R devel - Oct 2007 - R trunk (2.7) build fails with -fpic, needs -fPIC (PR#10372)

On Linux x86-64 (Ubuntu 6.06), the latest R sources from the
Subversion trunk fail to build with the following "recompile with
-fPIC" error:

  $ ./configure --with-x=yes --prefix=$inst_dir --enable-R-shlib
--with-tcltk=/usr/lib/tcl8.4 --with-tcl-config=/usr/lib/tcl8.4/tclConfig.sh
  $ make

  /usr/bin/ld: ../appl/approx.o: relocation R_X86_64_32 against `a local
symbol' can not be used when making a shared object; recompile with -fPIC
  ../appl/approx.o: could not read symbols: Bad value

This is easy to fix by changing 4 lines in the configure script from
"-fpic" to -fPIC", as shown in the patch below.

I saw this failure on an Intel x86-64 server, running Ubuntu 6.06:

  $ uname -srvm
  Linux 2.6.20.4 #1 SMP PREEMPT Sat Mar 31 07:46:01 EDT 2007 x86_64

  $ cat /etc/lsb-release
  DISTRIB_ID=Ubuntu
  DISTRIB_RELEASE=6.06
  DISTRIB_CODENAME=dapper
  DISTRIB_DESCRIPTION="Ubuntu 6.06.1 LTS"

  $ grep name /proc/cpuinfo
  model name      :                   Intel(R) Xeon(TM) CPU 3.80GHz
  model name      :                   Intel(R) Xeon(TM) CPU 3.80GHz

  $ dpkg -l libc6
  ||/ Name     Version              Description
 
+++-========-====================-================================================
ii  libc6    2.3.6-0ubuntu20.4    GNU C Library: Shared libraries and Timezone
data

  $ apt-cache show libc6 | grep Architecture | uniq
  Architecture: amd64

Here's a patch which fixes the problem:


$ svn diff configure
Index: configure
==================================================================--- configure
(revision 43265)
+++ configure	(working copy)
@@ -32806,7 +32806,7 @@
       cpicflags="-fPIC"
       ;;
     *)
-      cpicflags="-fpic"
+      cpicflags="-fPIC"
       ;;
   esac
   shlib_ldflags="-shared"
@@ -32817,7 +32817,7 @@
       fpicflags="-fPIC"
       ;;
     *)
-      fpicflags="-fpic"
+      fpicflags="-fPIC"
       ;;
   esac
 fi
@@ -32827,7 +32827,7 @@
       cxxpicflags="-fPIC"
       ;;
     *)
-      cxxpicflags="-fpic"
+      cxxpicflags="-fPIC"
       ;;
   esac
   shlib_cxxldflags="-shared"
@@ -47768,7 +47768,7 @@
       fcpicflags="-fPIC"
       ;;
     *)
-      fcpicflags="-fpic"
+      fcpicflags="-fPIC"
       ;;
   esac
 fi

-- 
Andrew Piskorski <atp at piskorski.com>
http://www.piskorski.com/

atp at piskorski.com wrote:
> On Linux x86-64 (Ubuntu 6.06), the latest R sources from the
> Subversion trunk fail to build with the following "recompile with
> -fPIC" error:
>
>   $ ./configure --with-x=yes --prefix=$inst_dir --enable-R-shlib
--with-tcltk=/usr/lib/tcl8.4 --with-tcl-config=/usr/lib/tcl8.4/tclConfig.sh
>   $ make
>
>   /usr/bin/ld: ../appl/approx.o: relocation R_X86_64_32 against `a local
symbol' can not be used when making a shared object; recompile with -fPIC
>   ../appl/approx.o: could not read symbols: Bad value
>
> This is easy to fix by changing 4 lines in the configure script from
> "-fpic" to -fPIC", as shown in the patch below.
>
> I saw this failure on an Intel x86-64 server, running Ubuntu 6.06:
>
>   $ uname -srvm
>   Linux 2.6.20.4 #1 SMP PREEMPT Sat Mar 31 07:46:01 EDT 2007 x86_64
>
>   $ cat /etc/lsb-release
>   DISTRIB_ID=Ubuntu
>   DISTRIB_RELEASE=6.06
>   DISTRIB_CODENAME=dapper
>   DISTRIB_DESCRIPTION="Ubuntu 6.06.1 LTS"
>
>   $ grep name /proc/cpuinfo
>   model name      :                   Intel(R) Xeon(TM) CPU 3.80GHz
>   model name      :                   Intel(R) Xeon(TM) CPU 3.80GHz
>
>   $ dpkg -l libc6
>   ||/ Name     Version              Description
>  
+++-========-====================-================================================>
ii  libc6    2.3.6-0ubuntu20.4    GNU C Library: Shared libraries and Timezone
data
>
>   $ apt-cache show libc6 | grep Architecture | uniq
>   Architecture: amd64
>
> Here's a patch which fixes the problem:
>
>
> $ svn diff configure
> Index: configure
> ==================================================================> ---
configure	(revision 43265)
> +++ configure	(working copy)
> @@ -32806,7 +32806,7 @@
>        cpicflags="-fPIC"
>        ;;
>      *)
> -      cpicflags="-fpic"
> +      cpicflags="-fPIC"
>        ;;
>    esac
>    shlib_ldflags="-shared"
> @@ -32817,7 +32817,7 @@
>        fpicflags="-fPIC"
>        ;;
>      *)
> -      fpicflags="-fpic"
> +      fpicflags="-fPIC"
>        ;;
>    esac
>  fi
> @@ -32827,7 +32827,7 @@
>        cxxpicflags="-fPIC"
>        ;;
>      *)
> -      cxxpicflags="-fpic"
> +      cxxpicflags="-fPIC"
>        ;;
>    esac
>    shlib_cxxldflags="-shared"
> @@ -47768,7 +47768,7 @@
>        fcpicflags="-fPIC"
>        ;;
>      *)
> -      fcpicflags="-fpic"
> +      fcpicflags="-fPIC"
>        ;;
>    esac
>  fi
>
>   
Fedora 7 seems perfectly happy with -fpic, and that patch looks 
unhealthy (for one thing, you shouldn't mess with that script directly, 
but use autoconf and aclocal on oter source files, for another, you are 
prescribing that -fPIC is to be used for all architectures.

Whic compiler/linker is this?

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

On Thu, Oct 25, 2007 at 12:19:13AM +0200, Peter Dalgaard wrote:
> Fedora 7 seems perfectly happy with -fpic,
Well, Ubuntu 6.06 x86-64 sure seems to hate it, but all I know about
-fpic vs. -fPIC is what I read here:

 
http://gcc.gnu.org/onlinedocs/gcc-4.0.3/gcc/Code-Gen-Options.html#index-fpic-1556
 
http://gcc.gnu.org/onlinedocs/gcc-4.2.2/gcc/Code-Gen-Options.html#index-fpic-1667
> Whic compiler/linker is this?
$ gcc --version | grep gcc
gcc (GCC) 4.0.3 (Ubuntu 4.0.3-1ubuntu5)
$ ld --version | grep ld
GNU ld version 2.16.91 20060118 Debian GNU/Linux

$ COLUMNS=140 dpkg -l binutils gcc-4.0
+++-==========-=============================-=============================================ii
binutils   2.16.1cvs20060117-1ubuntu2.1  The GNU assembler, linker and binary
utilities
ii  gcc-4.0    4.0.3-1ubuntu5                The GNU C compiler

-- 
Andrew Piskorski <atp at piskorski.com>
http://www.piskorski.com/