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
