On Fri, Dec 13, 2019 at 11:28:50AM +0100, Martin Reindl wrote:
On Thu, Dec 12, 2019 at 02:16:24PM +0100, Ingo Feinerer wrote:
update math/R 3.6.1 -> 3.6.2
[...]
Works for me on amd64.
+1 on arm64 with my Rscripts.
But does this need extra WANTLIBs?
R-3.6.2(math/R):
Missing: flang.2 from flang-8.0.1.20191107 (/usr/local/lib/R/modules/lapack.so)
Missing: flangrti.5 from flang-8.0.1.20191107
(/usr/local/lib/R/modules/lapack.so)
Missing: pgmath.4 from libpgmath-8.0.1.20191107
(/usr/local/lib/R/modules/lapack.so)
Extra: c++.3 c++abi.1
WANTLIB += flang flangrti pgmath
*** Error 1 in target 'port-lib-depends-check' (ignored)
R uses flang on arm64 (changed in math/R by bcallah@ on 2019-05-08):
MODULES = fortran
.if ${MACHINE_ARCH:Maarch64}
MODFORTRAN_COMPILER = flang
.else
MODFORTRAN_COMPILER = gfortran
.endif
Fortunately, infrastructure/mk/fortran.port.mk sets MODFORTRAN_WANTLIB
according to the value of MODFORTRAN_COMPILER (either gfortran or flang).
So I just added MODFORTRAN_WANTLIB to WANTLIB. amd64 is still happy with this
and I think it addresses your observation on arm64 (I don't have an arm64
system to test).
@martin or @bcallah: could you please confirm this?
Best regards,
Ingo
Index: Makefile
===================================================================
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.112
diff -u -p -r1.112 Makefile
--- Makefile 5 Jul 2019 19:27:30 -0000 1.112
+++ Makefile 17 Dec 2019 15:48:33 -0000
@@ -1,9 +1,9 @@
# $OpenBSD: Makefile,v 1.112 2019/07/05 19:27:30 feinerer Exp $
COMMENT= powerful math/statistics/graphics language
-DISTNAME= R-3.6.1
+DISTNAME= R-3.6.2
-SO_VERSION= 35.1
+SO_VERSION= 36.0
.for _lib in R Rblas Rlapack
SHARED_LIBS += ${_lib} ${SO_VERSION}
.endfor
@@ -16,7 +16,7 @@ MAINTAINER= Ingo Feinerer <feinerer@logi
# GPLv2+
PERMIT_PACKAGE= Yes
-WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB}
+WANTLIB += ${COMPILER_LIBCXX} ${MODTK_WANTLIB} ${MODFORTRAN_WANTLIB}
WANTLIB += ICE SM X11 Xext Xmu Xss Xt bz2 c cairo crypto curl
WANTLIB += glib-2.0 gobject-2.0 iconv icui18n icuuc intl jpeg lzma m
WANTLIB += nghttp2 pango-1.0 pangocairo-1.0 pcre pcre2-8 png readline ssl
tiff z
Index: distinfo
===================================================================
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.44
diff -u -p -r1.44 distinfo
--- distinfo 5 Jul 2019 19:27:30 -0000 1.44
+++ distinfo 17 Dec 2019 15:48:33 -0000
@@ -1,2 +1,2 @@
-SHA256 (R-3.6.1.tar.gz) = W6qevT5xrOzcw9ox2QQvsXTVWkKCn4MV8kVwgJeLE4k=
-SIZE (R-3.6.1.tar.gz) = 30463021
+SHA256 (R-3.6.2.tar.gz) = vWWkXN37iPNzcPvO5KyN0/GuvuvkfC+Wj9l3C6K7yVQ=
+SIZE (R-3.6.2.tar.gz) = 33311930
Index: patches/patch-configure
===================================================================
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.39
diff -u -p -r1.39 patch-configure
--- patches/patch-configure 5 Jul 2019 19:27:30 -0000 1.39
+++ patches/patch-configure 17 Dec 2019 15:48:33 -0000
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.39 2019/07
Index: configure
--- configure.orig
+++ configure
-@@ -41831,8 +41831,8 @@ fi
+@@ -42057,8 +42057,8 @@ fi
fi
if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
if ${r_cv_header_zlib_h+:} false; then :
$as_echo_n "(cached) " >&6
else
-@@ -41847,7 +41847,7 @@ else
+@@ -42073,7 +42073,7 @@ else
#include <zlib.h>
int main() {
#ifdef ZLIB_VERNUM
Index: pkg/PLIST
===================================================================
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.42
diff -u -p -r1.42 PLIST
--- pkg/PLIST 29 Apr 2019 08:52:48 -0000 1.42
+++ pkg/PLIST 17 Dec 2019 15:48:33 -0000
@@ -114,7 +114,7 @@ lib/R/library/KernSmooth/html/
lib/R/library/KernSmooth/html/00Index.html
lib/R/library/KernSmooth/html/R.css
lib/R/library/KernSmooth/libs/
-lib/R/library/KernSmooth/libs/KernSmooth.so
+@so lib/R/library/KernSmooth/libs/KernSmooth.so
lib/R/library/KernSmooth/po/
lib/R/library/KernSmooth/po/de/
lib/R/library/KernSmooth/po/de/LC_MESSAGES/
@@ -163,7 +163,7 @@ lib/R/library/MASS/html/
lib/R/library/MASS/html/00Index.html
lib/R/library/MASS/html/R.css
lib/R/library/MASS/libs/
-lib/R/library/MASS/libs/MASS.so
+@so lib/R/library/MASS/libs/MASS.so
lib/R/library/MASS/po/
lib/R/library/MASS/po/de/
lib/R/library/MASS/po/de/LC_MESSAGES/
@@ -273,7 +273,7 @@ lib/R/library/Matrix/include/Matrix.h
lib/R/library/Matrix/include/Matrix_stubs.c
lib/R/library/Matrix/include/cholmod.h
lib/R/library/Matrix/libs/
-lib/R/library/Matrix/libs/Matrix.so
+@so lib/R/library/Matrix/libs/Matrix.so
lib/R/library/Matrix/po/
lib/R/library/Matrix/po/de/
lib/R/library/Matrix/po/de/LC_MESSAGES/
@@ -404,7 +404,7 @@ lib/R/library/class/html/
lib/R/library/class/html/00Index.html
lib/R/library/class/html/R.css
lib/R/library/class/libs/
-lib/R/library/class/libs/class.so
+@so lib/R/library/class/libs/class.so
lib/R/library/class/po/
lib/R/library/class/po/de/
lib/R/library/class/po/de/LC_MESSAGES/
@@ -453,7 +453,7 @@ lib/R/library/cluster/html/
lib/R/library/cluster/html/00Index.html
lib/R/library/cluster/html/R.css
lib/R/library/cluster/libs/
-lib/R/library/cluster/libs/cluster.so
+@so lib/R/library/cluster/libs/cluster.so
lib/R/library/cluster/po/
lib/R/library/cluster/po/de/
lib/R/library/cluster/po/de/LC_MESSAGES/
@@ -580,7 +580,7 @@ lib/R/library/foreign/html/
lib/R/library/foreign/html/00Index.html
lib/R/library/foreign/html/R.css
lib/R/library/foreign/libs/
-lib/R/library/foreign/libs/foreign.so
+@so lib/R/library/foreign/libs/foreign.so
lib/R/library/foreign/po/
lib/R/library/foreign/po/de/
lib/R/library/foreign/po/de/LC_MESSAGES/
@@ -743,8 +743,8 @@ lib/R/library/grDevices/icc/
lib/R/library/grDevices/icc/srgb
lib/R/library/grDevices/icc/srgb.flate
lib/R/library/grDevices/libs/
-lib/R/library/grDevices/libs/cairo.so
-lib/R/library/grDevices/libs/grDevices.so
+@so lib/R/library/grDevices/libs/cairo.so
+@so lib/R/library/grDevices/libs/grDevices.so
lib/R/library/graphics/
lib/R/library/graphics/DESCRIPTION
lib/R/library/graphics/INDEX
@@ -786,7 +786,7 @@ lib/R/library/graphics/html/
lib/R/library/graphics/html/00Index.html
lib/R/library/graphics/html/R.css
lib/R/library/graphics/libs/
-lib/R/library/graphics/libs/graphics.so
+@so lib/R/library/graphics/libs/graphics.so
lib/R/library/grid/
lib/R/library/grid/DESCRIPTION
lib/R/library/grid/INDEX
@@ -856,7 +856,7 @@ lib/R/library/grid/html/
lib/R/library/grid/html/00Index.html
lib/R/library/grid/html/R.css
lib/R/library/grid/libs/
-lib/R/library/grid/libs/grid.so
+@so lib/R/library/grid/libs/grid.so
lib/R/library/lattice/
lib/R/library/lattice/CITATION
lib/R/library/lattice/DESCRIPTION
@@ -895,7 +895,7 @@ lib/R/library/lattice/html/
lib/R/library/lattice/html/00Index.html
lib/R/library/lattice/html/R.css
lib/R/library/lattice/libs/
-lib/R/library/lattice/libs/lattice.so
+@so lib/R/library/lattice/libs/lattice.so
lib/R/library/lattice/po/
lib/R/library/lattice/po/de/
lib/R/library/lattice/po/de/LC_MESSAGES/
@@ -937,7 +937,7 @@ lib/R/library/methods/html/
lib/R/library/methods/html/00Index.html
lib/R/library/methods/html/R.css
lib/R/library/methods/libs/
-lib/R/library/methods/libs/methods.so
+@so lib/R/library/methods/libs/methods.so
lib/R/library/mgcv/
lib/R/library/mgcv/CITATION
lib/R/library/mgcv/DESCRIPTION
@@ -968,7 +968,7 @@ lib/R/library/mgcv/html/
lib/R/library/mgcv/html/00Index.html
lib/R/library/mgcv/html/R.css
lib/R/library/mgcv/libs/
-lib/R/library/mgcv/libs/mgcv.so
+@so lib/R/library/mgcv/libs/mgcv.so
lib/R/library/mgcv/po/
lib/R/library/mgcv/po/de/
lib/R/library/mgcv/po/de/LC_MESSAGES/
@@ -1022,7 +1022,7 @@ lib/R/library/nlme/html/
lib/R/library/nlme/html/00Index.html
lib/R/library/nlme/html/R.css
lib/R/library/nlme/libs/
-lib/R/library/nlme/libs/nlme.so
+@so lib/R/library/nlme/libs/nlme.so
lib/R/library/nlme/mlbook/
lib/R/library/nlme/mlbook/README
lib/R/library/nlme/mlbook/ch04.R
@@ -1085,7 +1085,7 @@ lib/R/library/nnet/html/
lib/R/library/nnet/html/00Index.html
lib/R/library/nnet/html/R.css
lib/R/library/nnet/libs/
-lib/R/library/nnet/libs/nnet.so
+@so lib/R/library/nnet/libs/nnet.so
lib/R/library/nnet/po/
lib/R/library/nnet/po/de/
lib/R/library/nnet/po/de/LC_MESSAGES/
@@ -1133,7 +1133,7 @@ lib/R/library/parallel/html/
lib/R/library/parallel/html/00Index.html
lib/R/library/parallel/html/R.css
lib/R/library/parallel/libs/
-lib/R/library/parallel/libs/parallel.so
+@so lib/R/library/parallel/libs/parallel.so
lib/R/library/rpart/
lib/R/library/rpart/DESCRIPTION
lib/R/library/rpart/INDEX
@@ -1176,7 +1176,7 @@ lib/R/library/rpart/html/
lib/R/library/rpart/html/00Index.html
lib/R/library/rpart/html/R.css
lib/R/library/rpart/libs/
-lib/R/library/rpart/libs/rpart.so
+@so lib/R/library/rpart/libs/rpart.so
lib/R/library/rpart/po/
lib/R/library/rpart/po/de/
lib/R/library/rpart/po/de/LC_MESSAGES/
@@ -1230,7 +1230,7 @@ lib/R/library/spatial/html/
lib/R/library/spatial/html/00Index.html
lib/R/library/spatial/html/R.css
lib/R/library/spatial/libs/
-lib/R/library/spatial/libs/spatial.so
+@so lib/R/library/spatial/libs/spatial.so
lib/R/library/spatial/po/
lib/R/library/spatial/po/de/
lib/R/library/spatial/po/de/LC_MESSAGES/
@@ -1297,7 +1297,7 @@ lib/R/library/splines/html/
lib/R/library/splines/html/00Index.html
lib/R/library/splines/html/R.css
lib/R/library/splines/libs/
-lib/R/library/splines/libs/splines.so
+@so lib/R/library/splines/libs/splines.so
lib/R/library/stats/
lib/R/library/stats/COPYRIGHTS.modreg
lib/R/library/stats/DESCRIPTION
@@ -1331,7 +1331,7 @@ lib/R/library/stats/html/
lib/R/library/stats/html/00Index.html
lib/R/library/stats/html/R.css
lib/R/library/stats/libs/
-lib/R/library/stats/libs/stats.so
+@so lib/R/library/stats/libs/stats.so
lib/R/library/stats4/
lib/R/library/stats4/DESCRIPTION
lib/R/library/stats4/INDEX
@@ -1384,6 +1384,9 @@ lib/R/library/survival/doc/
lib/R/library/survival/doc/adjcurve.R
lib/R/library/survival/doc/adjcurve.Rnw
lib/R/library/survival/doc/adjcurve.pdf
+lib/R/library/survival/doc/approximate.R
+lib/R/library/survival/doc/approximate.Rnw
+lib/R/library/survival/doc/approximate.pdf
lib/R/library/survival/doc/compete.R
lib/R/library/survival/doc/compete.Rnw
lib/R/library/survival/doc/compete.pdf
@@ -1391,9 +1394,10 @@ lib/R/library/survival/doc/concordance.R
lib/R/library/survival/doc/concordance.Rnw
lib/R/library/survival/doc/concordance.pdf
lib/R/library/survival/doc/index.html
-lib/R/library/survival/doc/multi.R
lib/R/library/survival/doc/multi.Rnw
lib/R/library/survival/doc/multi.pdf
+lib/R/library/survival/doc/other.Rnw
+lib/R/library/survival/doc/other.pdf
lib/R/library/survival/doc/population.R
lib/R/library/survival/doc/population.Rnw
lib/R/library/survival/doc/population.pdf
@@ -1403,9 +1407,6 @@ lib/R/library/survival/doc/splines.pdf
lib/R/library/survival/doc/survival.R
lib/R/library/survival/doc/survival.Rnw
lib/R/library/survival/doc/survival.pdf
-lib/R/library/survival/doc/tests.R
-lib/R/library/survival/doc/tests.Rnw
-lib/R/library/survival/doc/tests.pdf
lib/R/library/survival/doc/tiedtimes.R
lib/R/library/survival/doc/tiedtimes.Rnw
lib/R/library/survival/doc/tiedtimes.pdf
@@ -1427,7 +1428,7 @@ lib/R/library/survival/html/
lib/R/library/survival/html/00Index.html
lib/R/library/survival/html/R.css
lib/R/library/survival/libs/
-lib/R/library/survival/libs/survival.so
+@so lib/R/library/survival/libs/survival.so
lib/R/library/tcltk/
lib/R/library/tcltk/DESCRIPTION
lib/R/library/tcltk/INDEX
@@ -1472,7 +1473,7 @@ lib/R/library/tcltk/html/
lib/R/library/tcltk/html/00Index.html
lib/R/library/tcltk/html/R.css
lib/R/library/tcltk/libs/
-lib/R/library/tcltk/libs/tcltk.so
+@so lib/R/library/tcltk/libs/tcltk.so
lib/R/library/tools/
lib/R/library/tools/DESCRIPTION
lib/R/library/tools/INDEX
@@ -1500,7 +1501,7 @@ lib/R/library/tools/html/
lib/R/library/tools/html/00Index.html
lib/R/library/tools/html/R.css
lib/R/library/tools/libs/
-lib/R/library/tools/libs/tools.so
+@so lib/R/library/tools/libs/tools.so
lib/R/library/translations/
lib/R/library/translations/DESCRIPTION
lib/R/library/translations/da/
@@ -1855,15 +1856,15 @@ lib/R/library/utils/html/00Index.html
lib/R/library/utils/html/R.css
lib/R/library/utils/iconvlist
lib/R/library/utils/libs/
-lib/R/library/utils/libs/utils.so
+@so lib/R/library/utils/libs/utils.so
lib/R/library/utils/misc/
lib/R/library/utils/misc/exDIF.csv
lib/R/library/utils/misc/exDIF.dif
lib/R/modules/
-lib/R/modules/R_X11.so
-lib/R/modules/R_de.so
-lib/R/modules/internet.so
-lib/R/modules/lapack.so
+@so lib/R/modules/R_X11.so
+@so lib/R/modules/R_de.so
+@so lib/R/modules/internet.so
+@so lib/R/modules/lapack.so
lib/R/share/
lib/R/share/R/
lib/R/share/R/REMOVE.R
