UPDATE: math/R

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UPDATE: math/R

Ingo Feinerer-2
Dear useRs,

update math/R 3.5.3 -> 3.6.0

- SHARED_LIBS: increase major version number

  check_sym reports added and removed symbols.

- CONFIGURE_ENV: Do not set F77 anymore (as we set FC)

  3.6.0 release notes mention:

  "Macro F77 is always set to the value of FC, so the latter should
  be set to user-select the Fortran compiler for both fixed-form
  and free-form Fortran.  In particular, gfortran is now the first
  choice for F77, not f95."

  and

  "Make macros F77, FCPIFCPLAGS and SHLIB_OPENMP_FCFLAGS are
  deprecated in favour of FC, FPICFLAGS and SHLIB_OPENMP_FFLAGS
  respectively."

- CONFIGURE_ENV: MAKEINFO -> TEXI2ANY

  3.6.0 release notes mention:

  "The configure macro MAKEINFO has been updated to TEXI2ANY."

- patch-src_modules_internet_libcurl_c was merged upstream.

- PLIST change:

  3.6.0 release notes mention:

  "The f77_f2c script has been removed: it no longer sufficed to
  compile the .f files in R."

- The `tan(1+1000i)` test still fails (see
  https://marc.info/?l=openbsd-tech&m=150737856618497&w=2).

Works for me on amd64.

OK?

Best regards,
Ingo

Index: Makefile
===================================================================
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.107
diff -u -p -r1.107 Makefile
--- Makefile 17 Mar 2019 07:16:32 -0000 1.107
+++ Makefile 26 Apr 2019 15:05:02 -0000
@@ -1,9 +1,9 @@
 # $OpenBSD: Makefile,v 1.107 2019/03/17 07:16:32 feinerer Exp $
 
 COMMENT= powerful math/statistics/graphics language
-DISTNAME= R-3.5.3
+DISTNAME= R-3.6.0
 
-SO_VERSION= 34.2
+SO_VERSION= 35.0
 .for _lib in R Rblas Rlapack
 SHARED_LIBS += ${_lib} ${SO_VERSION}
 .endfor
@@ -79,14 +79,13 @@ CONFIGURE_ARGS= --disable-java \
  --with-tcl-config=${MODTCL_CONFIG} \
  --with-tk-config=${MODTK_CONFIG}
 
-CONFIGURE_ENV= F77="${MODFORTRAN_COMPILER}" \
- FC="${MODFORTRAN_COMPILER}" \
+CONFIGURE_ENV= FC="${MODFORTRAN_COMPILER}" \
  FFLAGS="${FFLAGS}" \
  CPPFLAGS="-I${LOCALBASE}/include" \
  LDFLAGS="-L${LOCALBASE}/lib -Wl,-R${LOCALBASE}/lib/R/lib" \
  LIBnn=lib \
- MAKEINFO="${LOCALBASE}/bin/gtexi2any" \
  R_DYLIB_VERSION=${SO_VERSION} \
+ TEXI2ANY="${LOCALBASE}/bin/gtexi2any" \
  TEXI2DVI="${LOCALBASE}/bin/gtexi2dvi" \
  rdocdir="${PREFIX}/share/doc/R"
 
Index: distinfo
===================================================================
RCS file: /cvs/ports/math/R/distinfo,v
retrieving revision 1.42
diff -u -p -r1.42 distinfo
--- distinfo 17 Mar 2019 07:16:32 -0000 1.42
+++ distinfo 26 Apr 2019 15:05:02 -0000
@@ -1,2 +1,2 @@
-SHA256 (R-3.5.3.tar.gz) = K/o3t71wnwA9a4oXLd+20D3dLWctYJZDlSMDn3qOZ4w=
-SIZE (R-3.5.3.tar.gz) = 30205979
+SHA256 (R-3.6.0.tar.gz) = NvysPkUmZhWOYkWcb8gQrcJHxxCe1xxbbDrV/Cv1dQk=
+SIZE (R-3.6.0.tar.gz) = 30449618
Index: patches/patch-configure
===================================================================
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.37
diff -u -p -r1.37 patch-configure
--- patches/patch-configure 17 Mar 2019 07:16:32 -0000 1.37
+++ patches/patch-configure 26 Apr 2019 15:05:02 -0000
@@ -3,7 +3,7 @@ $OpenBSD: patch-configure,v 1.37 2019/03
 Index: configure
 --- configure.orig
 +++ configure
-@@ -42293,8 +42293,8 @@ fi
+@@ -41796,8 +41796,8 @@ fi
 
  fi
  if test "${have_zlib}" = yes; then
@@ -14,7 +14,7 @@ Index: configure
  if ${r_cv_header_zlib_h+:} false; then :
    $as_echo_n "(cached) " >&6
  else
-@@ -42309,7 +42309,7 @@ else
+@@ -41812,7 +41812,7 @@ else
  #include <zlib.h>
  int main() {
  #ifdef ZLIB_VERNUM
Index: patches/patch-src_modules_internet_libcurl_c
===================================================================
RCS file: patches/patch-src_modules_internet_libcurl_c
diff -N patches/patch-src_modules_internet_libcurl_c
--- patches/patch-src_modules_internet_libcurl_c 21 Feb 2019 20:04:34 -0000 1.1
+++ /dev/null 1 Jan 1970 00:00:00 -0000
@@ -1,32 +0,0 @@
-$OpenBSD: patch-src_modules_internet_libcurl_c,v 1.1 2019/02/21 20:04:34 tb Exp $
-
-Avoid use-after-free.  Upstream SVN commit #76143.
-
-Index: src/modules/internet/libcurl.c
---- src/modules/internet/libcurl.c.orig
-+++ src/modules/internet/libcurl.c
-@@ -641,12 +641,12 @@ in_do_curlDownload(SEXP call, SEXP op, SEXP args, SEXP
-
-     n_err += curlMultiCheckerrs(mhnd);
-
-+    long status = 0L;
-     for (int i = 0; i < nurls; i++) {
- if (out[i]) {
-    fclose(out[i]);
-    double dl;
-    curl_easy_getinfo(hnd[i], CURLINFO_SIZE_DOWNLOAD, &dl);
--    long status;
-    curl_easy_getinfo(hnd[i], CURLINFO_RESPONSE_CODE, &status);
-    // should we do something about incomplete transfers?
-    if (status != 200 && dl == 0. && strchr(mode, 'w'))
-@@ -655,10 +655,6 @@ in_do_curlDownload(SEXP call, SEXP op, SEXP args, SEXP
- curl_multi_remove_handle(mhnd, hnd[i]);
- curl_easy_cleanup(hnd[i]);
-     }
--    // This can show an invalid read: can it be improved?
--    long status = 0L;
--    if(nurls == 1)
-- curl_easy_getinfo(hnd[0], CURLINFO_RESPONSE_CODE, &status);
-     curl_multi_cleanup(mhnd);
-     if (!cacheOK) curl_slist_free_all(slist1);
-
Index: pkg/PLIST
===================================================================
RCS file: /cvs/ports/math/R/pkg/PLIST,v
retrieving revision 1.41
diff -u -p -r1.41 PLIST
--- pkg/PLIST 23 Dec 2018 08:03:45 -0000 1.41
+++ pkg/PLIST 26 Apr 2019 15:05:04 -0000
@@ -25,7 +25,6 @@ lib/R/bin/check
 lib/R/bin/config
 lib/R/bin/exec/
 @bin lib/R/bin/exec/R
-lib/R/bin/f77_f2c
 lib/R/bin/javareconf
 lib/R/bin/libtool
 lib/R/bin/mkinstalldirs
@@ -1168,6 +1167,8 @@ lib/R/library/rpart/doc/usercode.pdf
 lib/R/library/rpart/help/
 lib/R/library/rpart/help/AnIndex
 lib/R/library/rpart/help/aliases.rds
+lib/R/library/rpart/help/figures/
+lib/R/library/rpart/help/figures/rpart.png
 lib/R/library/rpart/help/paths.rds
 lib/R/library/rpart/help/rpart.rdb
 lib/R/library/rpart/help/rpart.rdx
@@ -1399,6 +1400,9 @@ lib/R/library/survival/doc/population.pd
 lib/R/library/survival/doc/splines.R
 lib/R/library/survival/doc/splines.Rnw
 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
@@ -1414,6 +1418,8 @@ lib/R/library/survival/doc/validate.pdf
 lib/R/library/survival/help/
 lib/R/library/survival/help/AnIndex
 lib/R/library/survival/help/aliases.rds
+lib/R/library/survival/help/figures/
+lib/R/library/survival/help/figures/logo.png
 lib/R/library/survival/help/paths.rds
 lib/R/library/survival/help/survival.rdb
 lib/R/library/survival/help/survival.rdx

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Re: UPDATE: math/R

Klemens Nanni-2
OK kn