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 checking for acroread4... no 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 checking for ieee754.h... yes 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 checking for sys/time.h... yes 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 checking for dgemm_ in -lessl... no 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 checking for iconv.h... yes checking for iconv... yes checking whether iconv() accepts "UTF-8", "latin1" and "UCS-*"... yes checking for iconvlist... no checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking wctype.h usability... yes checking wctype.h presence... yes checking for wctype.h... yes checking whether mbrtowc exists and is declared... yes checking whether wcrtomb exists and is declared... yes checking whether wcscoll exists and is declared... yes checking whether wcsftime exists and is declared... yes checking whether mbstowcs exists and is declared... yes checking whether wcstombs exists and is declared... yes checking whether wctrans exists and is declared... yes checking whether iswblank exists and is declared... no checking whether wctype exists and is declared... yes checking whether iswctype exists and is declared... yes 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 checking for /usr/include/tcl8.3/generic/tcl.h... no checking /usr/include/tcl8.3/tcl.h usability... no checking /usr/include/tcl8.3/tcl.h presence... no checking for /usr/include/tcl8.3/tcl.h... no checking /usr/include/tcl.h usability... no checking /usr/include/tcl.h presence... no checking for /usr/include/tcl.h... no checking for tcl.h... no checking for BSD networking... yes checking if jpeglib version >= 6b... no checking for main in -lz... yes checking if libpng version >= 1.0.5... no checking rpc/types.h usability... yes checking rpc/types.h presence... yes checking for rpc/types.h... yes checking for rpc/xdr.h... yes checking for XDR support... yes checking whether zlib support needs to be compiled... yes 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 checking for javac... /usr/bin/javac checking whether Java interpreter works... no checking for f95... no checking for fort... no checking for xlf95... no checking for ifc... no checking for efc... no 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 checking for gmsgfmt... /usr/bin/msgfmt checking for xgettext... no 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 checking for wint_t... yes checking for inttypes.h... yes checking for stdint.h... yes checking for intmax_t... yes checking whether printf() supports POSIX/XSI format strings... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for getpagesize... yes 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 checking for CFPreferencesCopyAppValue... no checking for CFLocaleCopyCurrent... no 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 checking argz.h usability... yes checking argz.h presence... yes checking for argz.h... yes checking for limits.h... (cached) yes checking for locale.h... (cached) yes checking nl_types.h usability... yes checking nl_types.h presence... yes checking for nl_types.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes 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 checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for asprintf... yes checking for fwprintf... yes checking for getcwd... yes checking for getegid... yes checking for geteuid... yes checking for getgid... yes checking for getuid... yes checking for mempcpy... yes checking for munmap... yes checking for putenv... (cached) yes checking for setenv... yes checking for setlocale... yes checking for snprintf... (cached) yes checking for stpcpy... yes checking for strcasecmp... yes checking for strdup... (cached) yes checking for strtoul... yes checking for tsearch... yes checking for wcslen... yes checking for __argz_count... yes checking for __argz_stringify... yes checking for __argz_next... yes checking for __fsetlocking... yes checking whether _snprintf is declared... no checking whether _snwprintf is declared... no checking whether feof_unlocked is declared... yes checking whether fgets_unlocked is declared... no checking whether getc_unlocked is declared... yes checking for iconv... yes checking for iconv declaration... 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 checking for LC_MESSAGES... yes checking for bison... bison checking version of bison... 1.875, ok checking for CFPreferencesCopyAppValue... (cached) no checking for CFLocaleCopyCurrent... (cached) no checking whether NLS is requested... yes checking whether included gettext is requested... no checking for GNU gettext in libc... yes checking whether to use NLS... yes checking where the gettext function comes from... libc configure: creating ./config.status config.status: creating Makeconf config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/html/Makefile config.status: creating doc/html/search/Makefile config.status: creating doc/manual/Makefile config.status: creating etc/Makefile config.status: creating etc/Makeconf config.status: creating etc/Renviron config.status: creating etc/ldpaths config.status: creating m4/Makefile config.status: creating po/Makefile.in config.status: creating share/Makefile config.status: creating src/Makefile config.status: creating src/appl/Makefile config.status: creating src/extra/Makefile config.status: creating src/extra/bzip2/Makefile config.status: creating src/extra/intl/Makefile config.status: creating src/extra/pcre/Makefile config.status: creating src/extra/xdr/Makefile config.status: creating src/extra/zlib/Makefile config.status: creating src/include/Makefile config.status: creating src/include/Rmath.h0 config.status: creating src/include/R_ext/Makefile config.status: creating src/library/Recommended/Makefile config.status: creating src/library/Makefile config.status: creating src/library/base/DESCRIPTION config.status: creating src/library/base/Makefile config.status: creating src/library/datasets/DESCRIPTION config.status: creating src/library/datasets/Makefile config.status: creating src/library/graphics/DESCRIPTION config.status: creating src/library/graphics/Makefile config.status: creating src/library/grDevices/DESCRIPTION config.status: creating src/library/grDevices/Makefile config.status: creating src/library/grDevices/src/Makefile config.status: creating src/library/grid/DESCRIPTION config.status: creating src/library/grid/Makefile config.status: creating src/library/grid/src/Makefile config.status: creating src/library/methods/DESCRIPTION config.status: creating src/library/methods/Makefile config.status: creating src/library/methods/src/Makefile config.status: creating src/library/profile/Makefile config.status: creating src/library/stats/DESCRIPTION config.status: creating src/library/stats/Makefile config.status: creating src/library/stats/src/Makefile config.status: creating src/library/stats4/DESCRIPTION config.status: creating src/library/stats4/Makefile config.status: creating src/library/splines/DESCRIPTION config.status: creating src/library/splines/Makefile config.status: creating src/library/splines/src/Makefile config.status: creating src/library/tcltk/DESCRIPTION config.status: creating src/library/tcltk/Makefile config.status: creating src/library/tcltk/src/Makefile config.status: creating src/library/tools/DESCRIPTION config.status: creating src/library/tools/Makefile config.status: creating src/library/tools/src/Makefile config.status: creating src/library/utils/DESCRIPTION config.status: creating src/library/utils/Makefile config.status: creating src/main/Makefile config.status: creating src/modules/Makefile config.status: creating src/modules/X11/Makefile config.status: creating src/modules/internet/Makefile config.status: creating src/modules/lapack/Makefile config.status: creating src/modules/vfonts/Makefile 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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