From nobody Sun Oct 3 11:27:21 2021 X-Original-To: ports-bugs@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id DE75817B59A6 for ; Sun, 3 Oct 2021 11:27:21 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4HMhQd5h63z4q9g for ; Sun, 3 Oct 2021 11:27:21 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2610:1c1:1:606c::50:1d]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 9FBE625136 for ; Sun, 3 Oct 2021 11:27:21 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org ([127.0.1.5]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id 193BRLco029928 for ; Sun, 3 Oct 2021 11:27:21 GMT (envelope-from bugzilla-noreply@freebsd.org) Received: (from www@localhost) by kenobi.freebsd.org (8.15.2/8.15.2/Submit) id 193BRL8a029927 for ports-bugs@FreeBSD.org; Sun, 3 Oct 2021 11:27:21 GMT (envelope-from bugzilla-noreply@freebsd.org) X-Authentication-Warning: kenobi.freebsd.org: www set sender to bugzilla-noreply@freebsd.org using -f From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 258887] math/R: fails to build with clang/openmp 13 due to old mgcv Date: Sun, 03 Oct 2021 11:27:21 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Only Me X-Bugzilla-Who: dim@FreeBSD.org X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: jrm@freebsd.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter flagtypes.name Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated List-Id: Ports bug reports List-Archive: https://lists.freebsd.org/archives/freebsd-ports-bugs List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-ports-bugs@freebsd.org X-BeenThere: freebsd-ports-bugs@freebsd.org MIME-Version: 1.0 X-ThisMailContainsUnwantedMimeParts: N https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D258887 Bug ID: 258887 Summary: math/R: fails to build with clang/openmp 13 due to old mgcv Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: jrm@freebsd.org Reporter: dim@FreeBSD.org Assignee: jrm@freebsd.org Flags: maintainer-feedback?(jrm@freebsd.org) During an exp-run for llvm 13 (see bug 258209), it turned out that math/R f= ails to build with clang 13 (http://gohan04.nyi.freebsd.org/data/mainamd64PR258209-default/2021-09-30_0= 6h20m28s/logs/errors/R-4.1.1_1.log): begin installing recommended package mgcv * installing *source* package =E2=80=98mgcv=E2=80=99 ... ** package =E2=80=98mgcv=E2=80=99 successfully unpacked and MD5 sums checked ** using non-staged installation ** libs gmake[4]: Entering directory '/tmp/RtmpJN7T4d/R.INSTALLb1494371d851/mgcv/sr= c' cc -I"/wrkdirs/usr/ports/math/R/work/R-4.1.1/include" -DNDEBUG=20=20 -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=20=20 -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=20=20 -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=3D{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=3D{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 *after* includi= ng , 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 >=20 > * minor update for clang compatibility. basically, in most of the .c files, "#include " was moved before "#include ". Locally, I was able to 'fix' it by replacing /wrkdirs/usr/ports/math/R/work/R-4.1.1/src/library/Recommended/mgcv.tgz wit= h 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, a= nd added to the port Makefile, somehow? Any ideas are welcome. --=20 You are receiving this mail because: You are the assignee for the bug.=