Displaying 13 results from an estimated 13 matches for "lhdf5".
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hdf5
2011 Feb 18
1
hdf5 library install issue
...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 ANSI C... none needed
checking for library containing inflate... -lz
checking for library containing H5open... -lhdf5
checking for sufficiently new HDF5... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/share/apps/R-core-2.12.1_SHLIB/lib64/R/include
-I/share/apps/HDF5/include -I/usr/local/include -fpic -g -O2 -c
hdf5.c -o hdf5.o
gcc -std=gnu99 -shared -...
1999 Aug 16
1
configure / linking problem when using hdf5
.../unix/libunix.a ../appl/libappl.a ../nmath/libmath.a -lSM -lICE -L/usr/local/X11R6.3/lib -R/usr/local/X11R6.3/lib -lX11 -lsocket -lnsl -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -L/opt/SUNWspro/SC4.2/lib -L/usr/ccs/lib -L/usr/lib /opt/SUNWspro/SC4.2/lib/libM77.a -lF77 -lsunmath -lm -lcx -lreadline -lhdf5 -lz -ldl -ltermcap -lm
Undefined first referenced
symbol in file
compress2 /usr/local/lib/libhdf5.a(H5Z.o)
ld: fatal: Symbol referencing errors. No output written to ../../bin/R.X11
-------------
Which happens because there was an -L/usr/local/X11R6.3/lib
be...
2010 Mar 03
1
linking hdf5, requires setting LD_LIBRARY_PATH
...irectly in src of the hdf5 package):
gcc -I/home/jbullard/projects/me/R-builder/lib64/R/include
-I/home/jbullard/scratch/hdf5_install/include -I/usr/local/include -fpic
-g -O2 -std=gnu99 -c hdf5.c -o hdf5.o
gcc -shared -L/usr/local/lib64 -o hdf5.so hdf5.o
-L/home/jbullard/scratch/hdf5_install/lib -lhdf5 -lz -lm
-L/home/jbullard/projects/me/R-builder/lib64/R/lib -lR
I then start R and get the following error:
Error in dyn.load("hdf5.so") :
unable to load shared library '/home/jbullard/scratch/hdf5/src/hdf5.so':
libhdf5.so.6: cannot open shared object file: No such file or di...
2000 Jan 21
1
Compiling error R-0.90.1
...suggestion are greatly appreciated.
Alvaro Novo
ps. I am including here lines from ./configure output that I found
potentially "problematic" or informative:
checking whether the C compiler (gcc ) is a cross-compiler... no
checking for sin in -lmoto... (cached) no
checking for main in -lhdf5... (cached) no
checking for main in -ldxml... (cached) no
checking for main in -lblas... (cached) no
checking for opendir in -ldir... (cached) no
checking for dl.h... (cached) no
checking for floatingpoint.h... (cached) no
checking for ieeefp.h... (cached) no
checking for blkcnt_t... (cached) no
ch...
1999 Oct 20
0
[szimeras@irisa.fr: R installation problem]
...uggestions about this problem?
Thank you very much for your time
Dr. Stelios Zimeras
Below I give you the results from the ./configure running (all the
others are yes)
checking whether gcc needs -traditional... no
checking for g77... no
checking for sin in -lmoto... no
chechecking for main in -lhdf5... no
cking for main in -lncurses... no
checking for main in -ldxml... no
checking for main in -lblas_risc... no
checking for rl_callback_read_char in -lreadline... no
checking for ANSI C header files... no
checking for vfork.h... no
checking for working vfork... no
checking for __setfpucw... no
ch...
2002 Mar 01
1
HDF 5 install - how to pass configure flag to the R CMD command
...es
checking whether we are cross compiling... no
checking for executable suffix...
checking for object suffix... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for library containing inflate... -lz
checking for library containing H5open... -lhdf5
checking for sufficiently new HDF5... yes
configure: creating ./config.status
config.status: creating src/Makevars
But how can I give the configure command line flag to the R CMD INSTALL
command?
Raphael
On Friday 01 March 2002 10:07, you wrote:
> As part of the HDF5 package, you have util...
1999 Oct 12
1
Compilation problem with R
...ver 65.1 in my UNIX machine, but I have some
difficulties. In particular
running the ./configure I have the following results (I give only the
no, all the others are yes)
checking whether gcc needs -traditional... no
checking for g77... no
checking for sin in -lmoto... no
chechecking for main in -lhdf5... no
cking for main in -lncurses... no
checking for main in -ldxml... no
checking for main in -lblas_risc... no
checking for rl_callback_read_char in -lreadline... no
checking for ANSI C header files... no
checking for vfork.h... no
checking for working vfork... no
checking for __setfpucw... no
ch...
2002 Mar 01
1
Building hdf5 on Windows
.../
#ifdef __cplusplus
extern "C"
#endif
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
char H5open ();
int
main ()
{
H5open ();
;
return 0;
}
configure:1809: gcc -o conftest.exe -g -O2 conftest.c -lhdf5 -lm >&5
C:\xtra\R\compile\bin\..\lib\gcc-lib\mingw32\2.95.3-6\..\..\..\..\mingw32\bi
n\ld.exe: cannot find -lhdf5
configure:1812: $? = 1
configure: failed program was:
#line 1790 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error...
2010 May 20
0
Installation problem with "geepack"
...{ return v_ + n_; }
^
icpc -shared -i-dynamic -mieee-fp -prec-div -O2 -axSSE2,SSE3,SSEE3,SSE4.1,SSE4.2,AVX -lpthread -o geepack.so famstr.o gee2.o geesubs.o inter.o ordgee.o param.o utils.o -L/usr/global/R/2.11.0/lib64/R/lib -lR -L/usr/global/hdf5/1.8.3/lib -Wl,-R/usr/global/hdf5/1.8.3/lib -lhdf5 -lhdf5_hl -lcurl
installing to /gpfs/work/xzt1/my_Rlibs/geepack/libs
** R
** data
** inst
** preparing package for lazy loading
Loading required package: survival
Loading required package: splines
** help
*** installing help indices
** building package indices ...
** testing if installed package ca...
2000 Jan 29
1
HDF5 as a module
...:49:19 1.30
--- aclocal.m4 2000/01/29 00:22:35
***************
*** 543,570 ****
AC_MSG_WARN([I found f2c but not libf2c, or libF77 and libI77])
fi])
dnl
- dnl R_LIB_HDF5
- dnl
- AC_DEFUN(R_LIB_HDF5,
- [ AC_CHECK_LIB(hdf5, main,
- [ ac_save_LIBS="${LIBS}"
- LIBS="-lhdf5 ${LIBS}"
- AC_CACHE_CHECK([for HDF5 version >= 1.2],
- r_cv_lib_hdf5,
- AC_TRY_LINK(
- [#include <hdf5.h>],
- [ H5T_pers_t convtype = H5T_PERS_SOFT;
- H5Tclose ((hid_t) 0);],
- r_cv_lib_hdf5=yes,
- r_cv_lib_hdf5=no))
- if test "${r_cv_lib_hdf5}&...
1998 Dec 08
0
R compile problems with AIX
...0; }
configure:1890: checking for main in -ltermcap
configure:1905: gcc -o conftest -g -O2 conftest.c -ltermcap -lm 1>&5
configure:1979: checking for dlopen in -ldl
configure:1998: gcc -o conftest -g -O2 conftest.c -ldl -ltermcap -lm 1>&5
configure:2027: checking for main in -lhdf5
configure:2042: gcc -o conftest -g -O2 conftest.c -lhdf5 -ldl -ltermcap -lm 1>&5
collect2: ld returned 255 exit status
ld: 0706-006 Cannot find or open library file: -l hdf5
ld:open(): No such file or directory
configure: failed program was:
#line 2035 "configure"
#include &qu...
1998 Dec 08
0
R compile problems with AIX
...0; }
configure:1890: checking for main in -ltermcap
configure:1905: gcc -o conftest -g -O2 conftest.c -ltermcap -lm 1>&5
configure:1979: checking for dlopen in -ldl
configure:1998: gcc -o conftest -g -O2 conftest.c -ldl -ltermcap -lm 1>&5
configure:2027: checking for main in -lhdf5
configure:2042: gcc -o conftest -g -O2 conftest.c -lhdf5 -ldl -ltermcap -lm 1>&5
collect2: ld returned 255 exit status
ld: 0706-006 Cannot find or open library file: -l hdf5
ld:open(): No such file or directory
configure: failed program was:
#line 2035 "configure"
#include &qu...
1999 Jun 09
4
packages with FORTRAN code
Recent sensible changes to the dynload mechanism have made an old
problem resurface: how should we deal with packages which contain
Fortran code and may need to be linked against additional libraries
such as -lf2c?
The current consensus is that extra Fortran libraries maybe needed are
handled via the make variable FLIBS, and that `-lf2c' or `-lg2c' are
added by default if g77 is used.