Build Octave-3.0.0 with HDF5-1.8.0

[David Kredba]

Hello.

I am building Octave-3.0.0 on my LFS/BLFS system
(www.linuxfromscratch.org) with hdf5-1.8.0.

Gcc is 4.2.3.

The compilation fails with :

g++ -c  -fPIC -I. -I.. -I../liboctave -I../src -I../libcruft/misc
-DHAVE_CONFIG_H -mieee-fp -Wall -W -Wshadow -Wold-style-cast -g -O2
ls-hdf5.cc -o pic/ls-hdf5.o
ls-hdf5.cc: In function ‘bool hdf5_check_attr(hid_t, const char*)’:
ls-hdf5.cc:146: error: invalid conversion from ‘herr_t (**)(hid_t, void*)’
to ‘hid_t’
ls-hdf5.cc:146: error: invalid conversion from ‘void**’ to ‘herr_t
(**)(hid_t, void*)’
/usr/include/H5Epublic.h:173: error: too few arguments to function ‘herr_t
H5Eget_auto2(hid_t, herr_t (**)(hid_t, void*), void**)’
ls-hdf5.cc:146: error: at this point in file
/usr/include/H5Epublic.h:174: error: too few arguments to function ‘herr_t
H5Eset_auto2(hid_t, herr_t (*)(hid_t, void*), void*)’
ls-hdf5.cc:147: error: at this point in file
ls-hdf5.cc:159: error: invalid conversion from ‘herr_t (*)(hid_t, void*)’
to ‘hid_t’
ls-hdf5.cc:159: error: invalid conversion from ‘void*’ to ‘herr_t
(*)(hid_t, void*)’
/usr/include/H5Epublic.h:174: error: too few arguments to function ‘herr_t
H5Eset_auto2(hid_t, herr_t (*)(hid_t, void*), void*)’
ls-hdf5.cc:159: error: at this point in file
/usr/include/H5Gpublic.h: In function ‘herr_t hdf5_read_next_data(hid_t,
const char*, void*)’:
/usr/include/H5Gpublic.h:77: error: too few arguments to function ‘hid_t
H5Gopen2(hid_t, const char*, hid_t)’
ls-hdf5.cc:225: error: at this point in file
/usr/include/H5Dpublic.h:98: error: too few arguments to function ‘hid_t
H5Dopen2(hid_t, const char*, hid_t)’
ls-hdf5.cc:235: error: at this point in file
/usr/include/H5Dpublic.h:98: error: too few arguments to function ‘hid_t
H5Dopen2(hid_t, const char*, hid_t)’
ls-hdf5.cc:307: error: at this point in file
/usr/include/H5Gpublic.h: In function ‘std::string
read_hdf5_data(std::istream&, const std::string&, bool&, octave_value&,
std::string&)’:
/usr/include/H5Gpublic.h:77: error: too few arguments to function ‘hid_t
H5Gopen2(hid_t, const char*, hid_t)’
ls-hdf5.cc:550: error: at this point in file
/usr/include/H5Apublic.h: In function ‘herr_t hdf5_add_attr(hid_t, const
char*)’:
/usr/include/H5Apublic.h:45: error: too few arguments to function ‘hid_t
H5Acreate2(hid_t, const char*, hid_t, hid_t, hid_t, hid_t)’
ls-hdf5.cc:597: error: at this point in file
/usr/include/H5Dpublic.h: In function ‘int save_hdf5_empty(hid_t, const
char*, dim_vector)’:
/usr/include/H5Dpublic.h:95: error: too few arguments to function ‘hid_t
H5Dcreate2(hid_t, const char*, hid_t, hid_t, hid_t, hid_t, hid_t)’
ls-hdf5.cc:644: error: at this point in file
/usr/include/H5Dpublic.h: In function ‘int load_hdf5_empty(hid_t, const
char*, dim_vector&)’:
/usr/include/H5Dpublic.h:98: error: too few arguments to function ‘hid_t
H5Dopen2(hid_t, const char*, hid_t)’
ls-hdf5.cc:674: error: at this point in file
/usr/include/H5Gpublic.h: In function ‘bool add_hdf5_data(hid_t, const
octave_value&, const std::string&, const std::string&, bool, bool)’:
/usr/include/H5Gpublic.h:75: error: too few arguments to function ‘hid_t
H5Gcreate2(hid_t, const char*, hid_t, hid_t, hid_t)’
ls-hdf5.cc:752: error: at this point in file
/usr/include/H5Dpublic.h:95: error: too few arguments to function ‘hid_t
H5Dcreate2(hid_t, const char*, hid_t, hid_t, hid_t, hid_t, hid_t)’
ls-hdf5.cc:766: error: at this point in file
make[2]: *** [pic/ls-hdf5.o] Error 1
make[2]: Leaving directory `/root/octave-3.0.0/src'
make[1]: *** [src] Error 2
make[1]: Leaving directory `/root/octave-3.0.0'
make: *** [all] Error 2


The output from the configure script is :

./configure --prefix=/usr --sysconfdir=/etc

./configure --prefix=/usr --sysconfdir=/etc
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
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... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for AIX... no
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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking for library containing strerror... none required
defining man1dir to be $(mandir)/man1
defining man1ext to be .1
defining infofile to be $(infodir)/octave.info
defining octincludedir to be $(includedir)/octave-$(version)
defining fcnfiledir to be $(datadir)/octave/$(version)/m
defining localfcnfiledir to be $(datadir)/octave/site/m
defining localapifcnfiledir to be $(datadir)/octave/site/$(api_version)/m
defining localverfcnfiledir to be $(datadir)/octave/$(version)/site/m
defining octlibdir to be $(libdir)/octave-$(version)
defining archlibdir to be
$(libexecdir)/octave/$(version)/exec/$(canonical_host_type)
defining localarchlibdir to be
$(libexecdir)/octave/site/exec/$(canonical_host_type)
defining localapiarchlibdir to be
$(libexecdir)/octave/$(api_version)/site/exec/$(canonical_host_type)
defining localverarchlibdir to be
$(libexecdir)/octave/$(version)/site/exec/$(canonical_host_type)
defining octfiledir to be
$(libexecdir)/octave/$(version)/oct/$(canonical_host_type)
defining localoctfiledir to be
$(libexecdir)/octave/site/oct/$(canonical_host_type)
defining localapioctfiledir to be
$(libexecdir)/octave/site/oct/$(api_version)/$(canonical_host_type)
defining localveroctfiledir to be
$(libexecdir)/octave/$(version)/site/oct/$(canonical_host_type)
defining imagedir to be $(datadir)/octave/$(version)/imagelib
configure: defining __NO_MATH_INLINES avoids buggy GNU libc exp function
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for C++ support for new friend template declaration... yes
checking if C++ library is ISO compliant... yes
checking for broken C++ reinterpret_cast... no
checking for nm... nm
checking C++ ABI version used by g++... gnu_v3
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking how to run the C preprocessor... gcc -E
checking whether gcc needs -traditional... no
checking whether gcc accepts -mieee-fp... yes
configure: adding -mieee-fp to XTRA_CFLAGS
checking whether g++ accepts -mieee-fp... yes
configure: adding -mieee-fp to XTRA_CXXFLAGS
checking whether g++ prepends an underscore to external names... no
checking for sin in -lm... yes
checking qhull/qhull_a.h usability... yes
checking qhull/qhull_a.h presence... yes
checking for qhull/qhull_a.h... yes
checking for qh_qhull in -lqhull... yes
checking for pcre-config... yes
checking whether pcre.h defines the macros we need... yes
checking for regexec... yes
checking for gzclearerr in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for H5Pcreate in -lhdf5... yes
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Gget_num_objs in -lhdf5... yes
checking fftw3.h usability... yes
checking fftw3.h presence... yes
checking for fftw3.h... yes
checking for fftw_plan_dft_1d in -lfftw3... yes
checking glpk/glpk.h usability... no
checking glpk/glpk.h presence... no
checking for glpk/glpk.h... no
checking glpk.h usability... yes
checking glpk.h presence... yes
checking for glpk.h... yes
checking for glp_lpx_simplex in -lglpk... no
checking for _glp_lpx_simplex in -lglpk... yes
checking for curl_easy_escape in -lcurl... yes
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking for IEEE 754 data format... yes
checking for ranlib... ranlib
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran...
-L/usr/lib/gcc/i686-pc-linux-gnu/4.2.3
-L/usr/lib/gcc/i686-pc-linux-gnu/4.2.3/../../.. -lhdf5 -lz -lgfortranbegin
-lgfortran -lm
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
checking whether gfortran accepts -mieee-fp... yes
adding -mieee-fp to FFLAGS
configure: defining FFLAGS to be -O -mieee-fp
checking whether gfortran accepts -ffloat-store... yes
setting F77_FLOAT_STORE_FLAG to -ffloat-store
checking for sgemm_... no
checking for ATL_xerbla in -latlas... yes
checking for sgemm_ in -lf77blas... yes
checking for cblas_dgemm in -lcblas... yes
checking for cheev_... no
checking for cheev_ in -llapack... no
checking for cheev_ in -llapack_rs6k... no
checking for amd_postorder in -lamd... yes
checking for camd_postorder in -lcamd... no
checking suitesparse/umfpack.h usability... no
checking suitesparse/umfpack.h presence... no
checking for suitesparse/umfpack.h... no
checking ufsparse/umfpack.h usability... no
checking ufsparse/umfpack.h presence... no
checking for ufsparse/umfpack.h... no
checking umfpack/umfpack.h usability... no
checking umfpack/umfpack.h presence... no
checking for umfpack/umfpack.h... no
checking umfpack.h usability... yes
checking umfpack.h presence... yes
checking for umfpack.h... yes
checking for umfpack_zi_get_determinant in -lumfpack... yes
checking for UMFPACK seperate complex matrix and rhs split... yes
checking suitesparse/colamd.h usability... no
checking suitesparse/colamd.h presence... no
checking for suitesparse/colamd.h... no
checking ufsparse/colamd.h usability... no
checking ufsparse/colamd.h presence... no
checking for ufsparse/colamd.h... no
checking colamd/colamd.h usability... no
checking colamd/colamd.h presence... no
checking for colamd/colamd.h... no
checking colamd.h usability... yes
checking colamd.h presence... yes
checking for colamd.h... yes
checking for colamd in -lcolamd... yes
checking suitesparse/ccolamd.h usability... no
checking suitesparse/ccolamd.h presence... no
checking for suitesparse/ccolamd.h... no
checking ufsparse/ccolamd.h usability... no
checking ufsparse/ccolamd.h presence... no
checking for ufsparse/ccolamd.h... no
checking ccolamd/ccolamd.h usability... no
checking ccolamd/ccolamd.h presence... no
checking for ccolamd/ccolamd.h... no
checking ccolamd.h usability... yes
checking ccolamd.h presence... yes
checking for ccolamd.h... yes
checking for ccolamd in -lccolamd... yes
checking suitesparse/cholmod.h usability... no
checking suitesparse/cholmod.h presence... no
checking for suitesparse/cholmod.h... no
checking ufsparse/cholmod.h usability... no
checking ufsparse/cholmod.h presence... no
checking for ufsparse/cholmod.h... no
checking cholmod/cholmod.h usability... yes
checking cholmod/cholmod.h presence... yes
checking for cholmod/cholmod.h... yes
checking for cholmod_start in -lcholmod... yes
checking suitesparse/cs.h usability... no
checking suitesparse/cs.h presence... no
checking for suitesparse/cs.h... no
checking ufsparse/cs.h usability... no
checking ufsparse/cs.h presence... no
checking for ufsparse/cs.h... no
checking cxsparse/cs.h usability... yes
checking cxsparse/cs.h presence... yes
checking for cxsparse/cs.h... yes
checking for cs_di_sqr in -lcxsparse... yes
configure: defining FPICFLAG to be -fPIC
configure: defining CPICFLAG to be -fPIC
configure: defining CXXPICFLAG to be -fPIC
configure: defining SHLEXT to be so
configure: defining SHLLIB to be $(SHLEXT)
configure: defining SHLBIN to be
configure: defining SHLEXT_VER to be $(SHLEXT).$(version)
configure: defining SHLLIB_VER to be $(SHLLIB).$(version)
configure: defining SHLBIN_VER to be $(SHLBIN).$(version)
configure: defining SHLLINKEXT to be
configure: defining LIBPRE to be lib
configure: defining SH_LD to be $(CXX)
configure: defining SH_LDFLAGS to be -shared
configure: defining DL_LD to be $(SH_LD)
configure: defining DL_LDFLAGS to be $(SH_LDFLAGS)
configure: defining MKOCTFILE_DL_LDFLAGS to be -shared -Wl,-Bsymbolic
configure: defining SONAME_FLAGS to be -Wl,-soname -Wl,$@
configure: defining NO_OCT_FILE_STRIP to be false
configure: defining RLD_FLAG to be -Wl,-rpath -Wl,$(octlibdir)
configure: defining TEMPLATE_AR to be $(AR)
configure: defining TEMPLATE_ARFLAGS to be rc
configure: defining CRUFT_DLL_DEFS to be
configure: defining OCTAVE_DLL_DEFS to be
configure: defining OCTINTERP_DLL_DEFS to be
configure: defining library_path_var to be LD_LIBRARY_PATH
checking for gethostname... yes
checking for getpwnam... yes
checking for mode_t... yes
checking for off_t... yes
checking for pid_t... yes
checking for size_t... yes
checking for uid_t in sys/types.h... yes
checking for dev_t... yes
checking for ino_t... yes
checking for nlink_t... yes
checking for nlink_t... (cached) yes
checking for long long int... yes
checking for unsigned long long int... yes
checking for sigset_t... yes
checking for sig_atomic_t... yes
checking for short... yes
checking size of short... 2
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 4
checking for long long... yes
checking size of long long... 8
checking for working alloca.h... yes
checking for alloca... yes
checking for an ANSI C-conforming const... yes
checking whether including <string> defines NPOS... no
checking whether <new> defines placement delete operator... yes
checking whether C++ supports dynamic auto arrays... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking whether time.h and sys/time.h may both be included... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking curses.h usability... yes
checking curses.h presence... yes
checking for curses.h... yes
checking direct.h usability... no
checking direct.h presence... no
checking for direct.h... no
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking ieeefp.h usability... no
checking ieeefp.h presence... no
checking for ieeefp.h... no
checking for inttypes.h... (cached) yes
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 for memory.h... (cached) yes
checking nan.h usability... no
checking nan.h presence... no
checking for nan.h... no
checking ncurses.h usability... yes
checking ncurses.h presence... yes
checking for ncurses.h... yes
checking poll.h usability... yes
checking poll.h presence... yes
checking for poll.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking sys/poll.h usability... yes
checking sys/poll.h presence... yes
checking for sys/poll.h... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking for sys/stat.h... (cached) 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 for sys/types.h... (cached) yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking sys/utime.h usability... no
checking sys/utime.h presence... no
checking for sys/utime.h... no
checking termcap.h usability... yes
checking termcap.h presence... yes
checking for termcap.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking varargs.h usability... no
checking varargs.h presence... no
checking for varargs.h... no
checking sstream usability... yes
checking sstream presence... yes
checking for sstream... yes
checking termio.h usability... yes
checking termio.h presence... yes
checking for termio.h... yes
checking sgtty.h usability... yes
checking sgtty.h presence... yes
checking for sgtty.h... yes
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking fnmatch.h usability... yes
checking fnmatch.h presence... yes
checking for fnmatch.h... yes
checking conio.h usability... no
checking conio.h presence... no
checking for conio.h... no
checking for fnmatch... yes
checking for glob... yes
checking for atexit... yes
checking for basename... yes
checking for bcopy... yes
checking for bzero... yes
checking for canonicalize_file_name... yes
checking for chmod... yes
checking for dup2... yes
checking for endgrent... yes
checking for endpwent... yes
checking for execvp... yes
checking for fcntl... yes
checking for fork... yes
checking for getcwd... yes
checking for getegid... yes
checking for geteuid... yes
checking for getgid... yes
checking for getgrent... yes
checking for getgrgid... yes
checking for getgrnam... yes
checking for getpgrp... yes
checking for getpid... yes
checking for getppid... yes
checking for getpwent... yes
checking for getpwuid... yes
checking for gettimeofday... yes
checking for getuid... yes
checking for getwd... yes
checking for _kbhit... no
checking for kill... yes
checking for lgamma... yes
checking for link... yes
checking for localtime_r... yes
checking for lstat... yes
checking for memmove... yes
checking for mkdir... yes
checking for mkfifo... yes
checking for mkstemp... yes
checking for on_exit... yes
checking for pipe... yes
checking for poll... yes
checking for putenv... yes
checking for raise... yes
checking for readlink... yes
checking for realpath... yes
checking for rename... yes
checking for resolvepath... no
checking for rindex... yes
checking for rmdir... yes
checking for round... yes
checking for select... yes
checking for setgrent... yes
checking for setlocale... yes
checking for setpwent... yes
checking for setvbuf... yes
checking for sigaction... yes
checking for siglongjmp... yes
checking for sigpending... yes
checking for sigprocmask... yes
checking for sigsuspend... yes
checking for snprintf... yes
checking for stat... yes
checking for strcasecmp... yes
checking for strdup... yes
checking for strerror... yes
checking for stricmp... no
checking for strncasecmp... yes
checking for strnicmp... no
checking for strptime... yes
checking for strsignal... yes
checking for symlink... yes
checking for tempnam... yes
checking for tgamma... yes
checking for umask... yes
checking for uname... yes
checking for unlink... yes
checking for usleep... yes
checking for utime... yes
checking for vfprintf... yes
checking for vsprintf... yes
checking for vsnprintf... yes
checking for waitpid... yes
checking for _chmod... no
checking for _snprintf... no
checking for x_utime... no
checking for _utime32... no
checking for strftime... yes
checking whether strptime is broken... no
checking whether putenv uses malloc... no
checking mach-o/dyld.h usability... no
checking mach-o/dyld.h presence... no
checking for mach-o/dyld.h... no
checking for shl_load in -ldld... no
checking for shl_load... no
checking for shl_findsym... no
checking for LoadLibrary in -lwsock32... no
checking for LoadLibrary... no
checking for dlopen in -ldl... yes
checking for dlopen... yes
checking for dlsym... yes
checking for dlerror... yes
checking for dlclose... yes
checking whether g++ accepts -rdynamic... yes
checking for struct timeval... yes
checking whether gettimeofday can't accept two arguments... no
checking for finite... yes
checking for isnan... yes
checking for isinf... yes
checking for copysign... yes
checking for signbit... no
checking for _finite... no
checking for _isnan... no
checking for _copysign... no
checking whether signbit is declared... yes
checking for acosh... yes
checking for asinh... yes
checking for atanh... yes
checking for erf... yes
checking for erfc... yes
checking for exp2... yes
checking for log2... yes
checking for struct stat.st_blksize... yes
checking for struct stat.st_blocks... yes
checking for struct stat.st_rdev... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for struct tm.tm_zone... yes
checking whether closedir returns void... no
checking for struct group.gr_passwd... no
checking if mkdir takes one argument... no
checking for tputs in -lncurses... yes
checking for rl_set_keyboard_input_timeout in -lreadline... yes
checking for struct exception in math.h... yes
checking return type of signal handlers... void
checking whether sys_siglist is declared... yes
checking for type of signal functions... posix
checking if signal handlers must be reinstalled when invoked... no
checking for getrusage... yes
checking for times... yes
checking for gawk... gawk
checking for gfind... no
checking for find... find
checking for a usable sed... /bin/sed
checking for perl... perl
checking for python... python
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
defining LFLAGS to be -t -I
checking for bison... bison -y
checking whether ln -s works... yes
checking for nm... (cached) nm
checking for a BSD-compatible install... /usr/bin/install -c
checking for desktop-file-install... no
checking for gnuplot... gnuplot
checking for less... less
checking for gperf... gperf
checking for gs... gs
checking for makeinfo... makeinfo
checking for texi2dvi... texi2dvi
checking for texi2pdf... texi2pdf
configure: defining UGLY_DEFS to be -DPACKAGE_NAME=\\\\\"\\\\\"
-DPACKAGE_TARNAME=\\\\\"\\\\\" -DPACKAGE_VERSION=\\\\\"\\\\\"
-DPACKAGE_STRING=\\\\\"\\\\\" -DPACKAGE_BUGREPORT=\\\\\"\\\\\"
-DOCTAVE_SOURCE=1 -D_GNU_SOURCE=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1
-DSEPCHAR=\':\' -DSEPCHAR_STR=\\\\\":\\\\\" -D__NO_MATH_INLINES=1
-DCXX_NEW_FRIEND_TEMPLATE_DECL=1 -DCXX_ISO_COMPLIANT_LIBRARY=1
-DCXX_ABI=gnu_v3 -DHAVE_LIBM=1 -DHAVE_QHULL=1 -DHAVE_PCRE=1
-DHAVE_REGEXEC=1 -DHAVE_REGEX=1 -DHAVE_ZLIB_H=1 -DHAVE_ZLIB=1
-DHAVE_HDF5_H=1 -DHAVE_HDF5=1 -DHAVE_H5GGET_NUM_OBJS=1 -DHAVE_FFTW3=1
-DHAVE_GLPK_H=1 -DHAVE_GLPK=1 -DHAVE_CURL_CURL_H=1 -DHAVE_CURL=1
-DHAVE_IEEE754_DATA_FORMAT=1 -DF77_FUNC\(name,NAME\)=name\ \#\#\ _
-DF77_FUNC_\(name,NAME\)=name\ \#\#\ _ -DHAVE_BLAS=1 -DHAVE_UMFPACK_H=1
-DHAVE_UMFPACK=1 -DUMFPACK_SEPARATE_SPLIT=1 -DHAVE_COLAMD_H=1
-DHAVE_COLAMD=1 -DHAVE_CCOLAMD_H=1 -DHAVE_CCOLAMD=1
-DHAVE_CHOLMOD_CHOLMOD_H=1 -DHAVE_CHOLMOD=1 -DHAVE_CXSPARSE_CS_H=1
-DHAVE_CXSPARSE=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPWNAM=1 -DHAVE_DEV_T=1
-DHAVE_INO_T=1 -DHAVE_NLINK_T=1 -DHAVE_NLINK_T=1 -DHAVE_LONG_LONG_INT=1
-DHAVE_UNSIGNED_LONG_LONG_INT=1 -DHAVE_SIGSET_T=1 -DHAVE_SIG_ATOMIC_T=1
-DSIZEOF_SHORT=2 -DSIZEOF_INT=4 -DSIZEOF_LONG=4 -DSIZEOF_LONG_LONG=8
-DHAVE_ALLOCA_H=1 -DHAVE_ALLOCA=1 -DNPOS=std::string::npos
-DHAVE_PLACEMENT_DELETE=1 -DHAVE_DYNAMIC_AUTO_ARRAYS=1 -DSTDC_HEADERS=1
-DHAVE_DIRENT_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_SYS_WAIT_H=1
-DHAVE_ASSERT_H=1 -DHAVE_CURSES_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FCNTL_H=1
-DHAVE_FLOAT_H=1 -DHAVE_GRP_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_LIMITS_H=1
-DHAVE_LOCALE_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NCURSES_H=1 -DHAVE_POLL_H=1
-DHAVE_PWD_H=1 -DHAVE_STDINT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_SYS_IOCTL_H=1 -DHAVE_SYS_PARAM_H=1 -DHAVE_SYS_POLL_H=1
-DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_SELECT_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_SYS_TIME_H=1 -DHAVE_SYS_TIMES_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_UTSNAME_H=1 -DHAVE_TERMCAP_H=1 -DHAVE_UNISTD_H=1
-DHAVE_UTIME_H=1 -DHAVE_SSTREAM=1 -DHAVE_TERMIO_H=1 -DHAVE_SGTTY_H=1
-DHAVE_GLOB_H=1 -DHAVE_FNMATCH_H=1 -DHAVE_FNMATCH=1 -DHAVE_GLOB=1
-DHAVE_ATEXIT=1 -DHAVE_BASENAME=1 -DHAVE_BCOPY=1 -DHAVE_BZERO=1
-DHAVE_CANONICALIZE_FILE_NAME=1 -DHAVE_CHMOD=1 -DHAVE_DUP2=1
-DHAVE_ENDGRENT=1 -DHAVE_ENDPWENT=1 -DHAVE_EXECVP=1 -DHAVE_FCNTL=1
-DHAVE_FORK=1 -DHAVE_GETCWD=1 -DHAVE_GETEGID=1 -DHAVE_GETEUID=1
-DHAVE_GETGID=1 -DHAVE_GETGRENT=1 -DHAVE_GETGRGID=1 -DHAVE_GETGRNAM=1
-DHAVE_GETPGRP=1 -DHAVE_GETPID=1 -DHAVE_GETPPID=1 -DHAVE_GETPWENT=1
-DHAVE_GETPWUID=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_GETUID=1 -DHAVE_GETWD=1
-DHAVE_KILL=1 -DHAVE_LGAMMA=1 -DHAVE_LINK=1 -DHAVE_LOCALTIME_R=1
-DHAVE_LSTAT=1 -DHAVE_MEMMOVE=1 -DHAVE_MKDIR=1 -DHAVE_MKFIFO=1
-DHAVE_MKSTEMP=1 -DHAVE_ON_EXIT=1 -DHAVE_PIPE=1 -DHAVE_POLL=1
-DHAVE_PUTENV=1 -DHAVE_RAISE=1 -DHAVE_READLINK=1 -DHAVE_REALPATH=1
-DHAVE_RENAME=1 -DHAVE_RINDEX=1 -DHAVE_RMDIR=1 -DHAVE_ROUND=1
-DHAVE_SELECT=1 -DHAVE_SETGRENT=1 -DHAVE_SETLOCALE=1 -DHAVE_SETPWENT=1
-DHAVE_SETVBUF=1 -DHAVE_SIGACTION=1 -DHAVE_SIGLONGJMP=1
-DHAVE_SIGPENDING=1 -DHAVE_SIGPROCMASK=1 -DHAVE_SIGSUSPEND=1
-DHAVE_SNPRINTF=1 -DHAVE_STAT=1 -DHAVE_STRCASECMP=1 -DHAVE_STRDUP=1
-DHAVE_STRERROR=1 -DHAVE_STRNCASECMP=1 -DHAVE_STRPTIME=1
-DHAVE_STRSIGNAL=1 -DHAVE_SYMLINK=1 -DHAVE_TEMPNAM=1 -DHAVE_TGAMMA=1
-DHAVE_UMASK=1 -DHAVE_UNAME=1 -DHAVE_UNLINK=1 -DHAVE_USLEEP=1
-DHAVE_UTIME=1 -DHAVE_VFPRINTF=1 -DHAVE_VSPRINTF=1 -DHAVE_VSNPRINTF=1
-DHAVE_WAITPID=1 -DHAVE_STRFTIME=1 -DHAVE_LIBDL=1 -DHAVE_DLOPEN=1
-DHAVE_DLSYM=1 -DHAVE_DLERROR=1 -DHAVE_DLCLOSE=1 -DHAVE_DLOPEN_API=1
-DENABLE_DYNAMIC_LINKING=1 -DHAVE_TIMEVAL=1 -DHAVE_FINITE=1 -DHAVE_ISNAN=1
-DHAVE_ISINF=1 -DHAVE_COPYSIGN=1 -DHAVE_DECL_SIGNBIT=1 -DHAVE_ACOSH=1
-DHAVE_ASINH=1 -DHAVE_ATANH=1 -DHAVE_ERF=1 -DHAVE_ERFC=1 -DHAVE_EXP2=1
-DHAVE_LOG2=1 -DHAVE_STRUCT_STAT_ST_BLKSIZE=1
-DHAVE_STRUCT_STAT_ST_BLOCKS=1 -DHAVE_STRUCT_STAT_ST_RDEV=1
-DHAVE_STRUCT_TM_TM_ZONE=1 -DHAVE_TM_ZONE=1 -DUSE_READLINE=1
-DEXCEPTION_IN_MATH=1 -DRETSIGTYPE=void -DHAVE_DECL_SYS_SIGLIST=1
-DHAVE_POSIX_SIGNALS=1 -DRETSIGTYPE_IS_VOID=1 -DHAVE_GETRUSAGE=1
-DHAVE_TIMES=1 -DYYTEXT_POINTER=1 -DGNUPLOT_BINARY=\\\\\"gnuplot\\\\\"
checking whether gcc accepts -Wall... yes
adding -Wall to WARN_CFLAGS
checking whether gcc accepts -W... yes
adding -W to WARN_CFLAGS
checking whether gcc accepts -Wshadow... yes
adding -Wshadow to WARN_CFLAGS
checking whether g++ accepts -Wall... yes
adding -Wall to WARN_CXXFLAGS
checking whether g++ accepts -W... yes
adding -W to WARN_CXXFLAGS
checking whether g++ accepts -Wshadow... yes
adding -Wshadow to WARN_CXXFLAGS
checking whether g++ accepts -Wold-style-cast... yes
adding -Wold-style-cast to WARN_CXXFLAGS
configure: creating ./config.status
config.status: creating Makefile
config.status: creating octMakefile
config.status: creating Makeconf
config.status: creating test/Makefile
config.status: creating doc/Makefile
config.status: creating doc/faq/Makefile
config.status: creating doc/interpreter/Makefile
config.status: creating doc/liboctave/Makefile
config.status: creating doc/refcard/Makefile
config.status: creating emacs/Makefile
config.status: creating examples/Makefile
config.status: creating liboctave/Makefile
config.status: creating liboctave/oct-types.h
config.status: creating src/Makefile
config.status: creating src/mxarray.h
config.status: creating libcruft/Makefile
config.status: creating libcruft/Makerules
config.status: creating libcruft/amos/Makefile
config.status: creating libcruft/blas/Makefile
config.status: creating libcruft/daspk/Makefile
config.status: creating libcruft/dasrt/Makefile
config.status: creating libcruft/dassl/Makefile
config.status: creating libcruft/fftpack/Makefile
config.status: creating libcruft/lapack/Makefile
config.status: creating libcruft/minpack/Makefile
config.status: creating libcruft/misc/Makefile
config.status: creating libcruft/odepack/Makefile
config.status: creating libcruft/ordered-qz/Makefile
config.status: creating libcruft/quadpack/Makefile
config.status: creating libcruft/ranlib/Makefile
config.status: creating libcruft/slatec-fn/Makefile
config.status: creating libcruft/slatec-err/Makefile
config.status: creating libcruft/villad/Makefile
config.status: creating libcruft/blas-xtra/Makefile
config.status: creating libcruft/lapack-xtra/Makefile
config.status: creating config.h
config.status: config.h is unchanged
=== configuring in scripts (/root/octave-3.0.0/scripts)
configure: running /bin/sh ./configure '--prefix=/usr'
'--sysconfdir=/etc' 'CFLAGS=-g -O2' 'CXXFLAGS=-g -O2'
--cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
configure: creating ./config.status
config.status: creating Makefile
config.status: creating audio/Makefile
config.status: creating control/Makefile
config.status: creating control/base/Makefile
config.status: creating control/hinf/Makefile
config.status: creating control/obsolete/Makefile
config.status: creating control/system/Makefile
config.status: creating control/util/Makefile
config.status: creating deprecated/Makefile
config.status: creating elfun/Makefile
config.status: creating finance/Makefile
config.status: creating general/Makefile
config.status: creating geometry/Makefile
config.status: creating image/Makefile
config.status: creating io/Makefile
config.status: creating linear-algebra/Makefile
config.status: creating miscellaneous/Makefile
config.status: creating optimization/Makefile
config.status: creating path/Makefile
config.status: creating pkg/Makefile
config.status: creating plot/Makefile
config.status: creating polynomial/Makefile
config.status: creating quaternion/Makefile
config.status: creating set/Makefile
config.status: creating signal/Makefile
config.status: creating sparse/Makefile
config.status: creating specfun/Makefile
config.status: creating special-matrix/Makefile
config.status: creating startup/Makefile
config.status: creating statistics/Makefile
config.status: creating statistics/base/Makefile
config.status: creating statistics/distributions/Makefile
config.status: creating statistics/models/Makefile
config.status: creating statistics/tests/Makefile
config.status: creating strings/Makefile
config.status: creating time/Makefile
config.status: creating testfun/Makefile
configure:

Octave is now configured for i686-pc-linux-gnu

  Source directory:     .
  Installation prefix:  /usr
  C compiler:           gcc  -mieee-fp  -Wall -W -Wshadow -g -O2
  C++ compiler:         g++  -mieee-fp  -Wall -W -Wshadow -Wold-style-cast
-g -O2
  Fortran compiler:     gfortran -O -mieee-fp
  Fortran libraries:     -L/usr/lib/gcc/i686-pc-linux-gnu/4.2.3
-L/usr/lib/gcc/i686-pc-linux-gnu/4.2.3/../../.. -lhdf5 -lz
-lgfortranbegin -lgfortran -lm
  BLAS libraries:       -lcblas -lf77blas -latlas
  FFTW libraries:       -lfftw3
  GLPK libraries:       -lglpk
  UMFPACK libraries:    -lumfpack
  AMD libraries:        -lamd
  CAMD libraries:
  COLAMD libraries:     -lcolamd
  CCOLAMD libraries:    -lccolamd
  CHOLMOD libraries:    -lcholmod
  CXSPARSE libraries:   -lcxsparse
  HDF5 libraries:       -lhdf5
  CURL libraries:       -lcurl
  REGEX libraries:      -L/usr/lib -lpcre
  QHULL libraries:      -lqhull
  LIBS:                 -lreadline  -lncurses -ldl -lhdf5 -lz -lm
  Default pager:        less
  gnuplot:              gnuplot

  Do internal array bounds checking:  false
  Build static libraries:             false
  Build shared libraries:             true
  Dynamic Linking:                    true (dlopen)
  Include support for GNU readline:   true
  64-bit array dims and indexing:     false


Did I used proper version of HDF5? Configure is not complained about, so I
hope not.

Please help me solve this issue.

Thank you.

Best regards, David Kredba.

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[John W. Eaton]

On  5-Apr-2008, David Kredba wrote:

| I am building Octave-3.0.0 on my LFS/BLFS system
| (www.linuxfromscratch.org) with hdf5-1.8.0.
|
| Gcc is 4.2.3.
|
| The compilation fails with :
|
| g++ -c  -fPIC -I. -I.. -I../liboctave -I../src -I../libcruft/misc
| -DHAVE_CONFIG_H -mieee-fp -Wall -W -Wshadow -Wold-style-cast -g -O2
| ls-hdf5.cc -o pic/ls-hdf5.o
| ls-hdf5.cc: In function ?bool hdf5_check_attr(hid_t, const char*)?:
| ls-hdf5.cc:146: error: invalid conversion from ?herr_t (**)(hid_t, void*)?
| to ?hid_t?

| Did I used proper version of HDF5? Configure is not complained about, so I
| hope not.

The configure script generally doesn't check for version information,
but tries to check for required features as that is more likely to
work in the future.  Unfortunately, this appears to be a case where a
change in a library implementation breaks Octave.  Perhaps someone will
submit a patch for Octave that will fix the problem.  You might be
able to avoid it by using an earlier version of the HDF5 library, but
it would be better if Octave could be fixed to work with old and new
versions of HDF5.

jwe

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[Thomas Weber-8]

On 05/04/08 16:40 -0400, John W. Eaton wrote:
> The configure script generally doesn't check for version information,
> but tries to check for required features as that is more likely to
> work in the future.  Unfortunately, this appears to be a case where a
> change in a library implementation breaks Octave.  Perhaps someone will
> submit a patch for Octave that will fix the problem.  You might be
> able to avoid it by using an earlier version of the HDF5 library, but
> it would be better if Octave could be fixed to work with old and new
> versions of HDF5.

Incompatible change in HDF5. A work-around is proposed at
http://www.mail-archive.com/meep-discuss@.../msg01486.html

        ./configure CPPFLAGS="-DH5_USE_16_API"

        Thomas
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