Re: Fix to R package

2007-06-27 Thread David Fetter 
Ah, shoot!  I was hoping the patches would fix our 64-bit problem with R
not compiling.  :-(  I'm getting the following error when I try to
compile it:

/usr/local/bin/cc -std=gnu99 -I. -I../../../src/include
-I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -fpic
-fPIC -c Lapack.c -o Lapack.o
/usr/local/bin/cc -std=gnu99 -shared -L/usr/local/lib -o lapack.so
Lapack.o   -L../../../lib -lRlapack -L../../../lib -lRblas -lgfortran
-lm /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortranbegin.a 
/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a
/usr/local/bin/ld: skipping
incompatible /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/libgfortran.a 
when searching for -lgfortran
/usr/local/bin/ld: 
/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a(pow_i4_i4.o):
 relocation R_X86_64_32 against `a local symbol' can not be used when making a 
shared object; recompile with -fPIC
/usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../lib64/libgfortran.a:
 could not read symbols: Bad value
collect2: ld returned 1 exit status
make[4]: *** [lapack.so] Error 1
make[3]: *** [R] Error 2
make[2]: *** [R] Error 1
make[1]: *** [R] Error 1
make: *** [R] Error 1


On Wed, 2007-06-27 at 20:07 +0200, Ralf S. Engelschall wrote:
> On Wed, Jun 27, 2007, Dennis McRitchie wrote:
> 
> > I just uploaded a modified spec file for the R statistical package.
> >
> > The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR,
> > but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to
> > allow packages to be installed.
> 
> Now fixed in the latest "r" package of OpenPKG CURRENT -- together with
> another packaging bug. Thanks for your feedback and support.
> 
>Ralf S. Engelschall
>[EMAIL PROTECTED]
>www.engelschall.com
> 
> __
> OpenPKG http://openpkg.org
> Developer Communication List   openpkg-dev@openpkg.org
> 
-- 
David M. Fetter - Portland State University - UNIX Systems Administrator
"Reality is merely an illusion, albeit a very persistent one." ~Einstein


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Re: Fix to R package

2007-06-27 Thread Ralf S. Engelschall 
On Wed, Jun 27, 2007, Dennis McRitchie wrote:

> I just uploaded a modified spec file for the R statistical package.
>
> The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR,
> but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to
> allow packages to be installed.

Now fixed in the latest "r" package of OpenPKG CURRENT -- together with
another packaging bug. Thanks for your feedback and support.

   Ralf S. Engelschall
   [EMAIL PROTECTED]
   www.engelschall.com

__
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Developer Communication List   openpkg-dev@openpkg.org

Fix to R package

2007-06-27 Thread Dennis McRitchie 
I just uploaded a modified spec file for the R statistical package.

The fix is to patch *both* R scripts, and to patch not just R_HOME_DIR,
but also R_SHARE_DIR, R_INCLUDE_DIR, and R_DOC_DIR. This is necessary to
allow packages to be installed.

Dennis

Dennis McRitchie
Computational Science and Engineering Support (CSES)
Academic Services Department
Office of Information Technology
Princeton University
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[CONTRIB] ACCEPT: r.spec

2007-06-27 Thread OpenPKG Project Robot 
The following OpenPKG Contribution Area operation occurred.
uploaded RPM specfile "r.spec" accepted -- moved to contrib area.
No action is required on your part.

Information about r.spec follows:
| ##
| ##  r.spec -- OpenPKG RPM Package Specification
| ##  Copyright (c) 2000-2007 OpenPKG Foundation e.V. 
| ##  Copyright (c) 2000-2007 Ralf S. Engelschall 
| ##
| ##  Permission to use, copy, modify, and distribute this software for
| ##  any purpose with or without fee is hereby granted, provided that
| ##  the above copyright notice and this permission notice appear in all
| ##  copies.
| ##
| ##  THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
| ##  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
| ##  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
| ##  IN NO EVENT SHALL THE AUTHORS AND COPYRIGHT HOLDERS AND THEIR
| ##  CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
| ##  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
| ##  LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
| ##  USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
| ##  ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
| ##  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
| ##  OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
| ##  SUCH DAMAGE.
| ##
| 
| #   package information
| Name: r
| Summary:  The R Statistical Computing System
| URL:  http://www.r-project.org/
| Vendor:   The R Foundation
| Packager: OpenPKG Foundation e.V.
| Distribution: OpenPKG Community
| Class:EVAL
| Group:Algorithm
| License:  GPL
| Version:  2.5.0
| Release:  20070425
| 
| #   package options
| %option   with_x11  yes
| 
| #   list of sources
| Source0:  http://cran.r-project.org/src/base/R-2/R-%{version}.tar.gz
| 
| #   build information
| Prefix:   %{l_prefix}
| BuildRoot:%{l_buildroot}
| BuildPreReq:  OpenPKG, openpkg >= 20040130, gcc, gcc::with_fortran = yes, make
| PreReq:   OpenPKG, openpkg >= 20040130
| BuildPreReq:  readline, png, jpeg, zlib, bzip2, pcre
| PreReq:   readline, png, jpeg, zlib, bzip2, pcre
| %if "%{with_x11}" == "yes"
| BuildPreReq:  X11
| PreReq:   X11
| %endif
| AutoReq:  no
| AutoReqProv:  no
| 
| %description
|  R is a language and environment for statistical computing and
|  graphics. It is similar to the S language and environment which
|  was developed at Bell Laboratories (formerly AT&T, now Lucent
|  Technologies) by John Chambers and colleagues. R can be considered
|  as a different implementation of S. There are some important
|  differences, but much code written for S runs unaltered under R.
| 
|  R provides a wide variety of statistical (linear and nonlinear
|  modelling, classical statistical tests, time-series analysis,
|  classification, clustering, ...) and graphical techniques, and is
|  highly extensible. The S language is often the vehicle of choice
|  for research in statistical methodology, and R provides an Open
|  Source route to participation in that activity.
| 
| %track
| prog r = {
| version   = %{version}
| url   = http://cran.r-project.org/src/base/R-2/
| regex = R-(__VER__)\.tar\.gz
| }
| 
| %prep
| %setup -q -n R-%{version}
| 
| %build
| CC="%{l_cc}" \
| CFLAGS="%{l_cflags -O}" \
| CPPFLAGS="%{l_cppflags}" \
| LDFLAGS="%{l_ldflags}" \
| ./configure \
| --prefix=%{l_prefix} \
| --with-recommended-packages \
| --with-readline \
| --without-gnome \
| --disable-nls \
| --with-libpng \
| --with-jpeglib \
| --with-zlib \
| --with-bzlib \
| --with-pcre \
| %if "%{with_x11}" == "yes"
| --with-x \
| --x-includes=`%{l_rc} --query x11_incdir` \
| --x-libraries=`%{l_rc} --query x11_libdir`
| %else
| --without-x
| %endif
| %{l_make} %{l_mflags -O}
| 
| %install
| rm -rf $RPM_BUILD_ROOT
| %{l_make} %{l_mflags} install \
| prefix=$RPM_BUILD_ROOT%{l_prefix} \
| exec_prefix=$RPM_BUILD_ROOT%{l_prefix}
| %{l_shtool} subst \
| -e 's;^\(R_HOME_DIR\)=.*;\1=%{l_prefix}/lib/r;' \
| -e 's;^\(R_SHARE_DIR\)=.*;\1=%{l_prefix}/lib/r/share;' \
| -e 's;^\(R_INCLUDE_DIR\)=.*;\1=%{l_prefix}/lib/r/include;' \
| -e 's;^\(R_DOC_DIR\)=.*;\1=%{l_prefix}/lib/r/doc;' \
| $RPM_BUILD_ROOT%{l_prefix}/bin/R \
| $RPM_BUILD_ROOT%{l_prefix}/lib/R/bin/R
| mv  $RPM_BUILD_ROOT%{l_prefix}/lib/R \
| $RPM_BUILD_ROOT%{l_prefix}/lib/r
| %{l_rpmtool} files -v -ofiles -r$RPM_BUILD_ROOT %{l_files_std}
| 
| %files -f files
| 
| %clean
| rm -rf $RPM_BUILD_ROOT
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