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untarring hdf5small.tgz ...
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configure: creating ./config.status
configure: creating ./config.lt
config.lt: creating libtool
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/H5config.h
config.status: executing default-1 commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
chmod: tools/misc/h5cc: No such file or directory
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.7
Configured on: Thu Apr 12 08:43:40 EDT 2018
Configured by: biocbuild@veracruz1.bioconductor.org
Configure mode: production
Host system: i386-apple-darwin15.6.0
Uname information: Darwin veracruz1.bioconductor.org 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan 9 20:12:05 PST 2018; root:xnu-3248.73.5˜1/RELEASE_X86_64 x86_64
Byte sex: little-endian
Libraries:
Installation point: /Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/local/clang4/bin/clang
CFLAGS: -Wall -g -O2
H5_CFLAGS: -w
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
Shared C Library: no
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
+ for d in src
+ test src '!=' .
+ cd src
+ make lib
CC H5.lo
CC H5checksum.lo
CC H5dbg.lo
CC H5system.lo
CC H5timer.lo
CC H5trace.lo
CC H5A.lo
CC H5Abtree2.lo
CC H5Adense.lo
CC H5Adeprec.lo
CC H5Aint.lo
CC H5Atest.lo
CC H5AC.lo
CC H5B.lo
CC H5Bcache.lo
CC H5Bdbg.lo
CC H5B2.lo
CC H5B2cache.lo
CC H5B2dbg.lo
CC H5B2hdr.lo
CC H5B2int.lo
CC H5B2stat.lo
CC H5B2test.lo
CC H5C.lo
CC H5CS.lo
CC H5D.lo
CC H5Dbtree.lo
CC H5Dchunk.lo
CC H5Dcompact.lo
CC H5Dcontig.lo
CC H5Ddbg.lo
CC H5Ddeprec.lo
CC H5Defl.lo
CC H5Dfill.lo
CC H5Dint.lo
CC H5Dio.lo
CC H5Dlayout.lo
CC H5Dmpio.lo
CC H5Doh.lo
CC H5Dscatgath.lo
CC H5Dselect.lo
CC H5Dtest.lo
CC H5E.lo
CC H5Edeprec.lo
CC H5Eint.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fdbg.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fmpi.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fsuper.lo
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDdirect.lo
CC H5FDfamily.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmpi.lo
CC H5FDmpio.lo
CC H5FDmpiposix.lo
CC H5FDmulti.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDstdio.lo
CC H5FL.lo
CC H5FO.lo
CC H5FS.lo
CC H5FScache.lo
CC H5FSdbg.lo
CC H5FSsection.lo
CC H5FSstat.lo
CC H5FStest.lo
CC H5G.lo
CC H5Gbtree2.lo
CC H5Gcache.lo
CC H5Gcompact.lo
CC H5Gdense.lo
CC H5Gdeprec.lo
CC H5Gent.lo
CC H5Gint.lo
CC H5Glink.lo
CC H5Gloc.lo
CC H5Gname.lo
CC H5Gnode.lo
CC H5Gobj.lo
CC H5Goh.lo
CC H5Groot.lo
CC H5Gstab.lo
CC H5Gtest.lo
CC H5Gtraverse.lo
CC H5HF.lo
CC H5HFbtree2.lo
CC H5HFcache.lo
CC H5HFdbg.lo
CC H5HFdblock.lo
CC H5HFdtable.lo
CC H5HFhdr.lo
CC H5HFhuge.lo
CC H5HFiblock.lo
CC H5HFiter.lo
CC H5HFman.lo
CC H5HFsection.lo
CC H5HFspace.lo
CC H5HFstat.lo
CC H5HFtest.lo
CC H5HFtiny.lo
CC H5HG.lo
CC H5HGcache.lo
CC H5HGdbg.lo
CC H5HL.lo
CC H5HLcache.lo
CC H5HLdbg.lo
CC H5HLint.lo
CC H5HP.lo
CC H5I.lo
CC H5Itest.lo
CC H5L.lo
CC H5Lexternal.lo
CC H5make_libsettings.o
CCLD H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5make_libsettings > H5lib_settings.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5lib_settings.c ; exit 1)
CC H5lib_settings.lo
CC H5MF.lo
CC H5MFaggr.lo
CC H5MFdbg.lo
CC H5MFsection.lo
CC H5MM.lo
CC H5MP.lo
CC H5MPtest.lo
CC H5O.lo
CC H5Oainfo.lo
CC H5Oalloc.lo
CC H5Oattr.lo
CC H5Oattribute.lo
CC H5Obogus.lo
CC H5Obtreek.lo
CC H5Ocache.lo
CC H5Ochunk.lo
CC H5Ocont.lo
CC H5Ocopy.lo
CC H5Odbg.lo
CC H5Odrvinfo.lo
CC H5Odtype.lo
CC H5Oefl.lo
CC H5Ofill.lo
CC H5Oginfo.lo
CC H5Olayout.lo
CC H5Olinfo.lo
CC H5Olink.lo
CC H5Omessage.lo
CC H5Omtime.lo
CC H5Oname.lo
CC H5Onull.lo
CC H5Opline.lo
CC H5Orefcount.lo
CC H5Osdspace.lo
CC H5Oshared.lo
CC H5Ostab.lo
CC H5Oshmesg.lo
CC H5Otest.lo
CC H5Ounknown.lo
CC H5P.lo
CC H5Pacpl.lo
CC H5Pdapl.lo
CC H5Pdcpl.lo
CC H5Pdeprec.lo
CC H5Pdxpl.lo
CC H5Pfapl.lo
CC H5Pfcpl.lo
CC H5Pfmpl.lo
CC H5Pgcpl.lo
CC H5Pint.lo
CC H5Plapl.lo
CC H5Plcpl.lo
CC H5Pocpl.lo
CC H5Pocpypl.lo
CC H5Pstrcpl.lo
CC H5Ptest.lo
CC H5R.lo
CC H5Rdeprec.lo
CC H5RC.lo
CC H5RS.lo
CC H5S.lo
CC H5Sall.lo
CC H5Sdbg.lo
CC H5Shyper.lo
CC H5Smpio.lo
CC H5Snone.lo
CC H5Spoint.lo
CC H5Sselect.lo
CC H5Stest.lo
CC H5SL.lo
CC H5SM.lo
CC H5SMbtree2.lo
CC H5SMcache.lo
CC H5SMmessage.lo
CC H5SMtest.lo
CC H5ST.lo
CC H5T.lo
CC H5Tarray.lo
CC H5Tbit.lo
CC H5Tcommit.lo
CC H5Tcompound.lo
CC H5Tconv.lo
CC H5Tcset.lo
CC H5Tdbg.lo
CC H5Tdeprec.lo
CC H5Tenum.lo
CC H5Tfields.lo
CC H5Tfixed.lo
CC H5Tfloat.lo
CC H5detect-H5detect.o
CCLD H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5detect > H5Tinit.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5Tinit.c ; exit 1)
CC H5Tinit.lo
CC H5Tnative.lo
CC H5Toffset.lo
CC H5Toh.lo
CC H5Topaque.lo
CC H5Torder.lo
CC H5Tpad.lo
CC H5Tprecis.lo
CC H5Tstrpad.lo
CC H5Tvisit.lo
CC H5Tvlen.lo
CC H5TS.lo
CC H5V.lo
CC H5WB.lo
CC H5Z.lo
CC H5Zdeflate.lo
CC H5Zfletcher32.lo
CC H5Znbit.lo
CC H5Zshuffle.lo
CC H5Zszip.lo
CC H5Zscaleoffset.lo
CC H5Ztrans.lo
CCLD libhdf5ForBioC.la
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5CS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Dmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Fmpi.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDdirect.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpiposix.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5MFdbg.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Obogus.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Smpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5TS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Zszip.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5CS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Dmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Fmpi.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDdirect.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpiposix.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5MFdbg.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Obogus.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Smpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5TS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Zszip.o) has no symbols
configure: HDF5_INCLUDE=hdf5/src
configure: HDF5_LIB=hdf5/src/.libs/libhdf5ForBioC.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5.c -o H5.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5A.c -o H5A.o
H5A.c:153:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, buf );
^
H5A.c:186:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, buf );
^
H5A.c:213:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
H5A.c:220:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5D.c -o H5D.o
H5D.c:220:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:217:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:232:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^
H5D.c:268:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:265:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
^
H5D.c:273:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, intbuf );
^
H5D.c:254:16: warning: variable 'intbuf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:258:9: note: uninitialized use occurs here
if (intbuf == 0) {
^˜˜˜˜˜
H5D.c:254:12: note: remove the 'if' if its condition is always true
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:244:17: note: initialize the variable 'intbuf' to silence this warning
void* intbuf;
^
= NULL
H5D.c:438:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:435:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
^
H5D.c:450:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^
H5D.c:471:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:468:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtype_id);
^
H5D.c:479:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, bufSTR );
^
H5D.c:490:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, bufSTR );
^
H5D.c:525:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tenum_insert (enumtype, st, &i);
^
H5D.c:536:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:533:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
^
H5D.c:550:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^
H5D.c:603:13: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:600:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
^
H5D.c:625:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^
H5D.c:619:18: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:625:94: note: uninitialized use occurs here
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^˜˜
H5D.c:619:14: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:612:18: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:625:94: note: uninitialized use occurs here
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^˜˜
H5D.c:612:14: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:607:15: note: initialize the variable 'buf' to silence this warning
void * buf;
^
= NULL
H5D.c:660:9: warning: unused variable 'mem_type_id' [-Wunused-variable]
hid_t mem_type_id = -1;
^
24 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5E.c -o H5E.o
H5E.c:76:3: warning: unused label 'Rf_error' [-Wunused-label]
error:
^˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
^
H5E.c:87:16: warning: unused variable 'indent' [-Wunused-variable]
const int indent = 4;
^
H5E.c:112:3: warning: unused label 'Rf_error' [-Wunused-label]
error:
^˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
^
H5E.c:121:12: warning: unused variable 'eee' [-Wunused-variable]
herr_t eee = H5Ewalk(estack_id, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data);
^
H5E.c:153:12: warning: unused variable 'eee' [-Wunused-variable]
herr_t eee = H5Ewalk(estack_id, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data);
^
5 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5F.c -o H5F.o
H5F.c:116:33: warning: incompatible pointer types passing 'char (*)[size + 1]' to parameter of type 'char *' [-Wincompatible-pointer-types]
size = H5Fget_name( obj_id, &name, size+1);
^˜˜˜˜
hdf5/src/H5Fpublic.h:174:48: note: passing argument to parameter 'name' here
H5_DLL ssize_t H5Fget_name(hid_t obj_id, char *name, size_t size);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5G.c -o H5G.o
H5G.c:66:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Gget_info( group_id, &group_info );
^
H5G.c:113:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Gget_info_by_name( loc_id, group_name, &group_info, H5P_DEFAULT );
^
H5G.c:163:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Gget_info_by_idx( loc_id, group_name, index_type, order, n, &group_info, H5P_DEFAULT );
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5I.c -o H5I.o
H5I.c:24:24: warning: incompatible pointer types passing 'char (*)[st + 1]' to parameter of type 'char *' [-Wincompatible-pointer-types]
H5Iget_name( obj_id, &name, st+1 );
^˜˜˜˜
hdf5/src/H5Ipublic.h:85:44: note: passing argument to parameter 'name' here
H5_DLL ssize_t H5Iget_name(hid_t id, char *name/*out*/, size_t size);
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5L.c -o H5L.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5O.c -o H5O.o
H5O.c:13:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aiterate( obj_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &opAcount, &n);
^
H5O.c:56:3: warning: implicit declaration of function 'addHandle' is invalid in C99 [-Wimplicit-function-declaration]
addHandle(hid);
^
H5O.c:69:5: warning: implicit declaration of function 'removeHandle' is invalid in C99 [-Wimplicit-function-declaration]
removeHandle(object_id);
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5P.c -o H5P.o
H5P.c:688:16: warning: unused variable 'libver_low' [-Wunused-variable]
H5F_libver_t libver_low = INTEGER(_libver_low)[0];
^
H5P.c:689:16: warning: unused variable 'libver_high' [-Wunused-variable]
H5F_libver_t libver_high = INTEGER(_libver_high)[0];
^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5S.c -o H5S.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5T.c -o H5T.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c H5constants.c -o H5constants.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c HandleList.cpp -o HandleList.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c HandleListWrap.c -o HandleListWrap.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c h5dump.c -o h5dump.o
h5dump.c:85:27: warning: implicit declaration of function 'H5Oget_num_attrs' is invalid in C99 [-Wimplicit-function-declaration]
newElement->num_attrs = H5Oget_num_attrs(oid);
^
h5dump.c:114:27: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%lu", size[newElement->rank-1]);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
h5dump.c:116:38: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%s x %lu", tmp, size[i]);
˜˜˜ ^˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
h5dump.c:124:22: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
h5dump.c:126:34: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%s x %lu", tmp, maxsize[i]);
˜˜˜ ^˜˜˜˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
h5dump.c:314:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToLinfoTree, &data );
^
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c h5ls.c -o h5ls.o
h5ls.c:99:22: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%lu", size[newElement->rank-1]);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
h5ls.c:101:34: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%s x %lu", tmp, size[i]);
˜˜˜ ^˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
h5ls.c:109:24: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
h5ls.c:111:36: warning: format specifies type 'unsigned long' but the argument has type 'hsize_t' (aka 'unsigned long long') [-Wformat]
sprintf(tmp, "%s x %lu", tmp, maxsize[i]);
˜˜˜ ^˜˜˜˜˜˜˜˜˜
%llu
/usr/include/secure/_stdio.h:47:56: note: expanded from macro 'sprintf'
__builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__)
^˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c h5writeDataFrame.c -o h5writeDataFrame.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c printdatatype.c -o printdatatype.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -Wall -g -O2 -c wrap.c -o wrap.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5T.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5writeDataFrame.o printdatatype.o wrap.o hdf5/src/.libs/libhdf5ForBioC.a -lz -lm -L. -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/include"
cp hdf5/src/*.h /Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/include
mkdir -p "/Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/lib"
cp hdf5/src/.libs/libhdf5ForBioC.a /Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/lib/libhdf5.a
installing to /Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rhdf5)
