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This commit is contained in:
Ertuğrul Erata
2016-07-20 19:22:15 +03:00
parent 8e992833e8
commit 10be24d1b7
12 changed files with 377 additions and 0 deletions
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programming/language/R/actions.py
+61
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@@ -0,0 +1,61 @@
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Licensed under the GNU General Public License, version 3.
# See the file http://www.gnu.org/licenses/gpl.txt
from pisi.actionsapi import autotools
from pisi.actionsapi import pisitools
from pisi.actionsapi import shelltools
from pisi.actionsapi import get
def setup():
shelltools.export("R_HOME_DIR", "/usr/lib/R")
shelltools.export("BLAS_LIBS","/usr/lib")
shelltools.export("LAPACK_LIBS","-L/usr/lib -llapack -lblas")
autotools.aclocal("-I m4")
autotools.autoconf()
autotools.configure("--prefix=/usr \
--with-recommended-packages \
--enable-R-profiling \
--enable-R-shlib \
--enable-shared \
--enable-prebuilt-html \
--disable-openmp \
--with-blas=-lblas \
--with-lapack \
--without-tcltk \
--with-readline \
--with-system-pcre \
--with-system-zlib \
--with-system-bzlib \
--with-system-xz \
rdocdir=/usr/share/doc/R \
rincludedir=/usr/include \
--with-x")
def build():
shelltools.export("R_HOME","")
autotools.make()
# build math library
shelltools.cd("src/nmath/standalone")
autotools.make("-j1")
#def check():
#shelltools.export("R_HOME","")
#autotools.make("check")
def install():
autotools.rawInstall("DESTDIR=%s" % get.installDIR())
# install math library remove static libs
autotools.install("-C src/nmath/standalone")
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")
programming/language/R/comar/package.py
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#!/usr/bin/python
import os
def postInstall(fromVersion, fromRelease, toVersion, toRelease):
os.system("R CMD javareconf")
programming/language/R/files/99R
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R_HOME_DIR=/usr/lib/R
R_HOME=/usr/lib/R
programming/language/R/files/R-2.11.1-parallel.patch
+11
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--- 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
@@ -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
programming/language/R/files/R-2.13.1-zlib_header_fix.patch
+13
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@@ -0,0 +1,13 @@
--- 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)
programming/language/R/files/Rscript.patch
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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"
programming/language/R/files/config_site.patch
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diff -Nuar R-2.12.1.orig//config.site R-2.12.1/config.site
--- R-2.12.1.orig//config.site 2010-11-14 01:05:06.000000000 +0200
+++ R-2.12.1/config.site 2010-12-22 07:11:10.429000021 +0200
@@ -28,7 +28,7 @@
## The paper size for the local (PostScript) printer.
## It must either be left blank or set to one of 'a4' or 'letter'.
## If left blank the system will use 'a4'.
-## R_PAPERSIZE=a4
+ R_PAPERSIZE=a4
## Set the default behavior of R when ending a session
## Set this to one of '--save' or '--no-save' depending whether you
@@ -207,23 +207,26 @@
## If unset configure searches in turn for (currently)
## firefox mozilla galeon opera xdg-open kfmclient gnome-moz-remote open
## and uses the full path.
-## R_BROWSER=
+R_BROWSER=xdg-open
+
+## Default pdf viewer
+R_PDFVIEWER=xdg-open
## BLAS and LAPACK settings
## Use BLAS_LIBS for all '-L' and '-l' options needed for linking
## against an external BLAS implementation.
-## BLAS_LIBS=
+## BLAS_LIBS=/usr/lib
## Use LAPACK_LIBS for all '-L' and '-l' options needed for linking
## against an external LAPACK implementation.
## Note that (see R-admin) that our main intention is to allow a
## LAPACK-containing BLAS to be used, so this is rarely needed, and
## it is not used if the BLAS already contains LAPACK.
-## LAPACK_LIBS=
+## LAPACK_LIBS="-L/usr/lib -llapack -lblas"
## Make name.
## Set this if you want to use a make by another name.
## For example, if your GNU make is called 'gmake', use 'MAKE=gmake'.
-## MAKE=
+MAKE=gmake
## Tar name
## Set this to prefer a tar which has the capability to automagically
programming/language/R/files/dont_use_atlas.patch
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@@ -0,0 +1,42 @@
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)();
programming/language/R/files/ld.so.conf
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@@ -0,0 +1 @@
/usr/lib/R/lib
programming/language/R/files/lib64.patch
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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
programming/language/R/pspec.xml
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<?xml version="1.0" ?>
<!DOCTYPE PISI SYSTEM "http://www.pisilinux.org/projeler/pisi/pisi-spec.dtd">
<PISI>
<Source>
<Name>R</Name>
<Homepage>http://www.r-project.org</Homepage>
<Packager>
<Name>PisiLinux Community</Name>
<Email>admins@pisilinux.org</Email>
</Packager>
<License>GPLv2</License>
<License>LGPLv2.1</License>
<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="df853188d3e2b1c2d32393016401c432a5192c4d" type="targz">http://cran.r-project.org/src/base/R-3/R-3.3.1.tar.gz</Archive>
<BuildDependencies>
<Dependency>libXmu-devel</Dependency>
<Dependency>icu4c-devel</Dependency>
<Dependency>jdk7-openjdk</Dependency>
<Dependency>xdg-utils</Dependency>
<Dependency>blas-devel</Dependency>
<Dependency>lapack-devel</Dependency>
<Dependency>libXt-devel</Dependency>
<Dependency>libSM-devel</Dependency>
<Dependency>cairo-devel</Dependency>
<Dependency>pango-devel</Dependency>
<Dependency>libjpeg-turbo-devel</Dependency>
<Dependency>tiff-devel</Dependency>
<Dependency>libgfortran</Dependency>
<Dependency>xz-devel</Dependency>
<Dependency>readline-devel</Dependency>
<Dependency>curl-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-->
</Patches>
</Source>
<Package>
<Name>R</Name>
<RuntimeDependencies>
<Dependency>blas</Dependency>
<Dependency>make</Dependency>
<Dependency>tiff</Dependency>
<Dependency>libXt</Dependency>
<Dependency>icu4c</Dependency>
<Dependency>libSM</Dependency>
<Dependency>cairo</Dependency>
<Dependency>pango</Dependency>
<Dependency>libXmu</Dependency>
<Dependency>lapack</Dependency>
<Dependency>xdg-utils</Dependency>
<Dependency>libgfortran</Dependency>
<Dependency>jre7-openjdk</Dependency>
<Dependency>libjpeg-turbo</Dependency>
<Dependency>xz</Dependency>
<Dependency>curl</Dependency>
<Dependency>zlib</Dependency>
<Dependency>bzip2</Dependency>
<Dependency>glib2</Dependency>
<Dependency>libX11</Dependency>
<Dependency>libpng</Dependency>
<Dependency>libpcre</Dependency>
<Dependency>readline</Dependency>
</RuntimeDependencies>
<Files>
<Path fileType="config">/etc</Path>
<Path fileType="executable">/usr/bin</Path>
<Path fileType="library">/usr/lib/R</Path>
<Path fileType="man">/usr/share/man</Path>
</Files>
<AdditionalFiles>
<AdditionalFile target="/etc/env.d/99R" owner="root" permission="0644">99R</AdditionalFile>
<AdditionalFile target="/etc/ld.so.conf.d/99-R.conf" owner="root" permission="0644">ld.so.conf</AdditionalFile>
</AdditionalFiles>
<Provides>
<COMAR script="package.py">System.Package</COMAR>
</Provides>
</Package>
<Package>
<Name>R-mathlib</Name>
<IsA>library</IsA>
<Summary>Math library for R</Summary>
<RuntimeDependencies>
<Dependency version="current">R</Dependency>
</RuntimeDependencies>
<Files>
<Path fileType="library">/usr/lib</Path>
<Path fileType="header">/usr/include/Rmath.h</Path>
</Files>
</Package>
<Package>
<Name>R-docs</Name>
<IsA>data:doc</IsA>
<Summary>Documents for R</Summary>
<Files>
<Path fileType="doc">/usr/share/doc/R</Path>
</Files>
</Package>
<Package>
<Name>R-devel</Name>
<Summary>Development files for R</Summary>
<RuntimeDependencies>
<Dependency release="current">R</Dependency>
</RuntimeDependencies>
<Files>
<Path fileType="header">/usr/include</Path>
<Path fileType="library">/usr/lib/pkgconfig/libR.pc</Path>
<Path fileType="library">/usr/lib/pkgconfig/libRmath.pc</Path>
</Files>
</Package>
<History>
<Update release="1">
<Date>2016-06-27</Date>
<Version>3.3.1</Version>
<Comment>First release</Comment>
<Name>Ertuğrul Erata</Name>
<Email>ertugrulerata@gmail.com</Email>
</Update>
</History>
</PISI>
programming/language/R/translations.xml
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<?xml version="1.0" ?>
<PISI>
<Source>
<Name>R</Name>
<Summary xml:lang="tr">R özgür istatistik ve grafik ortamı</Summary>
<Description xml:lang="tr">R özgür istatistik ve grafik ortamı</Description>
</Source>
<Package>
<Name>R-devel</Name>
<Summary xml:lang="tr">R için geliştirme dosyaları</Summary>
</Package>
<Package>
<Name>R-docs</Name>
<Summary xml:lang="tr">R belgeleri</Summary>
</Package>
<Package>
<Name>R-mathlib</Name>
<Summary xml:lang="tr">R Mathlib kitaplığı</Summary>
</Package>
</PISI>