diff --git a/programming/language/R-lang/actions.py b/programming/language/R-lang/actions.py index 605d453244..1e7371f76b 100644 --- a/programming/language/R-lang/actions.py +++ b/programming/language/R-lang/actions.py @@ -17,6 +17,9 @@ def setup(): autotools.aclocal("-I m4") autotools.autoconf() autotools.configure("--prefix=/usr \ + --libdir=/usr/lib \ + --sysconfdir=/etc/R \ + --datarootdir=/usr/share \ --with-recommended-packages \ --enable-R-profiling \ --enable-R-shlib \ @@ -27,12 +30,9 @@ def setup(): --with-lapack \ --without-tcltk \ --with-readline \ - --with-system-pcre \ - --with-system-zlib \ - --with-system-bzlib \ - --with-system-xz \ + rsharedir=/usr/share/R/ \ rdocdir=/usr/share/doc/R \ - rincludedir=/usr/include \ + rincludedir=/usr/include/R \ --with-x") def build(): @@ -41,7 +41,7 @@ def build(): # build math library shelltools.cd("src/nmath/standalone") - autotools.make("-j1") + autotools.make("shared") #def check(): #shelltools.export("R_HOME","") @@ -51,11 +51,11 @@ def install(): autotools.rawInstall("DESTDIR=%s" % get.installDIR()) # install math library remove static libs - autotools.install("-C src/nmath/standalone") + autotools.rawInstall("-C src/nmath/standalone DESTDIR=%s" % get.installDIR()) + pisitools.rename("/usr/lib/libRmath.so","libRmath.so.0.0.0") pisitools.dosym("/usr/lib/libRmath.so.0.0.0","/usr/lib/libRmath.so.0") pisitools.dosym("/usr/lib/libRmath.so.0.0.0","/usr/lib/libRmath.so") - pisitools.remove("/usr/lib/libRmath.a") diff --git a/programming/language/R-lang/files/R-2.13.1-zlib_header_fix.patch b/programming/language/R-lang/files/R-2.13.1-zlib_header_fix.patch deleted file mode 100644 index 0e1482e65b..0000000000 --- a/programming/language/R-lang/files/R-2.13.1-zlib_header_fix.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- src/main/unzip.h.orig 2011-09-24 19:35:53.000000000 -0700 -+++ src/main/unzip.h 2011-09-24 19:37:06.000000000 -0700 -@@ -58,6 +58,10 @@ - #define ZLIB_FILEFUNC_SEEK_END (2) - #define ZLIB_FILEFUNC_SEEK_SET (0) - -+#ifndef OF -+#define OF(x) x -+#endif -+ - #define ZLIB_FILEFUNC_MODE_READ (1) - #define ZLIB_FILEFUNC_MODE_WRITE (2) - #define ZLIB_FILEFUNC_MODE_READWRITEFILTER (3) diff --git a/programming/language/R-lang/files/R-2.11.1-parallel.patch b/programming/language/R-lang/files/R-3.4.1-parallel.patch similarity index 71% rename from programming/language/R-lang/files/R-2.11.1-parallel.patch rename to programming/language/R-lang/files/R-3.4.1-parallel.patch index d1e19ef671..6fac15b9ff 100644 --- a/programming/language/R-lang/files/R-2.11.1-parallel.patch +++ b/programming/language/R-lang/files/R-3.4.1-parallel.patch @@ -1,11 +1,11 @@ ---- src/include/Makefile.in.orig 2010-06-15 18:18:54.000000000 +0000 -+++ src/include/Makefile.in 2010-06-15 18:19:48.000000000 +0000 +--- a/src/include/Makefile.in 2017-07-05 23:09:09.682703655 +0000 ++++ b/src/include/Makefile.in 2017-07-05 23:06:56.533612308 +0000 @@ -81,7 +81,7 @@ Rmath.h0: $(srcdir)/Rmath.h0.in $(top_builddir)/config.status @cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ - + -install: installdirs install-intl-@USE_INCLUDED_LIBINTL@ +install: $(OBJ_HEADERS) installdirs install-intl-@USE_INCLUDED_LIBINTL@ @for d in $(SUBDIRS); do \ (cd $${d} && $(MAKE) $@) || exit 1; \ - done \ No newline at end of file + done diff --git a/programming/language/R-lang/files/R-3.4.1-rmath-shared.patch b/programming/language/R-lang/files/R-3.4.1-rmath-shared.patch new file mode 100644 index 0000000000..8bc6233de6 --- /dev/null +++ b/programming/language/R-lang/files/R-3.4.1-rmath-shared.patch @@ -0,0 +1,21 @@ +--- a/src/nmath/standalone/Makefile.in 2017-07-05 23:20:26.098087600 +0000 ++++ b/src/nmath/standalone/Makefile.in 2017-07-05 23:21:55.087480310 +0000 +@@ -64,7 +64,8 @@ + Rexeclibdir_LTLIBRARIES = $(libRmath_la) + libRmath_la_SOURCES = $(SOURCES) + libRmath_la_OBJECTS = $(OBJECTS:.o=.lo) +-libRmath_la_LDFLAGS = ++libRmath_la_LDFLAGS = -Wl,-soname=libRmath.so ++libRmath_la_LIBADD = $(LIBM) + + CLEANFILES = Makedeps *.d *.o *.lo test check.log $(SOURCES) + DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES) +@@ -127,7 +128,7 @@ + + ## under peculiar circumstances, $(LIBM) here helps. + $(libRmath_la): $(libRmath_la_OBJECTS) +- $(DYLIB_LINK) -o $@ $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(LIBM) ++ $(DYLIB_LINK) $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(libRmath_la_LIBADD) -o $@ + + test: $(srcdir)/test.c + $(CC) -o $@ $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(srcdir)/test.c \ diff --git a/programming/language/R-lang/files/Rscript.patch b/programming/language/R-lang/files/Rscript.patch deleted file mode 100644 index 8792da4162..0000000000 --- a/programming/language/R-lang/files/Rscript.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Nuar R-2.7.1.orig/src/unix/Makefile.in R-2.7.1/src/unix/Makefile.in ---- R-2.7.1.orig/src/unix/Makefile.in 2008-06-23 12:38:27.000000000 +0300 -+++ R-2.7.1/src/unix/Makefile.in 2008-06-24 16:40:23.000000000 +0300 -@@ -66,7 +66,7 @@ - - ## we need to build at install time to capture the correct 'rhome' - install-Rscript: -- $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -DR_HOME='"$(rhome)"' -o Rscript \ -+ $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -DR_HOME='"/usr/lib/R/"' -o Rscript \ - $(srcdir)/Rscript.c - @$(MKINSTALLDIRS) "$(DESTDIR)$(Rexecbindir)" - @$(INSTALL_PROGRAM) Rscript "$(DESTDIR)$(Rexecbindir)/Rscript" diff --git a/programming/language/R-lang/files/dont_use_atlas.patch b/programming/language/R-lang/files/dont_use_atlas.patch deleted file mode 100644 index ed9afd2ed2..0000000000 --- a/programming/language/R-lang/files/dont_use_atlas.patch +++ /dev/null @@ -1,42 +0,0 @@ -diff -Nuar R-2.11.0.orig/configure.ac R-2.11.0/configure.ac ---- R-2.11.0.orig/configure.ac 2010-04-01 01:10:02.000000000 +0300 -+++ R-2.11.0/configure.ac 2010-05-02 18:42:50.276871339 +0300 -@@ -2508,7 +2508,6 @@ - if test "${acx_blas_ok}" = "yes"; then - ## Try to figure out which BLAS was used. - case "${BLAS_LIBS0}" in -- *-latlas*) r_blas=ATLAS ;; - *-lsgemm*) r_blas=PhiPack ;; - *sunperf*) r_blas=SunPerf ;; - *-lessl*) r_blas=ESSL ;; -diff -Nuar R-2.11.0.orig/m4/R.m4 R-2.11.0/m4/R.m4 ---- R-2.11.0.orig/m4/R.m4 2010-03-28 01:10:03.000000000 +0200 -+++ R-2.11.0/m4/R.m4 2010-05-02 18:44:38.987876278 +0300 -@@ -2536,19 +2536,6 @@ - fi - fi - --## BLAS linked to by default? (happens on some supercomputers) --if test "${acx_blas_ok}" = no; then -- AC_CHECK_FUNC(${dgemm}, [acx_blas_ok=yes]) --fi -- --## BLAS in ATLAS library? (http://math-atlas.sourceforge.net/) --if test "${acx_blas_ok}" = no; then -- AC_CHECK_LIB(atlas, ATL_xerbla, -- [AC_CHECK_LIB(f77blas, ${dgemm}, -- [acx_blas_ok=yes -- BLAS_LIBS="-lf77blas -latlas"], -- [], [-latlas])]) --fi - - ## BLAS in PhiPACK libraries? (requires generic BLAS lib, too) - if test "${acx_blas_ok}" = no; then -@@ -2744,7 +2731,6 @@ - F77_SYMBOL(drotmg)(); - F77_SYMBOL(dsbmv)(); - F77_SYMBOL(dscal)(); -- F77_SYMBOL(dsdot)(); - F77_SYMBOL(dspmv)(); - F77_SYMBOL(dspr)(); - F77_SYMBOL(dspr2)(); diff --git a/programming/language/R-lang/files/lib64.patch b/programming/language/R-lang/files/lib64.patch deleted file mode 100644 index 0eec18e033..0000000000 --- a/programming/language/R-lang/files/lib64.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff -Nuar R-3.0.1.orig/configure.ac R-3.0.1/configure.ac ---- R-3.0.1.orig/configure.ac 2013-03-25 01:05:05.000000000 +0200 -+++ R-3.0.1/configure.ac 2013-05-18 23:41:55.803629789 +0300 -@@ -137,7 +137,7 @@ - linux*) - ## Not all distros use this: some choose to march out of step - case "${host_cpu}" in -- x86_64|mips64|ppc64|powerpc64|sparc64|s390x) -+ mips64|ppc64|powerpc64|sparc64|s390x) - if test -d /usr/lib64; then - libnn=lib64 - fi -diff -Nuar R-3.0.1.orig/src/scripts/R.sh.in R-3.0.1/src/scripts/R.sh.in ---- R-3.0.1.orig/src/scripts/R.sh.in 2013-03-06 01:02:41.000000000 +0200 -+++ R-3.0.1/src/scripts/R.sh.in 2013-05-18 23:42:28.075630689 +0300 -@@ -7,13 +7,13 @@ - linux*) - run_arch=`uname -m` - case "$run_arch" in -- x86_64|mips64|ppc64|powerpc64|sparc64|s390x) -+ mips64|ppc64|powerpc64|sparc64|s390x) - libnn=lib64 - libnn_fallback=lib - ;; - *) - libnn=lib -- libnn_fallback=lib64 -+ libnn_fallback=lib - ;; - esac - if [ -x "@prefix@/${libnn}/R/bin/exec/R" ]; then diff --git a/programming/language/R-lang/pspec.xml b/programming/language/R-lang/pspec.xml index c9e865da60..83aa014f3e 100644 --- a/programming/language/R-lang/pspec.xml +++ b/programming/language/R-lang/pspec.xml @@ -13,7 +13,7 @@ app:console A free software environment for statistical computing and graphics This package includes the core R userspace and all R development components. - http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz + http://cran.r-project.org/src/base/R-3/R-3.5.2.tar.gz libXmu-devel icu4c-devel @@ -31,14 +31,11 @@ xz-devel readline-devel curl-devel + minizip-devel - - - R-2.11.1-parallel.patch - R-2.13.1-zlib_header_fix.patch - + R-3.4.1-parallel.patch + R-3.4.1-rmath-shared.patch @@ -74,6 +71,7 @@ /usr/bin /usr/lib/R /usr/share/man + /usr/share/R 99R @@ -94,6 +92,7 @@ /usr/lib /usr/include/Rmath.h + /usr/include/R/Rmath.h /usr/lib/pkgconfig/libRmath.pc @@ -120,6 +119,13 @@ + + 2018-12-23 + 3.5.2 + Version bump. + Ertuğrul Erata + ertugrulerata@gmail.com + 2018-09-09 3.5.1