From ripley at stats.ox.ac.uk  Tue Aug 30 18:23:28 2005
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 30 Aug 2005 17:23:28 +0100 (BST)
Subject: [Rd] compile R with Portland Group compiler
In-Reply-To: <43148303.8040805@lindaspaces.com>
References: <430B63FB.1000908@lindaspaces.com>
	<Pine.LNX.4.61.0508232211550.21594@gannet.stats>
	<430C9DA7.5020809@lindaspaces.com>
	<Pine.LNX.4.61.0508241730270.17771@gannet.stats>
	<43148303.8040805@lindaspaces.com>
Message-ID: <Pine.LNX.4.61.0508301721170.16651@gannet.stats>

Thank you for the report.

/* */ is standard C.  simpleaffy is not a CRAN package: we test those with 
enough flags (-Wall -pedantic) that the use of // is flagged and would get 
reported to the maintainer/submitter.

On Tue, 30 Aug 2005, Jennifer Lai wrote:

> Hi,
>   After getting some help from Portland Group, I was able to pass the 
> initial stage of building R with Portland Group Compiler on AMD Opeteron.
>
> For anyone who is interested in building R with PG compiler, here is a list 
> of set flags used in config.site,
> CC=/usr/pgi/linux86-64/6.0/bin/pgcc
> CFLAGS='-g -O2 -mieee-fp'
> CPPFLAGS='-I/usr/pgi/linux86-64/6.0/include 
> -I/usr/pgi/linux86-64/6.0/include/CC'
> F77=/usr/pgi/linux86-64/6.0/bin/pgf77
> FFLAGS=-O2
> CPICFLAGS=-fpic
> FPICFLAGS=-fpic
> SHLIB_LDFLAGS=-shared
> LDFLAGS='-L/usr/pgi/linux86-64/6.0/libso -L/usr/lib64'
> CXX=/usr/pgi/linux86-64/6.0/bin/pgCC
> CXXPICFLAGS=-fpic
> SHLIB_CXXLDFLAGS=-shared
>
> After installing R, I went ahead to install simpleaffy package. However, came 
> across the following errors.
>
> PGC-S-0035-Syntax error: Recovery attempted by replacing '/' by double 
> 0.00000000000000000E+0 (simpleaffy.c: 455)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier by by 
> '!=' (simpleaffy.c: 455)
> PGC-S-0035-Syntax error: Recovery attempted by replacing integer 15 by '!=' 
> (simpleaffy.c: 455)
> PGC-S-0039-Use of undeclared variable added (simpleaffy.c: 455)
> PGC-S-0037-Syntax error: Recovery attempted by deleting identifier march 
> (simpleaffy.c: 455)
> PGC-S-0039-Use of undeclared variable Crispin (simpleaffy.c: 455)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier with by 
> '!=' (simpleaffy.c: 455)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier in by 
> '!=' (simpleaffy.c: 455)
> PGC-S-0039-Use of undeclared variable deals (simpleaffy.c: 455)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier largest 
> by '!=' (simpleaffy.c: 455)
> PGC-S-0039-Use of undeclared variable ties (simpleaffy.c: 455)
> PGC-S-0035-Syntax error: Recovery attempted by replacing '...' by ',' 
> (simpleaffy.c: 455)
> PGC-S-0039-Use of undeclared variable the (simpleaffy.c: 455)
> PGC-S-0039-Use of undeclared variable ranks (simpleaffy.c: 455)
> PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors
> make: *** [simpleaffy.o] Error 2
> ERROR: compilation failed for package 'simpleaffy'
>
> Apparently, PG compiler doesn't like "//" style for comments. So, by changing 
> "//" to "/* */" style fixed above errors.
> The commenting style errors also happened in other packages, such as affy.
> Since "/* */" comment style is acceptable by both PG Compiler and gcc, it is 
> probably worthwhile to use "/* */" consistently throughout R packages.
>
>
> Regards,
> Jennifer
>
> Prof Brian Ripley wrote:
>
>> Let us be clear: some things in config.log are designed to fail, so only 
>> unexpected errors are a cause to look there.  The regex.c warnings are it 
>> seems from an over-zealous compiler.
>> 
>> The problems here seem to be the unknown use of .lo (which it seems to have 
>> coped with) and a problem in the PG's own libc, which it seems cannot be 
>> used in a shared object.  That issue discussed in the R-admin manual, and 
>> seems something you do need to take up with PG.  The crucial part is
>> 
>>> /usr/bin/ld: /usr/pgi/linux86-64/6.0/lib/libpgc.a(fastmath.o): relocation
>>> R_X86_64_PC32 against `__fvdlog' can not be used when making a shared 
>>> object;
>>> recompile with -fPIC
>> 
>> 
>> which is asking you to recompile their static library.  If you can't use a 
>> dynamic library then this is fatal.
>> 
>> 
>> On Wed, 24 Aug 2005, Jennifer Lai wrote:
>> 
>>> I downloaded R-devel and compiled it with pgcc. This time, instead of 
>>> breaking in src/main, compilation breaks in src/modules with the following 
>>> error messages.
>>> 
>>> Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
>>> Copyright 2000-2005, STMicroelectronics, Inc.  All Rights Reserved.
>>> /usr/pgi/linux86-64/6.0/bin/pgcc -shared  -L/usr/pgi/linux86-64/6.0/lib 
>>> -L/usr/lib64 -o R_X11.so  dataentry.lo devX11.lo rotated.lo rbitmap.lo 
>>> -lSM -lICE -L/usr/X11R6/lib64 -lX11  -ljpeg -lpng -lz
>>> File with unknown suffix passed to linker: dataentry.lo
>>> File with unknown suffix passed to linker: devX11.lo
>>> File with unknown suffix passed to linker: rotated.lo
>>> File with unknown suffix passed to linker: rbitmap.lo
>>> /usr/bin/ld: /usr/pgi/linux86-64/6.0/lib/libpgc.a(fastmath.o): relocation 
>>> R_X86_64_PC32 against `__fvdlog' can not be used when making a shared 
>>> object; recompile with -fPIC
>>> /usr/bin/ld: final link failed: Bad value
>>> make[4]: *** [R_X11.so] Error 2
>>> make[4]: Leaving directory `/home/cuser/R-devel/src/modules/X11'
>>> make[3]: *** [R] Error 2
>>> make[3]: Leaving directory `/home/cuser/R-devel/src/modules/X11'
>>> make[2]: *** [R] Error 1
>>> make[2]: Leaving directory `/home/cuser/R-devel/src/modules'
>>> make[1]: *** [R] Error 1
>>> make[1]: Leaving directory `/home/cuser/R-devel/src'
>>> make: *** [R] Error 1
>>> 
>>> Though src/main directory compiled successfully, I do still get warning 
>>> messages from src/main/regex.c compilation.
>>> PGC-W-0155-64-bit integral value truncated  (/usr/include/wctype.h: 109)
>>> PGC-W-0155-64-bit integral value truncated  (/usr/include/wctype.h: 110)
>>> PGC-W-0155-64-bit integral value truncated  (/usr/include/wctype.h: 111)
>>> PGC-W-0155-64-bit integral value truncated  (/usr/include/wctype.h: 112)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #5 
>>> (regex.c: 3288)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 4464)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 4591)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 4635)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 4737)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 4792)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #4 
>>> (regex.c: 4793)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 4861)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 4904)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument 
>> 
>> #3
>> 
>>> (regex.c: 4954)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #4 
>>> (regex.c: 4961)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 5057)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 5581)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 5596)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 5628)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 5641)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 5669)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 5858)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 6230)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #6 
>>> (regex.c: 7035)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 7803)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #2 
>>> (regex.c: 7814)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #3 
>>> (regex.c: 7826)
>>> PGC-W-0155-Long value is passed to a nonprototyped function - argument #7 
>>> (regex.c: 10722)
>>> PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with warnings
>>> 
>>> 
>>> One last thing that I notice is the errors messages in config.log. Should 
>>> I consult these error messages with Portland Group, or R-devel can help me 
>>> out on this?
>>> 
>>> Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
>>> Copyright 2000-2005, STMicroelectronics, Inc.  All Rights Reserved.
>>> PGC-S-0040-Illegal use of symbol, choke (conftest.c: 21)
>>> PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors
>>> configure:4222: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | /* end confdefs.h.  */
>>> |
>>> | int
>>> | main ()
>>> | {
>>> | #ifndef __GNUC__
>>> |        choke me
>>> | #endif
>>> |
>>> |   ;
>>> |   return 0;
>>> | }
>>> 
>>> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier me by 
>>> ';' (conftest.c: 2)
>>> PGC-W-0057-Old-style declaration used; int assumed (conftest.c: 2)
>>> PGC/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors
>>> configure:4453: $? = 2
>>> configure: failed program was:
>>> | #ifndef __cplusplus
>>> |   choke me
>>> | #endif
>>> 
>>> PGFTN-S-0034-Syntax error at or near end of line (conftest.F: 3)
>>> 0 inform,   0 warnings,   1 severes, 0 fatal for main
>>> PGFTN/x86-64 Linux/x86-64 6.0-5: compilation completed with severe errors
>>> configure:5400: $? = 2
>>> configure: failed program was:
>>> |       program main
>>> | #ifndef __GNUC__
>>> |        choke me
>>> | #endif
>>> |
>>> |       end
>>> 
>>> configure:5665: /usr/pgi/linux86-64/6.0/bin/pgCC -c 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc >&5
>>> "conftest.cc", line 21: error: identifier "choke" is undefined
>>>        choke me
>>>        ^
>>> 
>>> "conftest.cc", line 21: warning: variable "me" was declared but never
>>>         referenced
>>>        choke me
>>>              ^
>>> 
>>> 1 error detected in the compilation of "conftest.cc".
>>> configure:5671: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | /* end confdefs.h.  */
>>> |
>>> | int
>>> | main ()
>>> | {
>>> | #ifndef __GNUC__
>>> |        choke me
>>> | #endif
>>> |
>>> |   ;
>>> |   return 0;
>>> | }
>>> 
>>> configure:5841: /usr/pgi/linux86-64/6.0/bin/pgCC -c -g 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc >&5
>>> "conftest.cc", line 20: error: identifier "exit" is undefined
>>> exit (42);
>>> ^
>>> 
>>> 1 error detected in the compilation of "conftest.cc".
>>> configure:5847: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | /* end confdefs.h.  */
>>> |
>>> | int
>>> | main ()
>>> | {
>>> | exit (42);
>>> |   ;
>>> |   return 0;
>>> | }
>>> configure:5796: /usr/pgi/linux86-64/6.0/bin/pgCC -c -g 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc >&5
>>> "conftest.cc", line 16: error: namespace "std" has no member "exit"
>>> extern "C" void std::exit (int) throw (); using std::exit;
>>>                      ^
>>> 
>>> "conftest.cc", line 16: error: namespace "std" has no member "exit"
>>> extern "C" void std::exit (int) throw (); using std::exit;
>>>                                                      ^
>>> 
>>> 2 errors detected in the compilation of "conftest.cc".
>>> configure:5802: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | /* end confdefs.h.  */
>>> | extern "C" void std::exit (int) throw (); using std::exit;
>>> | #include <stdlib.h>
>>> | int
>>> | main ()
>>> | {
>>> | exit (42);
>>> |   ;
>>> |   return 0;
>>> | }
>>> configure:5796: /usr/pgi/linux86-64/6.0/bin/pgCC -c -g 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc >&5
>>> "conftest.cc", line 16: error: namespace "std" has no member "exit"
>>> extern "C" void std::exit (int); using std::exit;
>>>                      ^
>>> 
>>> "conftest.cc", line 16: error: namespace "std" has no member "exit"
>>> extern "C" void std::exit (int); using std::exit;
>>>                                             ^
>>> 
>>> 2 errors detected in the compilation of "conftest.cc".
>>> configure:5802: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | /* end confdefs.h.  */
>>> | extern "C" void std::exit (int); using std::exit;
>>> | #include <stdlib.h>
>>> | int
>>> | main ()
>>> | {
>>> | exit (42);
>>> |   ;
>>> |   return 0;
>>> | }
>>> configure:5796: /usr/pgi/linux86-64/6.0/bin/pgCC -c -g 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc >&5
>>> "/usr/include/stdlib.h", line 640: error: omission of exception 
>>> specification
>>>         is incompatible with previous function "exit" (declared at line 16
>>>         of "conftest.cc")
>>> extern void exit (int __status) __THROW __attribute__ ((__noreturn__));
>>>                                                                       ^
>>> 
>>> 1 error detected in the compilation of "conftest.cc".
>>> configure:5802: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | /* end confdefs.h.  */
>>> | extern "C" void exit (int) throw ();
>>> | #include <stdlib.h>
>>> | int
>>> | main ()
>>> | {
>>> | exit (42);
>>> |   ;
>>> |   return 0;
>>> | }
>>> configure:5796: /usr/pgi/linux86-64/6.0/bin/pgCC -c -g 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc >&5
>>> NOTE: your evaluation license will expire in 14 days, 5.7 hours.
>>> For a permanent license, please read the order acknowledgement
>>> that you received.  Connect to https://www.pgroup.com/License with
>>> the username and password in the order acknowledgement.
>>> 
>>>   Name:    lai
>>>   User:    lai
>>>   Email:    lai at lindaspaces.com
>>>   Hostid:    PGI=00001AE0193111621CB217
>>> configure:5802: $? = 0
>>> configure:5806: test -z
>>>            || test ! -s conftest.err
>>> configure:5809: $? = 0
>>> configure:5812: test -s conftest.o
>>> configure:5815: $? = 0
>>> configure:5841: /usr/pgi/linux86-64/6.0/bin/pgCC -c -g 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc >&5
>>> NOTE: your evaluation license will expire in 14 days, 5.7 hours.
>>> For a permanent license, please read the order acknowledgement
>>> that you received.  Connect to https://www.pgroup.com/License with
>>> the username and password in the order acknowledgement.
>>> 
>>>   Name:    lai
>>>   User:    lai
>>>   Email:    lai at lindaspaces.com
>>>   Hostid:    PGI=00001AE0193111621CB217
>>> configure:5847: $? = 0
>>> configure:5851: test -z
>>>            || test ! -s conftest.err
>>> configure:5854: $? = 0
>>> configure:5857: test -s conftest.o
>>> configure:5860: $? = 0
>>> configure:5888: checking how to run the C++ preprocessor
>>> configure:5919: /usr/pgi/linux86-64/6.0/bin/pgCC -E 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc
>>> configure:5925: $? = 0
>>> configure:5957: /usr/pgi/linux86-64/6.0/bin/pgCC -E 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc
>>> "conftest.cc", line 19: catastrophic error: could not open source file
>>>         "ac_nonexistent.h"
>>> #include <ac_nonexistent.h>
>>>                            ^
>>> 
>>> 1 catastrophic error detected in the compilation of "conftest.cc".
>>> Compilation terminated.
>>> configure:5963: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | #ifdef __cplusplus
>>> | extern "C" void exit (int);
>>> | #endif
>>> | /* end confdefs.h.  */
>>> | #include <ac_nonexistent.h>
>>> configure:6002: result: /usr/pgi/linux86-64/6.0/bin/pgCC -E
>>> configure:6026: /usr/pgi/linux86-64/6.0/bin/pgCC -E 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc
>>> configure:6032: $? = 0
>>> configure:6064: /usr/pgi/linux86-64/6.0/bin/pgCC -E 
>>> -I/usr/pgi/linux86-64/6.0/include -I/usr/pgi/linux86-64/6.0/include/CC 
>>> conftest.cc
>>> "conftest.cc", line 19: catastrophic error: could not open source file
>>>         "ac_nonexistent.h"
>>> #include <ac_nonexistent.h>
>>>                            ^
>>> 
>>> 1 catastrophic error detected in the compilation of "conftest.cc".
>>> Compilation terminated.
>>> configure:6070: $? = 2
>>> configure: failed program was:
>>> | /* confdefs.h.  */
>>> |
>>> | #define PACKAGE_NAME "R"
>>> | #define PACKAGE_TARNAME "R"
>>> | #define PACKAGE_VERSION "2.2.0"
>>> | #define PACKAGE_STRING "R 2.2.0"
>>> | #define PACKAGE_BUGREPORT "r-bugs at R-project.org"
>>> | #define PACKAGE "R"
>>> | #define VERSION "2.2.0"
>>> | #define R_PLATFORM "x86_64-unknown-linux-gnu"
>>> | #define R_CPU "x86_64"
>>> | #define R_VENDOR "unknown"
>>> | #define R_OS "linux-gnu"
>>> | #define Unix 1
>>> | #ifdef __cplusplus
>>> | extern "C" void exit (int);
>>> | #endif
>>> | /* end confdefs.h.  */
>>> | #include <ac_nonexistent.h>
>>> 
>>> 
>>> Thank you in advance for your help!
>>> 
>>> Sincerely,
>>> Jennifer
>>> 
>>> Prof Brian Ripley wrote:
>>> 
>>>> regex.c is not our code, but from glibc.  Could you please try R-devel 
>>>> instead, which has a later version of glibc.  Since 2.1.1 is not longer 
>>>> part of the developement, we cannot help with that, but we can help wih 
>>>> R-devel.
>>>> 
>>>> I see the later regex.c does use prototypes.  But bitset is an integer 
>>>> type, so that may be a compiler error.
>>>> 
>>>> (It is on my list to try Intel and PG compilers on AMD64 as we have 
>>>> licences, but not very high priority.)
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> 
>> 
>
>
>

-- 
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



[Rd] compile R with Portland Group compiler
Prof Brian Ripley