[MINC-users] MINC installation issue

[Thomas Funck]

Hi,

I had minc installed and working but something went wrong with my libraries and so now I am trying to reinstall it (from source). However for the life of me I can't find the correct HDF5 version to install it with. 

I've tried older versions of HDF5 (1.6.9) and  I get the following errors when trying to use the minc2 library:

/usr/bin/ld: warning: libhdf5.so.7, needed by /usr/local/neuro/lib//libminc2.so, not found (try using -rpath or -rpath-link)
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Acreate1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eauto_is_v2'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eget_auto1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Aiterate1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Dcreate1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Gcreate1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eset_auto2'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Gopen2'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Acreate2'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eget_auto2'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Pget_filter1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Dopen1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Eset_auto1'
/usr/local/neuro/lib//libminc2.so: undefined reference to `H5Gopen1'



On the other hand, when I install HDF5(1.8.9) I get the following errors:


libsrc/hdf_convenience.c: In function ‘hdf_id_add’:
libsrc/hdf_convenience.c:83:9: error: too few arguments to function ‘H5Gopen2’
/usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_var_add’:
libsrc/hdf_convenience.c:185:9: error: too few arguments to function ‘H5Dopen2’
/usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_put_dimorder’:
libsrc/hdf_convenience.c:621:5: error: too few arguments to function ‘H5Acreate2’
/usr/local/neuro/include/H5Apublic.h:44:16: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_set_length’:
libsrc/hdf_convenience.c:928:28: error: too few arguments to function ‘H5Acreate2’
/usr/local/neuro/include/H5Apublic.h:44:16: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_attput’:
libsrc/hdf_convenience.c:1106:37: error: too few arguments to function ‘H5Dcreate2’
/usr/local/neuro/include/H5Dpublic.h:104:14: note: declared here
libsrc/hdf_convenience.c:1110:13: error: incompatible type for argument 2 of ‘H5Aiterate2’
/usr/local/neuro/include/H5Apublic.h:74:16: note: expected ‘H5_index_t’ but argument is of type ‘unsigned int *’
libsrc/hdf_convenience.c:1110:13: error: incompatible type for argument 3 of ‘H5Aiterate2’
/usr/local/neuro/include/H5Apublic.h:74:16: note: expected ‘H5_iter_order_t’ but argument is of type ‘herr_t (*)(hid_t,  const char *, void *)’
libsrc/hdf_convenience.c:1110:13: error: too few arguments to function ‘H5Aiterate2’
/usr/local/neuro/include/H5Apublic.h:74:16: note: declared here
libsrc/hdf_convenience.c:1189:9: error: too few arguments to function ‘H5Acreate2’
/usr/local/neuro/include/H5Apublic.h:44:16: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_vardef’:
libsrc/hdf_convenience.c:1384:9: error: too few arguments to function ‘H5Dcreate2’
/usr/local/neuro/include/H5Dpublic.h:104:14: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_copy_attr’:
libsrc/hdf_convenience.c:2060:4: error: too few arguments to function ‘H5Acreate2’
/usr/local/neuro/include/H5Apublic.h:44:16: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_open_dsets’:
libsrc/hdf_convenience.c:2122:6: error: too few arguments to function ‘H5Gopen2’
/usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here
libsrc/hdf_convenience.c:2133:6: error: too few arguments to function ‘H5Dopen2’
/usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_open’:
libsrc/hdf_convenience.c:2209:9: error: too few arguments to function ‘H5Dopen2’
/usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here
libsrc/hdf_convenience.c:2240:9: error: too few arguments to function ‘H5Dopen2’
/usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here
libsrc/hdf_convenience.c:2248:9: error: too few arguments to function ‘H5Dopen2’
/usr/local/neuro/include/H5Dpublic.h:108:14: note: declared here
libsrc/hdf_convenience.c:2259:5: error: too few arguments to function ‘H5Gopen2’
/usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here
libsrc/hdf_convenience.c:2265:5: error: too few arguments to function ‘H5Gopen2’
/usr/local/neuro/include/H5Gpublic.h:78:14: note: declared here
libsrc/hdf_convenience.c: In function ‘hdf_create’:
libsrc/hdf_convenience.c:2299:5: error: too few arguments to function ‘H5Gcreate2’
/usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here
libsrc/hdf_convenience.c:2303:5: error: too few arguments to function ‘H5Gcreate2’
/usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here
libsrc/hdf_convenience.c:2308:5: error: too few arguments to function ‘H5Gcreate2’
/usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here
libsrc/hdf_convenience.c:2313:5: error: too few arguments to function ‘H5Gcreate2’
/usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here
libsrc/hdf_convenience.c:2318:5: error: too few arguments to function ‘H5Gcreate2’
/usr/local/neuro/include/H5Gpublic.h:75:14: note: declared here

Any suggestion what HDF5 library I should use?

Many thanks for the help!

Thomas