Problem compiling in extra/xdr

On Mon, 18 Jul 2011, Prof Brian Ripley wrote:

1) R-help is the wrong list: see the posting guide.  I've moved this to 
R-devel.

2) A glibc system should not be compiling in that directory.  glibc 2.14 is 
rather recent and NEWS does say

* The RPC implementation in libc is obsoleted.  Old programs keep working
 but new programs cannot be linked with the routines in libc anymore.
 Programs in need of RPC functionality must be linked against TI-RPC.
 The TI-RPC implementation is IPv6 enabled and there are other benefits.

 Visible changes of this change include (obviously) the inability to link
 programs using RPC functions without referencing the TI-RPC library and 
the
 removal of the RPC headers from the glibc headers.
 Implemented by Ulrich Drepper.

So the answer seems to be that your libc is too new.
OK, thanks. I should have remembered the info about RPC in the glibc-2.14 
news. Then there will presumably be a problem building current R on current 
Fedora?
What is 'current Fedora'?  glibc 2.14 postdates the current release, 
Fedora 15, which uses 2.13.   I do not know what Fedora 16 will use in 
several months ....

The main problem will be that the xdr included in R is only for 
platforms with 32-bit longs -- but that may be true for your i686 
Linux.  It needs _X86_ defined to compile for i686: I would have 
expected that to be true on your platform, but am testing a cleaned-up 
version.  If that works it will appear in R-patched within 24 hours.

On Mon, 18 Jul 2011, Allin Cottrell wrote:

I'm building R 2.13.1 on i686-pc-linux-gnu, using gcc 4.6.1
and with glibc 2.14.

I get this error:

In file included from xdr.c:61:0:
./rpc/types.h:63:14: error: conflicting types for 'malloc'
make[4]: *** [xdr.o] Error 1

I can make the build proceed some by commenting out the declaration 
"extern char *malloc();" in xdr/rpc/types.h,
but then I get a slew of other errors:

xdr_float.c: In function 'xdr_float':
xdr_float.c:119:21: error: storage size of 'is' isn't known
xdr_float.c:120:20: error: storage size of 'vs' isn't known

and so on.

config.log is rather big to post here; I'm putting it at
http://www.wfu.edu/~cottrell/tmp/R.config.log .

--
Allin Cottrell
Department of Economics
Wake Forest University, NC

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

-- 
Allin Cottrell
Department of Economics
Wake Forest University

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
1) The current R-patched should compile src/extra/xdr on 32-bit Linux 
systems.

2) Longer-term or on a 64-bit platform the solution is to make use of 
libtirpc: you would need both this installed (common now) and its 
headers (unlikely).

Then if you arrange for /usr/include/tirpc to be in the C include path 
(not easy to do portably, but using C_INCLUDE_PATH will work on 
Linux), the tirpc versions should be found.

On Mon, 18 Jul 2011, Allin Cottrell wrote:

On Mon, 18 Jul 2011, Prof Brian Ripley wrote:

1) R-help is the wrong list: see the posting guide.  I've moved this to 
R-devel.

2) A glibc system should not be compiling in that directory.  glibc 2.14 
is rather recent and NEWS does say

* The RPC implementation in libc is obsoleted.  Old programs keep working
 but new programs cannot be linked with the routines in libc anymore.
 Programs in need of RPC functionality must be linked against TI-RPC.
 The TI-RPC implementation is IPv6 enabled and there are other benefits.

 Visible changes of this change include (obviously) the inability to link
 programs using RPC functions without referencing the TI-RPC library and 
the
 removal of the RPC headers from the glibc headers.
 Implemented by Ulrich Drepper.

So the answer seems to be that your libc is too new.
OK, thanks. I should have remembered the info about RPC in the glibc-2.14 
news. Then there will presumably be a problem building current R on current 
Fedora?
What is 'current Fedora'?  glibc 2.14 postdates the current release, Fedora 
15, which uses 2.13.   I do not know what Fedora 16 will use in several 
months ....

The main problem will be that the xdr included in R is only for platforms 
with 32-bit longs -- but that may be true for your i686 Linux.  It needs 
_X86_ defined to compile for i686: I would have expected that to be true on 
your platform, but am testing a cleaned-up version.  If that works it will 
appear in R-patched within 24 hours.

On Mon, 18 Jul 2011, Allin Cottrell wrote:

I'm building R 2.13.1 on i686-pc-linux-gnu, using gcc 4.6.1
and with glibc 2.14.

I get this error:

In file included from xdr.c:61:0:
./rpc/types.h:63:14: error: conflicting types for 'malloc'
make[4]: *** [xdr.o] Error 1

I can make the build proceed some by commenting out the declaration 
"extern char *malloc();" in xdr/rpc/types.h,
but then I get a slew of other errors:

xdr_float.c: In function 'xdr_float':
xdr_float.c:119:21: error: storage size of 'is' isn't known
xdr_float.c:120:20: error: storage size of 'vs' isn't known

and so on.

config.log is rather big to post here; I'm putting it at
http://www.wfu.edu/~cottrell/tmp/R.config.log .

--
Allin Cottrell
Department of Economics
Wake Forest University, NC

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

-- 
Allin Cottrell
Department of Economics
Wake Forest University

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

1) The current R-patched should compile src/extra/xdr on 32-bit Linux 
systems.

2) Longer-term or on a 64-bit platform the solution is to make use of 
libtirpc: you would need both this installed (common now) and its headers 
(unlikely).

Then if you arrange for /usr/include/tirpc to be in the C include path (not 
easy to do portably, but using C_INCLUDE_PATH will work on Linux), the tirpc 
versions should be found.
For the record, a more portable way is described in the R-admin manual 
in 2.13.1 patched and R-devel.
On Tue, 19 Jul 2011, Prof Brian Ripley wrote:

On Mon, 18 Jul 2011, Allin Cottrell wrote:

On Mon, 18 Jul 2011, Prof Brian Ripley wrote:

1) R-help is the wrong list: see the posting guide.  I've moved this to 
R-devel.

2) A glibc system should not be compiling in that directory.  glibc 2.14 
is rather recent and NEWS does say

* The RPC implementation in libc is obsoleted.  Old programs keep working
 but new programs cannot be linked with the routines in libc anymore.
 Programs in need of RPC functionality must be linked against TI-RPC.
 The TI-RPC implementation is IPv6 enabled and there are other benefits.

 Visible changes of this change include (obviously) the inability to link
 programs using RPC functions without referencing the TI-RPC library and 
the
 removal of the RPC headers from the glibc headers.
 Implemented by Ulrich Drepper.

So the answer seems to be that your libc is too new.
OK, thanks. I should have remembered the info about RPC in the glibc-2.14 
news. Then there will presumably be a problem building current R on 
current Fedora?
What is 'current Fedora'?  glibc 2.14 postdates the current release, Fedora 
15, which uses 2.13.   I do not know what Fedora 16 will use in several 
months ....

The main problem will be that the xdr included in R is only for platforms 
with 32-bit longs -- but that may be true for your i686 Linux.  It needs 
_X86_ defined to compile for i686: I would have expected that to be true on 
your platform, but am testing a cleaned-up version.  If that works it will 
appear in R-patched within 24 hours.

On Mon, 18 Jul 2011, Allin Cottrell wrote:

I'm building R 2.13.1 on i686-pc-linux-gnu, using gcc 4.6.1
and with glibc 2.14.

I get this error:

In file included from xdr.c:61:0:
./rpc/types.h:63:14: error: conflicting types for 'malloc'
make[4]: *** [xdr.o] Error 1

I can make the build proceed some by commenting out the declaration 
"extern char *malloc();" in xdr/rpc/types.h,
but then I get a slew of other errors:

xdr_float.c: In function 'xdr_float':
xdr_float.c:119:21: error: storage size of 'is' isn't known
xdr_float.c:120:20: error: storage size of 'vs' isn't known

and so on.

config.log is rather big to post here; I'm putting it at
http://www.wfu.edu/~cottrell/tmp/R.config.log .

--
Allin Cottrell
Department of Economics
Wake Forest University, NC

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

-- 
Allin Cottrell
Department of Economics
Wake Forest University

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595