[Rd] R-devel and PGI 6.0 compile error
Paul Gilbert
pgilbert at bank-banque-canada.ca
Thu May 18 17:59:37 CEST 2006
I am trying to compile R-devel (R-devel_2006-05-17.tar.gz) on Red Hat
Enterprise Linux AS release 3 (Taroon Update 7) using the Portland Group
compiler 6.0. (I have not yet successful compiled R on this
configuration, so I don't know if this is a new problem.) I get an error
pgcc -L/usr/local/pgi/linux86-64/6.0/libso -L/usr/lib64 -o dftables
dftables.o
../dftables chartables.h
../dftables: error while loading shared libraries: libpgc.so: cannot open
shared object file: No such file or directory
make[3]: *** [chartables.h] Error 127
The library containing libpgc.so is in both my LD_LIBRARY_PATH and in
LDFLAGS. More details are below. In configure I am also getting
checking whether C99 double complex is supported...
checking complex.h usability... no
checking complex.h presence... yes
configure: WARNING: complex.h: present but cannot be compiled
configure: WARNING: complex.h: check for missing prerequisite headers?
configure: WARNING: complex.h: see the Autoconf documentation
configure: WARNING: complex.h: section "Present But Cannot Be Compiled"
configure: WARNING: complex.h: proceeding with the preprocessor's result
configure: WARNING: complex.h: in the future, the compiler will take
precedence
configure: WARNING: ## ----------------------------------- ##
configure: WARNING: ## Report this to r-bugs at R-project.org ##
configure: WARNING: ## ----------------------------------- ##
checking for complex.h... yes
Paul Gilbert
_____________________
~/toolchain/R/clusterPGI/R-devel:../../src/R-devel/configure --with-x=no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script '../../src/R-devel/config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... no
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for working makeinfo... found
checking for gawk... gawk
checking for egrep... grep -E
checking whether ln -s works... yes
checking for ranlib... ranlib
checking for bison... bison -y
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for less... /usr/bin/less
checking for perl... /usr/bin/perl
checking whether perl version is at least 5.004... yes
checking for dvips... no
checking for tex... no
checking for latex... no
configure: WARNING: you cannot build DVI versions of the R manuals
checking for makeindex... no
checking for pdftex... no
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for makeinfo... /usr/bin/makeinfo
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for firefox... no
checking for mozilla... no
checking for netscape... no
checking for galeon... no
checking for kfmclient... no
checking for opera... no
checking for gnome-moz-remote... no
checking for open... /usr/bin/open
using default browser ... /usr/bin/open
checking for acroread... no
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checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for kghostview... no
checking for open... /usr/bin/open
checking for gcc... pgcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... no
checking whether pgcc accepts -g... yes
checking for pgcc option to accept ANSI C... none needed
checking how to run the C preprocessor... pgcc -E
checking how to run the C preprocessor... pgcc -E
defining F77 to be pgf77
checking whether we are using the GNU Fortran 77 compiler... no
checking whether pgf77 accepts -g... yes
checking whether we are using the GNU C++ compiler... no
checking whether pgCC accepts -g... yes
checking how to run the C++ preprocessor... pgCC -E
checking whether __attribute__((visibility())) is supported... no
checking whether pgcc accepts -fvisibility... yes
checking whether pgf77 accepts -fvisibility... yes
checking for a sed that does not truncate output... /bin/sed
checking for non-GNU ld... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from pgcc object... ok
checking for objdir... .libs
checking for ranlib... (cached) ranlib
checking for strip... strip
checking if pgcc static flag works... yes
checking for pgcc option to produce PIC...
checking if pgcc supports -c -o file.o... yes
checking whether the pgcc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
checking whether the pgCC linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking for pgCC option to produce PIC...
checking if pgCC supports -c -o file.o... yes
checking whether the pgCC linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for pgf77 option to produce PIC...
checking if pgf77 supports -c -o file.o... yes
checking whether the pgf77 linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking whether makeinfo version is at least 4.7... no
configure: WARNING: you cannot build info or html versions of the R manuals
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking dl.h usability... no
checking dl.h presence... no
checking for dl.h... no
checking for dlfcn.h... (cached) yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking fpu_control.h usability... yes
checking fpu_control.h presence... yes
checking for fpu_control.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking ieee754.h usability... yes
checking ieee754.h presence... yes
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checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking for strings.h... (cached) yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
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checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 8
checking for long long... yes
checking size of long long... 8
checking for long double... yes
checking size of long double... 8
checking whether we can compute C Make dependencies... yes, using cpp -M
checking whether pgcc supports -c -o FILE.lo... yes
checking how to get verbose linking output from pgf77... -v
checking for Fortran libraries of pgf77...
-L/usr/local/pgi/linux86-64/6.0/libso -L/usr/lib64' -L/usr/lib64
-L/usr/local/pgi/linux86-64/6.0/lib
-L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3 -lpgftnrtl -lnspgc -lpgc -lm
checking how to get verbose linking output from pgcc... -v
checking for C libraries of pgcc...
-L/usr/local/pgi/linux86-64/6.0/libso -L/usr/lib64' -L/usr/lib64
-L/usr/local/pgi/linux86-64/6.0/lib
-L/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3 -lnspgc -lpgc -lm
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no
extra underscore
checking whether pgf77 appends underscores to external names... yes
checking whether pgf77 appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether pgf77 and pgcc agree on int and double... yes
checking whether pgf77 and pgcc agree on double complex... yes
checking whether pgCC accepts -M for generating dependencies... yes
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking for fseeko... yes
checking for ftello... yes
checking for isblank... yes
checking for matherr... yes
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log2 exists and is declared... no
checking whether log10 exists and is declared... yes
checking whether rint exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking whether __va_copy exists and is declared... no
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether realpath exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether system exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether strcoll exists and is declared... yes
checking whether strerror exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether times exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... no
checking for finite... yes
checking for isnan... yes
checking whether isfinite is declared... no
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking for nl_langinfo and CODESET... yes
checking for acosh... yes
checking for asinh... yes
checking for atanh... yes
checking for mkdtemp... yes
checking for snprintf... yes
checking for strdup... yes
checking for strncasecmp... yes
checking for vsnprintf... yes
checking whether acosh is declared... yes
checking whether asinh is declared... yes
checking whether atanh is declared... yes
checking whether mkdtemp is declared... yes
checking whether snprintf is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking whether vsnprintf is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for __setfpucw... no
checking for working calloc... yes
checking for working finite... no
checking for working log... no
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking whether C99 double complex is supported...
checking complex.h usability... no
checking complex.h presence... yes
configure: WARNING: complex.h: present but cannot be compiled
configure: WARNING: complex.h: check for missing prerequisite headers?
configure: WARNING: complex.h: see the Autoconf documentation
configure: WARNING: complex.h: section "Present But Cannot Be Compiled"
configure: WARNING: complex.h: proceeding with the preprocessor's result
configure: WARNING: complex.h: in the future, the compiler will take
precedence
configure: WARNING: ## ----------------------------------- ##
configure: WARNING: ## Report this to r-bugs at R-project.org ##
configure: WARNING: ## ----------------------------------- ##
checking for complex.h... yes
checking for double complex... no
no
checking for cblas_cdotu_sub in vecLib framework... no
checking for dgemm_... no
checking for ATL_xerbla in -latlas... no
checking for dgemm_ in -lblas... yes
checking for dgemm_ in -ldgemm... no
checking for dgemm_ in -lsunperf... no
checking for dgemm_ in -lblas... (cached) yes
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checking for dgemm_ in -lblas... (cached) yes
checking whether double complex BLAS can be used... no
checking iconv.h usability... yes
checking iconv.h presence... yes
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checking wctype.h presence... yes
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checking whether iswblank exists and is declared... no
checking whether wctype exists and is declared... yes
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checking for wctrans_t... yes
checking for mbstate_t... yes
checking for X... disabled
using X11 ... no
checking for CFStringGetSystemEncoding in CoreFoundation framework... no
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories...
/usr/lib64/tclConfig.shchecking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories...
/usr/lib64/tkConfig.sh
checking /usr/include/tcl8.3/generic/tcl.h usability... no
checking /usr/include/tcl8.3/generic/tcl.h presence... no
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checking for BSD networking... yes
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checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
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checking for rpc/xdr.h... yes
checking for XDR support... yes
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checking mmap support for zlib... yes
checking whether bzip2 support needs to be compiled... yes
checking whether PCRE support needs to be compiled... yes
checking whether leap seconds are treated according to POSIX... yes
checking for setitimer... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGE_FILES value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... 1
checking for fseeko... (cached) yes
checking whether KERN_USRSTACK sysctl is supported... no
checking for lpr... lpr
checking for paperconf... false
checking for java... /usr/bin/java
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checking whether Java interpreter works... no
checking for f95... no
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checking for pgf95... pgf95
checking whether we are using the GNU Fortran compiler... no
checking whether pgf95 accepts -g... yes
checking for Fortran flag to compile .f90 files... none
checking for Fortran flag to compile .f95 files... none
checking for recommended packages... yes
checking whether NLS is requested... yes
checking whether make sets $(MAKE)... yes
checking for msgfmt... /usr/bin/msgfmt
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checking for msgmerge... /usr/bin/msgmerge
checking whether we are using the GNU C Library 2 or newer... yes
checking for library containing strerror... none required
checking for signed... yes
checking for inline... inline
checking for off_t... (cached) yes
checking for long long... (cached) yes
checking for long double... yes
checking for wchar_t... yes
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checking for stdlib.h... (cached) yes
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checking for working mmap... yes
checking whether we are using the GNU C Library 2.1 or newer... yes
checking whether integer division by zero raises SIGFPE... yes
checking for unsigned long long... yes
checking for inttypes.h... yes
checking whether the inttypes.h PRIxNN macros are broken... no
checking for stdint.h... (cached) yes
checking for SIZE_MAX... yes
checking for stdint.h... (cached) yes
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checking for GNU ld... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking for shared library run path origin... done
checking for ptrdiff_t... yes
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checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
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extern size_t iconv (iconv_t cd, char * *inbuf, size_t
*inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for nl_langinfo and CODESET... (cached) yes
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checking version of bison... 1.875, ok
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checking whether to use NLS... yes
checking where the gettext function comes from... libc
configure: creating ./config.status
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config.status: creating src/nmath/Makefile
config.status: creating src/nmath/standalone/Makefile
config.status: creating src/scripts/Makefile
config.status: creating src/scripts/COMPILE
config.status: creating src/scripts/INSTALL
config.status: creating src/scripts/REMOVE
config.status: creating src/scripts/R.sh
config.status: creating src/scripts/Rdconv
config.status: creating src/scripts/Rprof
config.status: creating src/scripts/SHLIB
config.status: creating src/scripts/Sd2Rd
config.status: creating src/scripts/build
config.status: creating src/scripts/check
config.status: creating src/unix/Makefile
config.status: creating tests/Makefile
config.status: creating tests/Embedding/Makefile
config.status: creating tests/Examples/Makefile
config.status: creating tests/Native/Makefile
config.status: creating tools/Makefile
config.status: creating src/include/config.h
config.status: executing default-1 commands
config.status: creating po/POTFILES
config.status: creating po/Makefile
config.status: executing stamp-h commands
R is now configured for x86_64-unknown-linux-gnu
Source directory: ../../src/R-devel
Installation directory: /usr/local
C compiler: pgcc -g -O2 -pc 64 -Kieee -fPIC
Fortran 77 compiler: pgf77 -g -O2 -pc 64 -Kieee -fPIC
C++ compiler: pgCC -g -O2 -pc 64 -Kieee -fPIC
Fortran 90/95 compiler: pgf95 -g -O2 -pc 64 -Kieee -fPIC
Interfaces supported:
External libraries: readline
Additional capabilities: iconv, MBCS, NLS
Options enabled: R profiling
Recommended packages: yes
configure: WARNING: you cannot build DVI versions of the R manuals
configure: WARNING: you cannot build info or html versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
~/toolchain/R/clusterPGI/R-devel:make
make[1]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/m4'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/m4'
make[1]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/tools'
make[1]: Nothing to be done for `R'.
make[1]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/tools'make[1]: Entering
directory `/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc'
make[2]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html'
make[3]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html'
make[3]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html'
make[3]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html/search'
make[4]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html/search'
make[4]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html/search'
make[3]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html/search'
make[2]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/html'
make[2]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/manual'
make[2]: Nothing to be done for `R'.
make[2]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc/manual'
make[2]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc'
make[2]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc'
make[1]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/doc'
make[1]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/etc'
make[1]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/etc'
make[1]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/share'
make[2]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/share'
mkdir -p -- ../share/R
mkdir -p -- ../share/encodings
mkdir -p -- ../share/licenses
mkdir -p -- ../share/make
mkdir -p -- ../share/perl
mkdir -p -- ../share/perl/R
mkdir -p -- ../share/perl/Text
mkdir -p -- ../share/sh
mkdir -p -- ../share/texmf
make[2]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/share'make[1]: Leaving
directory `/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/share'make[1]:
Entering directory `/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src'
make[2]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/scripts'
creating src/scripts/R.fe
make[3]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/scripts'
mkdir -p -- ../../bin
make[3]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/scripts'
make[2]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/scripts'
make[2]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/include'
mkdir -p -- ../../include
make[3]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/include/R_ext'
mkdir -p -- ../../../include/R_ext
make[3]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/include/R_ext'
make[2]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/include'
make[2]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra'
make[3]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/bzip2'
make[4]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/bzip2'
making blocksort.d from
.../../../../../src/R-devel/src/extra/bzip2/blocksort.c
making bzlib.d from ../../../../../src/R-devel/src/extra/bzip2/bzlib.c
making compress.d from ../../../../../src/R-devel/src/extra/bzip2/compress.c
making crctable.d from ../../../../../src/R-devel/src/extra/bzip2/crctable.c
making decompress.d from
.../../../../../src/R-devel/src/extra/bzip2/decompress.cmaking huffman.d
from ../../../../../src/R-devel/src/extra/bzip2/huffman.c
making randtable.d from
.../../../../../src/R-devel/src/extra/bzip2/randtable.c
make[4]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/bzip2'
make[4]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/bzip2'
pgcc -I../../../../../src/R-devel/src/extra/bzip2 -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c
.../../../../../src/R-devel/src/extra/bzip2/blocksort.c -o blocksort.o
pgcc -I../../../../../src/R-devel/src/extra/bzip2 -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c ../../../../../src/R-devel/src/extra/bzip2/bzlib.c -o
bzlib.o
pgcc -I../../../../../src/R-devel/src/extra/bzip2 -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c ../../../../../src/R-devel/src/extra/bzip2/compress.c
-o compress.o
pgcc -I../../../../../src/R-devel/src/extra/bzip2 -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c ../../../../../src/R-devel/src/extra/bzip2/crctable.c
-o crctable.o
pgcc -I../../../../../src/R-devel/src/extra/bzip2 -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c
.../../../../../src/R-devel/src/extra/bzip2/decompress.c -o
decompress.opgcc -I../../../../../src/R-devel/src/extra/bzip2 -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c ../../../../../src/R-devel/src/extra/bzip2/huffman.c
-o huffman.o
pgcc -I../../../../../src/R-devel/src/extra/bzip2 -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c
.../../../../../src/R-devel/src/extra/bzip2/randtable.c -o randtable.o
rm -f libbz2.a
ar cr libbz2.a blocksort.o bzlib.o compress.o crctable.o decompress.o
huffman.o randtable.o
ranlib libbz2.a
make[4]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/bzip2'
make[3]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/bzip2'
make[3]: Entering directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/pcre'
pgcc -I../../../../../src/R-devel/src/extra/pcre -I.
-I../../../src/include -I../../../../../src/R-devel/src/include
-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC -DHAVE_CONFIG_H -g -O2 -pc
64 -Kieee -fPIC -c ../../../../../src/R-devel/src/extra/pcre/dftables.c
-o dftables.o
pgcc -L/usr/local/pgi/linux86-64/6.0/libso -L/usr/lib64 -o dftables
dftables.o
../dftables chartables.h
../dftables: error while loading shared libraries: libpgc.so: cannot open
shared object file: No such file or directory
make[3]: *** [chartables.h] Error 127
make[3]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra/pcre'
make[2]: *** [R] Error 1
make[2]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src/extra'
make[1]: *** [R] Error 1
make[1]: Leaving directory
`/home/mfa/gilp/toolchain/R/clusterPGI/R-devel/src'
make: *** [R] Error 1
~/toolchain/R/clusterPGI/R-devel:
~/toolchain/R/clusterPGI/R-devel:
~/toolchain/R/clusterPGI/R-devel:
~/toolchain/R/clusterPGI/R-devel:set
BASH=/bin/bash
BASH_VERSINFO=([0]="2" [1]="05b" [2]="0" [3]="1" [4]="release"
[5]="x86_64-redhat-linux-gnu")
BASH_VERSION='2.05b.0(1)-release'
BSTINPUTS=/home/mfa/gilp/BOCcite:
CC=pgcc
CFLAGS='-g -O2 -pc 64 -Kieee -fPIC'
CMSS_MYSQL_HOST=mfa01518
CMSS_MYSQL_PWD=cmss
COLORS=/etc/DIR_COLORS.xterm
COLUMNS=80
CPPFLAGS='-I/usr/local/pgi/linux86-64/6.0/include
-I/usr/local/pgi/linux86-64/6.0/include/CC'
CVSDIRS='dse Mybin MyNotes papers cmss toolchain boc systems-config
HomeOnTheWeb'
CVSEDITOR=vi
CVSROOT=/home/mfa/gilp/cvsroot
CVS_RSH=ssh
CXX=pgCC
CXXFLAGS='-g -O2 -pc 64 -Kieee -fPIC'
DIRSTACK=()
DISPLAY=localhost:11.0
EUID=598
F77=pgf77
F95=pgf95
FCFLAGS='-g -O2 -pc 64 -Kieee -fPIC'
FFLAGS='-g -O2 -pc 64 -Kieee -fPIC'
GROUPS=()
GS_OPTIONS=-dAutoRotatePages=/None
G_BROKEN_FILENAMES=1
HISTFILE=/home/mfa/gilp/.bash_history
HISTFILESIZE=1000
HISTSIZE=1000
HOME=/home/mfa/gilp
HOSTNAME=node01
HOSTTYPE=x86_64
IFS=$' \t\n'
INPUTRC=/etc/inputrc
LANG=en_US.UTF-8
LANGVAR=en_US.UTF-8
LDFLAGS='-L/usr/local/pgi/linux86-64/6.0/libso -L/usr/lib64'
LD_LIBRARY_PATH='-L/usr/local/pgi/linux86-64/6.0/libso -L/usr/lib64'
LESSOPEN='|/usr/bin/lesspipe.sh %s'
LINES=24
LM_LICENSE_FILE=/usr/local/pgi/license.dat
LOGNAME=gilp
LS_COLORS='no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.bz=00;31:*.tz=00;31:*.rpm=00;31:*.cpio=00;31:*.jpg=00;35:*.gif=00;35:*.bmp=00;35:*.xbm=00;35:*.xpm=00;35:*.png=00;35:*.tif=00;35:'
MACHTYPE=x86_64-redhat-linux-gnu
MAIL=/var/spool/mail/gilp
MAILCHECK=60
MANPATH=/usr/local/pgi/linux86-64/6.0/man:/
MOABHOMEDIR=/usr/local/moab
OLDPWD=/home/mfa/gilp/toolchain/R/clusterPGI
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PADI_CLEANUP=cleanup.simple.server
PADI_STARTUP=simple.server
PATH=/usr/local/bin:/home/mfa/gilp/Mybin:/home/mfa/gilp/bin-cluster:/apps/bin:/usr/local/pgi/linux86-64/6.0/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/pbs/x86_64/bin:/usr/local/pbs/x86_64/sbin:/usr/local/moab/x86_64/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin
PBS_DEFAULT=cc-mgnt01
PGI=/usr/local/pgi/linux86-64/6.0
PIPESTATUS=([0]="2")
PPID=14266
PS1='\w:'
PS2='> '
PS4='+ '
PWD=/home/mfa/gilp/toolchain/R/clusterPGI/R-devel
SHELL=/bin/bash
SHELLOPTS=braceexpand:emacs:hashall:histexpand:history:interactive-comments:monitor
SHLIB_CXXLDFLAGS=-shared
SHLIB_LDFLAGS=-shared
SHLVL=1
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
SSH_CLIENT='172.20.0.1 56584 22'
SSH_CONNECTION='172.20.0.1 56584 172.20.101.1 22'
SSH_TTY=/dev/pts/1
SUPPORTED=en_US.UTF-8:en_US:en
TERM=xterm
TEXINPUTS=/home/mfa/gilp/BOCcite:
UID=598
USER=gilp
XARCH=x86_64
XCATPREFIX=/opt/xcat
XCATROOT=/opt/xcat
_=make
http_proxy=http://wwwproxy:8080
ssl_proxy=ftp://wwwproxy:8080
x=Linux
~/toolchain/R/clusterPGI/R-devel:
~/toolchain/R/clusterPGI/R-devel:
~/toolchain/R/clusterPGI/R-devel:uname -a
Linux node01 2.4.21-37.ELsmp #1 SMP Wed Sep 7 13:32:18 EDT 2005 x86_64
x86_64 x86_64 GNU/Linux
~/toolchain/R/clusterPGI/R-devel:
~/toolchain/R/clusterPGI/R-devel:ls -l
/usr/local/pgi/linux86-64/6.0/libso/*pgc*
-rw-r--r-- 1 909 1004 1456 Nov 4 2005
/usr/local/pgi/linux86-64/6.0/libso/libnspgc.a
-rw-r--r-- 1 909 1004 453956 Nov 4 2005
/usr/local/pgi/linux86-64/6.0/libso/libpgc.a
-rwxr-xr-x 2 909 1004 271084 Nov 4 2005
/usr/local/pgi/linux86-64/6.0/libso/libpgc.so
~/toolchain/R/clusterPGI/R-devel:
====================================================================================
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