grimbough / Rhdf5lib

Distribution of the HDF5 library in an R package
https://bioconductor.org/packages/Rhdf5lib/
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[Rosetta] Build failure on H5Tinit.c with Bus error #53

Open barracuda156 opened 1 year ago

barracuda156 commented 1 year ago

Not really sure what causes this:

  CC       H5SL.lo
In file included from H5SL.c:64:
H5private.h: In function 'H5SL_insert_common':
H5private.h:2437:11: warning: 'ret_value' may be used uninitialized [-Wmaybe-uninitialized]
 2437 |     return(ret_value);                                                        \
      |           ^
H5SL.c:760:18: note: 'ret_value' was declared here
  760 |     H5SL_node_t *ret_value;                     /* Return value */
      |                  ^~~~~~~~~
H5private.h: In function 'H5SL_search':
H5private.h:2437:11: warning: 'ret_value' may be used uninitialized [-Wmaybe-uninitialized]
 2437 |     return(ret_value);                                                        \
      |           ^
H5SL.c:1397:11: note: 'ret_value' was declared here
 1397 |     void *ret_value;                            /* Return value */
      |           ^~~~~~~~~
H5private.h: In function 'H5SL_find':
H5private.h:2437:11: warning: 'ret_value' may be used uninitialized [-Wmaybe-uninitialized]
 2437 |     return(ret_value);                                                        \
      |           ^
H5SL.c:1698:18: note: 'ret_value' was declared here
 1698 |     H5SL_node_t *ret_value;                     /* Return value */
      |                  ^~~~~~~~~
  CC       H5SM.lo
  CC       H5SMbtree2.lo
  CC       H5SMcache.lo
  CC       H5SMmessage.lo
  CC       H5SMtest.lo
  CC       H5ST.lo
  CC       H5T.lo
H5T.c: In function 'H5T__create':
H5T.c:3096:38: warning: duplicated 'if' condition [-Wduplicated-cond]
 3096 |                 else if(sizeof(long) == size)
      |                         ~~~~~~~~~~~~~^~~~~~~
H5T.c:3094:37: note: previously used here
 3094 |                 else if(sizeof(int) == size)
      |                         ~~~~~~~~~~~~^~~~~~~
H5T.c: In function 'H5T_nameof':
H5T.c:5246:23: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers]
 5246 |             ret_value = &(dt->path);
      |                       ^
  CC       H5Tarray.lo
  CC       H5Tbit.lo
  CC       H5Tcommit.lo
  CC       H5Tcompound.lo
  CC       H5Tconv.lo
H5Tconv.c:7483:5: warning: "H5T_CONV_INTERNAL_LLONG_LDOUBLE" is not defined, evaluates to 0 [-Wundef]
 7483 | #if H5T_CONV_INTERNAL_LLONG_LDOUBLE
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5Tconv.c:7551:5: warning: "H5T_CONV_INTERNAL_ULLONG_LDOUBLE" is not defined, evaluates to 0 [-Wundef]
 7551 | #if H5T_CONV_INTERNAL_ULLONG_LDOUBLE
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5Tconv.c:8247:5: warning: "H5T_CONV_INTERNAL_LDOUBLE_LLONG" is not defined, evaluates to 0 [-Wundef]
 8247 | #if H5T_CONV_INTERNAL_LDOUBLE_LLONG
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  CC       H5Tcset.lo
  CC       H5Tdbg.lo
  CC       H5Tdeprec.lo
  CC       H5Tenum.lo
  CC       H5Tfields.lo
  CC       H5Tfixed.lo
  CC       H5Tfloat.lo
  CC       H5detect.o
  CCLD     H5detect
ld: warning: option -s is obsolete and being ignored
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -L/opt/local/lib -lMacportsLegacySupport -arch ppc |                  \
        sed -e 's/-L/:/g' -e 's/ //g'`"                               \
     ./H5detect > H5Tinit.c  ||                               \
        (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
        (rm -f H5Tinit.c ; exit 1)
/bin/sh: line 1:  8302 Bus error               LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -L/opt/local/lib -lMacportsLegacySupport -arch ppc |                    sed -e 's/-L/:/g' -e 's/ //g'`" ./H5detect > H5Tinit.c
make[3]: *** [H5Tinit.c] Error 1
make[2]: *** [lib] Error 1
make[1]: *** [lib] Error 1
make: *** [build-hdf5] Error 2
ERROR: compilation failed for package ‘Rhdf5lib’

This is on 10.6.8 Rosetta; I have definitely built Rhdf5lib successfully earlier, however only natively on PowerPC.

barracuda156 commented 1 year ago

@grimbough Still relevant for 1.23.2 built from 511632077dea4150cbf49e79323634cd3170415b