Bug 258887

Summary:	math/R: fails to build with clang/openmp 13 due to old mgcv
Product:	Ports & Packages	Reporter:	Dimitry Andric <dim>
Component:	Individual Port(s)	Assignee:	Joseph Mingrone <jrm>
Status:	Closed FIXED
Severity:	Affects Only Me	CC:	rhurlin
Priority:	---	Flags:	bugzilla: maintainer-feedback? (jrm)
Version:	Latest
Hardware:	Any
OS:	Any
Bug Depends on:
Bug Blocks:	258209

Description Dimitry Andric freebsd_committer

2021-10-03 11:27:21 UTC

During an exp-run for llvm 13 (see bug 258209), it turned out that math/R fails to build with clang 13 (http://gohan04.nyi.freebsd.org/data/mainamd64PR258209-default/2021-09-30_06h20m28s/logs/errors/R-4.1.1_1.log):

begin installing recommended package mgcv
* installing *source* package ‘mgcv’ ...
** package ‘mgcv’ successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
gmake[4]: Entering directory '/tmp/RtmpJN7T4d/R.INSTALLb1494371d851/mgcv/src'
cc -I"/wrkdirs/usr/ports/math/R/work/R-4.1.1/include" -DNDEBUG   -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include  -fopenmp -fpic  -O2 -pipe  -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -c coxph.c -o coxph.o
cc -I"/wrkdirs/usr/ports/math/R/work/R-4.1.1/include" -DNDEBUG   -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include  -fopenmp -fpic  -O2 -pipe  -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -c davies.c -o davies.o
cc -I"/wrkdirs/usr/ports/math/R/work/R-4.1.1/include" -DNDEBUG   -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include  -fopenmp -fpic  -O2 -pipe  -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing   -c discrete.c -o discrete.o
In file included from discrete.c:28:
/usr/include/omp.h:484:39: error: expected 'match' clause on 'omp declare variant' directive
    #pragma omp begin declare variant match(device={kind(host)})
                                      ^
/wrkdirs/usr/ports/math/R/work/R-4.1.1/include/Rinternals.h:1640:17: note: expanded from macro 'match'
#define match                   Rf_match
                                ^
In file included from discrete.c:28:
/usr/include/omp.h:487:39: error: expected 'match' clause on 'omp declare variant' directive
    #pragma omp begin declare variant match(device={kind(nohost)})
                                      ^
/wrkdirs/usr/ports/math/R/work/R-4.1.1/include/Rinternals.h:1640:17: note: expanded from macro 'match'
#define match                   Rf_match
                                ^
2 errors generated.

What happens here is that the mgcv package includes <omp.h> *after* including <R.h>, which causes the conflict between the "#define match" and the openm pragma line which uses match().

This problem was fixed in mgcv 1.8-37 (https://cran.r-project.org/web/packages/mgcv/ChangeLog) with the small mention:

> 1.8-37
> 
> * minor update for clang compatibility.

basically, in most of the .c files, "#include <omp.h>" was moved before "#include <R.h>".

Locally, I was able to 'fix' it by replacing /wrkdirs/usr/ports/math/R/work/R-4.1.1/src/library/Recommended/mgcv.tgz with a copy of https://cran.r-project.org/src/contrib/mgcv_1.8-37.tar.gz, but I am unsure how this can be done more correctly for the math/R port.

Maybe the mgcv_1.8-37.tar.gz file can be added as an additional distfile, and added to the port Makefile, somehow? Any ideas are welcome.

Comment 1 Joseph Mingrone freebsd_committer

2021-10-03 14:29:15 UTC

Could you test https://reviews.freebsd.org/D32280 ?

Comment 2 Dimitry Andric freebsd_committer

2021-10-03 19:00:53 UTC

(In reply to Joseph Mingrone from comment #1)
As noted in the review, it builds with clang 13, installs, and seems to run fine for me. Thanks for the quick fix!

Comment 3 commit-hook freebsd_committer

2021-10-03 20:32:08 UTC

A commit in branch main references this bug:

URL: https://cgit.FreeBSD.org/ports/commit/?id=16c89d12ec5c03f824e4925d18b8849c4ab1e86b

commit 16c89d12ec5c03f824e4925d18b8849c4ab1e86b
Author:     Joseph Mingrone <jrm@FreeBSD.org>
AuthorDate: 2021-10-03 14:20:38 +0000
Commit:     Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2021-10-03 20:28:52 +0000

    math/R: Fix build with clang/openmp 13

    The mgcv package is one of the recommended packages to be installed with
    R.  A problem with mgcv and clang/openmp 13 is that mgcv versions prior
    to 1.8-37 place 'include <omp.h>' after 'include <R.h>'.  This causes a
    conflict between '#define match' and an openmp pragma line, which uses
    match().  This problem was fixed in mgcv 1.8-37, so replace mgcv 1.8-36
    with this newer version.

    While here, incorporate formatting changes suggested by portclippy and
    portfmt.

    PR:             258887
    Approved by:    dim
    Differential Revision:  https://reviews.freebsd.org/D32280

 math/R/Makefile  | 18 ++++++++++++------
 math/R/distinfo  |  4 +++-
 math/R/pkg-plist |  2 --
 3 files changed, 15 insertions(+), 9 deletions(-)

Comment 4 Joseph Mingrone freebsd_committer

2021-10-03 20:33:11 UTC

Thanks for confirming.