rhdf5 2.6.0
Bernd Fischer
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/rhdf5 | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.6.0.tar.gz'
>>>>>>>
* installing *source* package ‘rhdf5’ ...
** libs
cd hdf5source && \
gunzip -dc hdf5small.tgz | tar xf -;
mv hdf5source/hdf5 .
cd hdf5 && \
./configure CC="llvm-gcc-4.2 -arch x86_64 -std=gnu99" CPP="llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E" CXX="llvm-g++-4.2 -arch x86_64" CXXCPP="llvm-g++-4.2 -arch x86_64 -E" F77="gfortran-4.2 -arch x86_64" --build="" --with-pic
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... bin/install-sh -c -d
checking for gawk... no
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checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... i386-apple-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
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checking for config apple... found
compiler 'llvm-gcc-4.2 -arch x86_64 -std=gnu99' is GNU gcc-4.2.1
No match to get fc_version_info for
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checking whether the C compiler works... yes
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checking dependency style of llvm-gcc-4.2 -arch x86_64 -std=gnu99... gcc3
checking if unsupported combinations of configure options are allowed... no
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checking whether llvm-g++-4.2 -arch x86_64 accepts -g... yes
checking dependency style of llvm-g++-4.2 -arch x86_64... gcc3
checking how to run the C++ preprocessor... llvm-g++-4.2 -arch x86_64 -E
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checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
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checking the maximum length of command line arguments... 196608
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checking whether the shell understands "+="... yes
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checking how to convert i386-apple-darwin10.8.0 file names to toolchain format... func_convert_file_noop
checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r
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checking for archiver @FILE support... no
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checking command to parse /usr/bin/nm output from llvm-gcc-4.2 -arch x86_64 -std=gnu99 object... ok
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checking whether the llvm-gcc-4.2 -arch x86_64 -std=gnu99 linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 dyld
checking how to hardcode library paths into programs... immediate
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checking for parallel support files... skipped
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checking for Default Virtual File Driver definition... yes
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checking whether exception handling functions is checked during data conversions... yes
checking whether data accuracy is guaranteed during data conversions... yes
checking if converting denormalized floating-point values is possible... yes
checking if converting floating-point values to long long is not working... false
checking if the machine has window style path name... no
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checking if accurately converting unsigned long to float values... yes
checking if accurately converting unsigned long long to floating-point values... yes
checking if accurately roundup converting floating-point to unsigned long long values... yes
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checking if correctly converting long double to unsigned int values... yes
checking if compiling unsigned long long to floating-point typecasts work... yes
checking if compiling long long to floating-point typecasts work... yes
checking if converting unsigned long long to long double with precision... yes
checking if overflows normally converting floating-point to integer values... yes
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checking if using special algorithm to convert (unsigned) long to long double values... no
checking if correctly converting long double to (unsigned) long long values... yes
checking if correctly converting (unsigned) long long to long double values... yes
checking if bad code for log2 routine is generated... no
checking if high level library is enabled... yes
checking additional programs should be built... no
checking if deprecated public symbols are available... yes
checking which version of public symbols to use by default... v18
checking Whether to perform strict file format checks... no
checking Whether to have library information embedded in the executables... yes
checking Whether to enable the h5dump packed bits feature... yes
checking if alignment restrictions are strictly enforced... no
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: Sat Apr 5 05:37:06 PDT 2014
Configured by: biocbuild@perceval.fhcrc.org
Configure mode: production
Host system: i386-apple-darwin10.8.0
Uname information: Darwin perceval.fhcrc.org 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3˜1/RELEASE_I386 i386
Byte sex: little-endian
Libraries:
Installation point: /private/tmp/RtmpY9CF6y/R.INSTALL151a734e171bb/rhdf5/src/hdf5/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/llvm-gcc-4.2 -arch x86_64 -std=gnu99 ( (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00))
CFLAGS:
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -w -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
Shared C Library: yes
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
cd hdf5/src && \
make
make all-am
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
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5CS.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Dmpio.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Fmpi.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDdirect.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpio.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpiposix.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5MFdbg.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Obogus.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Smpio.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5TS.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Zszip.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5CS.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Dmpio.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Fmpi.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5FDdirect.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpio.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpiposix.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5MFdbg.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Obogus.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Smpio.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5TS.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Zszip.o) has no symbols
cp hdf5/src/.libs/libhdf5ForBioC.a .
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5A.c -o H5A.o
H5A.c: In function ‘H5Aread_helper_INTEGER’:
H5A.c:153: warning: unused variable ‘herr’
H5A.c: In function ‘H5Aread_helper_FLOAT’:
H5A.c:186: warning: unused variable ‘herr’
H5A.c: In function ‘H5Aread_helper_STRING’:
H5A.c:213: warning: unused variable ‘herr’
H5A.c:220: warning: unused variable ‘herr’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5D.c -o H5D.o
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:116: warning: unused variable ‘status’
H5D.c:113: warning: unused variable ‘status’
H5D.c:128: warning: unused variable ‘herr’
H5D.c:141: warning: unused variable ‘status’
H5D.c:138: warning: unused variable ‘status’
H5D.c:149: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_FLOAT’:
H5D.c:195: warning: unused variable ‘status’
H5D.c:192: warning: unused variable ‘status’
H5D.c:207: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_STRING’:
H5D.c:228: warning: unused variable ‘status’
H5D.c:225: warning: unused variable ‘status’
H5D.c:236: warning: unused variable ‘herr’
H5D.c:244: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_ENUM’:
H5D.c:276: warning: unused variable ‘status’
H5D.c:287: warning: unused variable ‘status’
H5D.c:284: warning: unused variable ‘status’
H5D.c:301: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:352: warning: unused variable ‘status’
H5D.c:349: warning: unused variable ‘status’
H5D.c:374: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:407: warning: unused variable ‘mem_type_id’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5F.c -o H5F.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5G.c -o H5G.o
H5G.c: In function ‘_H5Gget_info’:
H5G.c:66: warning: unused variable ‘herr’
H5G.c: In function ‘_H5Gget_info_by_name’:
H5G.c:113: warning: unused variable ‘herr’
H5G.c: In function ‘_H5Gget_info_by_idx’:
H5G.c:163: warning: unused variable ‘herr’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5I.c -o H5I.o
H5I.c: In function ‘_H5Iget_name’:
H5I.c:24: warning: passing argument 2 of ‘H5Iget_name’ from incompatible pointer type
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5L.c -o H5L.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5O.c -o H5O.o
H5O.c: In function ‘H5Oget_num_attrs’:
H5O.c:13: warning: unused variable ‘herr’
H5O.c: In function ‘_H5Oopen’:
H5O.c:56: warning: implicit declaration of function ‘addHandle’
H5O.c: In function ‘_H5Oclose’:
H5O.c:69: warning: implicit declaration of function ‘removeHandle’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5S.c -o H5S.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5T.c -o H5T.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5constants.c -o H5constants.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c HandleList.cpp -o HandleList.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c h5dump.c -o h5dump.o
h5dump.c: In function ‘opAddToLinfoTree’:
h5dump.c:60: warning: implicit declaration of function ‘H5Oget_num_attrs’
h5dump.c:89: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5dump.c:91: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
h5dump.c:99: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5dump.c:101: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
h5dump.c: In function ‘_h5dump’:
h5dump.c:289: warning: unused variable ‘herr’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c h5ls.c -o h5ls.o
h5ls.c: In function ‘opAddToLinfoList’:
h5ls.c:80: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5ls.c:82: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
h5ls.c:90: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5ls.c:92: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c printdatatype.c -o printdatatype.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c wrap.c -o wrap.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o rhdf5.so H5A.o H5D.o H5F.o H5G.o H5I.o H5L.o H5O.o H5S.o H5T.o H5constants.o HandleList.o h5dump.o h5ls.o h5writeDataFrame.o printdatatype.o wrap.o libhdf5ForBioC.a -lz -lm -L. -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/rhdf5.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"