Merge pull request #6143 from ertugerata/master

update R-3.5.2
2018-12-23 23:51:41 +03:00
parent 0d7d774a9a 493bea286f
commit 8c822bdcb6
8 changed files with 46 additions and 117 deletions
@@ -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")


@@ -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)
@@ -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
+ 	done
@@ -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 \
@@ -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)$(Rexecbindir)/Rscript"
@@ -1,42 +0,0 @@
-diff -Nuar R-2.11.0.orig/configure.ac R-2.11.0/configure.ac
--- R-2.11.0.orig/configure.ac	2010-04-01 01:10:02.000000000 +0300
-+++ R-2.11.0/configure.ac	2010-05-02 18:42:50.276871339 +0300
-@@ -2508,7 +2508,6 @@
- if test "${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)();
@@ -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
@@ -13,7 +13,7 @@
        <IsA>app:console</IsA>
        <Summary>A free software environment for statistical computing and graphics</Summary>
        <Description>This package includes the core R userspace and all R development components.</Description>
-        <Archive sha1sum="9314d3d372b05546a33791fbc8dd579c92ebd16b" type="targz">http://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz</Archive>
+        <Archive sha1sum="057ea91daed3e68a12b2a473ee1283cf26f360e2" type="targz">http://cran.r-project.org/src/base/R-3/R-3.5.2.tar.gz</Archive>
        <BuildDependencies>
            <Dependency>libXmu-devel</Dependency>
            <Dependency>icu4c-devel</Dependency>
@@ -31,14 +31,11 @@
            <Dependency>xz-devel</Dependency>
            <Dependency>readline-devel</Dependency>
            <Dependency>curl-devel</Dependency>
+            <Dependency>minizip-devel</Dependency>
        </BuildDependencies>
        <Patches>
-            <!--<Patch level="1">Rscript.patch</Patch>-->
-            <!--<Patch level="1">dont_use_atlas.patch</Patch>
-            <Patch level="1">config_site.patch</Patch-->
-            <Patch level="0">R-2.11.1-parallel.patch</Patch>
-            <Patch level="0">R-2.13.1-zlib_header_fix.patch</Patch>
-            <!--Patch level="1">lib64.patch</Patch-->
+            <Patch>R-3.4.1-parallel.patch</Patch>
+            <Patch>R-3.4.1-rmath-shared.patch</Patch>
        </Patches>
    </Source>

@@ -74,6 +71,7 @@
            <Path fileType="executable">/usr/bin</Path>
            <Path fileType="library">/usr/lib/R</Path>
            <Path fileType="man">/usr/share/man</Path>
+            <Path fileType="data">/usr/share/R</Path>
        </Files>
        <AdditionalFiles>
            <AdditionalFile target="/etc/env.d/99R" owner="root" permission="0644">99R</AdditionalFile>
@@ -94,6 +92,7 @@
        <Files>
            <Path fileType="library">/usr/lib</Path>
            <Path fileType="header">/usr/include/Rmath.h</Path>
+            <Path fileType="header">/usr/include/R/Rmath.h</Path>
            <Path fileType="library">/usr/lib/pkgconfig/libRmath.pc</Path>
        </Files>
    </Package>
@@ -120,6 +119,13 @@
    </Package>

    <History>
+        <Update release="7">
+            <Date>2018-12-23</Date>
+            <Version>3.5.2</Version>
+            <Comment>Version bump.</Comment>
+            <Name>Ertuğrul Erata</Name>
+            <Email>ertugrulerata@gmail.com</Email>
+        </Update>
        <Update release="6">
            <Date>2018-09-09</Date>
            <Version>3.5.1</Version>