasper Daniel Hansen)
Date: Tue, 27 Sep 2016 10:17:29 -0400
Subject: [Rd] src/Makevars ignored ?
In-Reply-To: <b11e2a62-95bd-0d2f-66ba-2d6177f62bb9@pasteur.fr>
References: <5abedec3-552a-b141-a9e2-ef74e212b893@pasteur.fr>
	<22506.22668.727653.313373@max.nulle.part>
	<b11e2a62-95bd-0d2f-66ba-2d6177f62bb9@pasteur.fr>
Message-ID: <CAC2h7usqc7JQxkJG72k-NA4dqT+MR0BB_Qm4GBkROSVHux+6Yw@mail.gmail.com>

As a package author, it is in my opinion irresponsible to override these
system settings (which is why it is also impossible).  You have no idea
what system it is being deployed on, I mean, you don't even know if the
compiler is gcc. If a user wants (say) heavy optimization they will compile
R with optimization.  (For this reason I also don't think users should
modify their ~/.R/Makevars, unless for testing purposes).  The exception is
(in my opinion) if you need to decrease the level of optimization because
you know or suspect the compiler to generate wrong code.

What you should do, is use
  PKG_CFLAGS
as documented in R-exts, 1.2.1 under "Using Makevars".

Best,
Kasper


On Tue, Sep 27, 2016 at 9:23 AM, Eric Deveaud <edeveaud at pasteur.fr> wrote:

> Le 27/09/16 ? 13:31, Dirk Eddelbuettel a ?crit :
>
>
>> On 27 September 2016 at 09:37, Eric Deveaud wrote:
>> |      Hello,
>> |
>> | I'm tring to install a Rpackage that holds some C//C++ code
>> |
>> | as far as I understood the R library generic compilation mechanism,
>> | compilation of C//C++ sources is controled
>> |
>> | 1) at system level by the ocntentos RHOME/etc/Makeconf
>> | 2) at user level by the content of ~/.R/Makevars
>> | 3) at package level by the content of src/Makevars
>> |
>> | Problem I have is that src/Makevars is ignored
>> |
>> |
>> | see following example:
>> |
>> | R is compiled and use the following CC and CFLAGS definition
>> |
>> | bigmess:epactsR/src > R CMD config CC
>> | gcc -std=gnu99
>> | bigmess:epactsR/src > R CMD config CFLAGS
>> | -Wall -g
>> |
>> | so building C sources lead to the following
>> |
>> | bigmess:epactsR/src > R CMD SHLIB index.c
>> | gcc -std=gnu99 -I/local/gensoft2/adm/lib64/R/include -DNDEBUG
>> | -I/usr/local/include    -fpic  -Wall -g  -c index.c -o index.o
>> |
>> | normal, it uses defintion from RHOME/etc/Makeconf
>> |
>> |
>> | when I set upp a ~/.R/Makevars that overwrite CC and CFLAGS definition.
>> |
>> | bigmess:epactsR/src > cat ~/.R/Makevars
>> | CC=gcc
>> | CFLAGS=-O3
>> | bigmess:epactsR/src > R CMD SHLIB index.c
>> | gcc -I/local/gensoft2/adm/lib64/R/include -DNDEBUG
>> -I/usr/local/include
>> |     -fpic  -O3 -c index.c -o index.o
>> | gcc -std=gnu99 -shared -L/usr/local/lib64 -o index.so index.o
>> |
>> |
>> | OK CC and CFLAGS are honored and set accordingly to ~/.R/Makevars
>> |
>> |
>> | but when I try to use src/Makevars, it is ignored
>> |
>> | bigmess:epactsR/src > cat ~/.R/Makevars
>> | cat: /home/edeveaud/.R/Makevars: No such file or directory
>> | bigmess:epactsR/src > cat ./Makevars
>> | CC = gcc
>> | CFLAGS=-O3
>> | bigmess:epactsR/src > R CMD SHLIB index.c
>> | gcc -std=gnu99 -I/local/gensoft2/adm/lib64/R/include -DNDEBUG
>> | -I/usr/local/include    -fpic  -Wall -g  -c index.c -o index.o
>> |
>> |
>> | is there something I have missed, misunderstood or is there something
>> | wrong ?
>>
>> You have not demonstrated that src/Makevars is ignored -- as it clearly
>> isn't, given how thousands of CRAN packages use it.
>>
>> What you have done is demonstrate that you _cannot change CC and CXX_ in
>> src/Makevars.  And I think that was known, though maybe not as widely.
>>
>
>
>     Hello Dirk,
>
>
> so why ~/R/Makevars allows to change CC and not src/Makevars ?
>
> this is pretty confusing.
>
> in unix world mechanism of overwriting system default in user and package
> order is something standadr and consistent given the level
>
> priority is package specific stuff overwrite user configuration that
> overwrite system default
>
> mechanism of Makevars is NOT consistent
>
>
> furthermore diggng in $RHOME/bin/config one can see the following
>
>
> if test "${site}" = "yes"; then
> : ${R_MAKEVARS_SITE="${R_HOME}/etc${R_ARCH}/Makevars.site"}
>   if test -f "${R_MAKEVARS_SITE}"; then
>     makefiles="${makefiles} -f ${R_MAKEVARS_SITE}"
>   fi
> fi
> if test "${personal}" = "yes"; then
>   if test "${R_OSTYPE}" = "windows"; then
>     if test -f "${R_MAKEVARS_USER}"; then
>       makefiles="${makefiles} -f ${R_MAKEVARS_USER}"
>     elif test ${R_ARCH} = "/x64" -a -f "${HOME}/.R/Makevars.win64"; then
>       makefiles="${makefiles} -f ${HOME}/.R/Makevars.win64"
>     elif test -f "${HOME}/.R/Makevars.win"; then
>       makefiles="${makefiles} -f ${HOME}/.R/Makevars.win"
>     elif test -f "${HOME}/.R/Makevars"; then
>       makefiles="${makefiles} -f ${HOME}/.R/Makevars"
>     fi
>   else
>     . ${R_HOME}/etc${R_ARCH}/Renviron
>     if test -f "${R_MAKEVARS_USER}"; then
>       makefiles="${makefiles} -f ${R_MAKEVARS_USER}"
>     elif test -f "${HOME}/.R/Makevars-${R_PLATFORM}"; then
>       makefiles="${makefiles} -f ${HOME}/.R/Makevars-${R_PLATFORM}"
>     elif test -f "${HOME}/.R/Makevars"; then
>       makefiles="${makefiles} -f ${HOME}/.R/Makevars"
>     fi
>   fi
> fi
>
> it checks and honours R_MAKEVARS_USER, ~/.R/Makevars, but not src/Makevars
> I'm not really familiar with the R policy about code comilation, but I
> consider this a bug but maybee I'm wrong
>
>
> as a side note I solved the problem of overwritting CC for this particular
> package using MAKEFLAGS="CC=gcc" R CMD INSTALL package
>
>
>
>     best regards
>
>     Eric
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Rd] src/Makevars ignored ?
Kasper Daniel Hansen