UPDATE: math/R

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UPDATE: math/R

Ingo Feinerer-2
Dear useRs,

update math/R 3.6.1 -> 3.6.2

- SHARED_LIBS: increase major version number due to removals in dynamic
  export changes

  $ /usr/src/lib/check_sym libR.so.35.1 libR.so.36.0
  libR.so.35.1 --> libR.so.36.0
  Dynamic export changes:
  removed:
          dummy_ii
          dummy_ii_ptr

  PLT removed:
          intpr_

- Update line numbers in patch

- Several lines in PLIST are now marked with "@so" but these files are
  no longer in the installed package. Is this expected (i.e., ignored by
  the pkg_* machinery or just coincidence)?

  All tested packages seems to work without problems; I did not notice
  any errors due to the missing .so files.

Works for me on amd64.

OK?

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 12 Dec 2019 13:01:49 -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
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 12 Dec 2019 13:01:49 -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 12 Dec 2019 13:01:49 -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 12 Dec 2019 13:01:49 -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

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Re: UPDATE: math/R

Martin Reindl-3
On Thu, Dec 12, 2019 at 02:16:24PM +0100, Ingo Feinerer wrote:
> Dear useRs,
>
> 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)

-m

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Re: UPDATE: math/R

Ingo Feinerer-2
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

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Re: UPDATE: math/R

Brian Callahan-5
Hi Ingo --

On 2019-12-17 10:52, Ingo Feinerer wrote:

> 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?

I don't have access to my arm64 machine until Thursday; I can check then.

Alternatively, we can probably switch arm64 to using gfortran if that
makes life easier for people. The decision to use flang for arm64 dates
back to when the only fortran compiler on arm64 was flang. But I don't
think that's the case any more. I can cook up something if that's the
direction we choose to go.

Anyhow, I'll check on Thursday if no one else beats me to it and get
back to you.

~Brian

> 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

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Re: UPDATE: math/R

Martin Reindl-3
On Tue, Dec 17, 2019 at 11:07:43AM -0500, Brian Callahan wrote:

> Hi Ingo --
>
> On 2019-12-17 10:52, Ingo Feinerer wrote:
> > 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?
>
> I don't have access to my arm64 machine until Thursday; I can check then.
>
> Alternatively, we can probably switch arm64 to
> using gfortran if that makes life easier for
> people. The decision to use flang for arm64
> dates back to when the only fortran compiler on
> arm64 was flang. But I don't think that's the
> case any more. I can cook up something if that's
> the direction we choose to go.
>
> Anyhow, I'll check on Thursday if no one else
> beats me to it and get back to you.

With gfortran, R needs some extra -fPIC love I think. That's probably why you
switched it to flang.

From my point of view, it is better to set MODFORTRAN_WANTLIB for now and
stick to flang on arm64. I can confirm port-lib-depends-check is happy on
arm64 with the MODFORTRAN_WANTLIB addition.

-m

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Re: UPDATE: math/R

Brian Callahan-5


On 2019-12-18 02:47, Martin Reindl wrote:

> On Tue, Dec 17, 2019 at 11:07:43AM -0500, Brian Callahan wrote:
>> Hi Ingo --
>>
>> On 2019-12-17 10:52, Ingo Feinerer wrote:
>>> 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?
>> I don't have access to my arm64 machine until Thursday; I can check then.
>>
>> Alternatively, we can probably switch arm64 to
>> using gfortran if that makes life easier for
>> people. The decision to use flang for arm64
>> dates back to when the only fortran compiler on
>> arm64 was flang. But I don't think that's the
>> case any more. I can cook up something if that's
>> the direction we choose to go.
>>
>> Anyhow, I'll check on Thursday if no one else
>> beats me to it and get back to you.
> With gfortran, R needs some extra -fPIC love I think. That's probably why you
> switched it to flang.
>
>  From my point of view, it is better to set MODFORTRAN_WANTLIB for now and
> stick to flang on arm64. I can confirm port-lib-depends-check is happy on
> arm64 with the MODFORTRAN_WANTLIB addition.
>
> -m

Sounds good to me.

~Brian