rhdf5 2.2.0
Bernd Fischer
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/rhdf5 | | Last Changed Rev: 70050 / Revision: 74773 | | Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.2.0.tar.gz'
>>>>>>>
* installing *source* package 'rhdf5' ...
** libs
*** arch - i386
cd hdf5source && \
gunzip -dc hdf5small.tgz | tar xf -;
mv hdf5source/hdf5 .
cd hdf5 && \
./configure CC="gcc -arch i386 -std=gnu99" CPP="gcc -arch i386 -std=gnu99 -E" CXX="g++ -arch i386" CXXCPP="g++ -arch i386 -E" F77="gfortran -arch i386" --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
checking for mawk... 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-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
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 'gcc -arch i386 -std=gnu99' is GNU gcc-4.2.1
compiler 'gfortran' is GNU gfortran-4.2.3
checking for config ./config/site-specific/host-PERCEVAL.FHCRC.ORG... no
checking for config ./config/site-specific/host-FHCRC.ORG... no
checking for config ./config/site-specific/host-ORG... no
checking for gcc... gcc -arch i386 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
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checking dependency style of gcc -arch i386 -std=gnu99... gcc3
checking if unsupported combinations of configure options are allowed... no
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checking whether g++ -arch i386 accepts -g... yes
checking dependency style of g++ -arch i386... gcc3
checking how to run the C++ preprocessor... g++ -arch i386 -E
checking if c++ interface enabled... no
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checking whether make sets $(MAKE)... (cached) yes
checking for tr... /usr/bin/tr
checking if srcdir= and time commands work together... yes
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checking for a sed that does not truncate output... /usr/bin/sed
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checking for ld used by gcc -arch i386 -std=gnu99... /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld
checking if the linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -p
checking the name lister (/usr/bin/nm -p) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert i386-apple-darwin9.8.0 file names to i386-apple-darwin9.8.0 format... func_convert_file_noop
checking how to convert i386-apple-darwin9.8.0 file names to toolchain format... func_convert_file_noop
checking for /usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
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checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... no
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checking command to parse /usr/bin/nm -p output from gcc -arch i386 -std=gnu99 object... ok
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checking for otool64... no
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checking for ANSI C header files... yes
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checking whether the gcc -arch i386 -std=gnu99 linker (/usr/libexec/gcc/i686-apple-darwin9/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin9.8.0 dyld
checking how to hardcode library paths into programs... immediate
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checking whether stripping libraries is possible... yes
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checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes
checking make... checking how make searches directories... VPATH=DIR1 DIR2 ...
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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
checking if right maximum converting floating-point to unsigned long long values... no
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: Mon Mar 25 02:03:49 PDT 2013
Configured by: biocbuild@PERCEVAL.FHCRC.ORG
Configure mode: production
Host system: i386-apple-darwin9.8.0
Uname information: Darwin PERCEVAL.FHCRC.ORG 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4˜1/RELEASE_I386 i386
Byte sex: little-endian
Libraries:
Installation point: /private/tmp/RtmpTvgzT9/R.INSTALL2e7f5eba5cd1/rhdf5/src/hdf5/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc -arch i386 -std=gnu99 ( (GCC) 4.2.1 (Apple Inc. build 5577))
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
warning: no debug symbols in executable (-arch i386)
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
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 .
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5A.c -o H5A.o
H5A.c: In function 'H5Aread_helper_INTEGER':
H5A.c:152: warning: unused variable 'herr'
H5A.c: In function 'H5Aread_helper_FLOAT':
H5A.c:185: warning: unused variable 'herr'
H5A.c: In function 'H5Aread_helper_STRING':
H5A.c:219: warning: unused variable 'herr'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5D.c -o H5D.o
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:108: warning: unused variable 'status'
H5D.c:105: warning: unused variable 'status'
H5D.c:120: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_FLOAT':
H5D.c:142: warning: unused variable 'status'
H5D.c:139: warning: unused variable 'status'
H5D.c:154: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_STRING':
H5D.c:184: warning: unused variable 'status'
H5D.c:181: warning: unused variable 'status'
H5D.c:189: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_ENUM':
H5D.c:222: warning: unused variable 'status'
H5D.c:233: warning: unused variable 'status'
H5D.c:230: warning: unused variable 'status'
H5D.c:247: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:298: warning: unused variable 'status'
H5D.c:295: warning: unused variable 'status'
H5D.c:320: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_COMPOUND':
H5D.c:352: warning: unused variable 'mem_type_id'
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:285: warning: 'arraytype' may be used uninitialized in this function
H5D.c:302: warning: 'buf' may be used uninitialized in this function
H5D.c:274: warning: 'Rval' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5F.c -o H5F.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5L.c -o H5L.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5S.c -o H5S.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5T.c -o H5T.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5constants.c -o H5constants.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -fasm-blocks -c HandleList.cpp -o HandleList.o
HandleList.cpp: In function 'int removeHandle(hid_t)':
HandleList.cpp:175: warning: control reaches end of non-void function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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 3 has type 'long long unsigned int'
h5dump.c:91: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
h5dump.c:99: warning: format '%lu' expects type 'long unsigned int', but argument 3 has type 'long long unsigned int'
h5dump.c:101: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
h5dump.c: In function '_h5dump':
h5dump.c:289: warning: unused variable 'herr'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c h5ls.c -o h5ls.o
h5ls.c: In function 'opAddToLinfoList':
h5ls.c:80: warning: format '%lu' expects type 'long unsigned int', but argument 3 has type 'long long unsigned int'
h5ls.c:82: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
h5ls.c:90: warning: format '%lu' expects type 'long unsigned int', but argument 3 has type 'long long unsigned int'
h5ls.c:92: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c h5writeDataFrame.c -o h5writeDataFrame.o
h5writeDataFrame.c: In function '_h5writeDataFrame':
h5writeDataFrame.c:8: warning: unused variable 'level'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c printdatatype.c -o printdatatype.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c wrap.c -o wrap.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.11-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'rhdf5.Rnw'
** testing if installed package can be loaded
* DONE (rhdf5)
>>>>>>>
>>>>>>> FIXING LINKS FOR rhdf5.buildbin-libdir/rhdf5/libs/i386/rhdf5.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/i386/rhdf5.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/i386/rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/i386/rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/i386/rhdf5.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=rhdf5.buildbin-libdir --libs-only rhdf5_2.2.0.tar.gz'
>>>>>>>
* installing *source* package 'rhdf5' ...
** libs
*** arch - x86_64
cd hdf5source && \
gunzip -dc hdf5small.tgz | tar xf -;
mv hdf5source/hdf5 .
cd hdf5 && \
./configure CC="gcc -arch x86_64 -std=gnu99" CPP="gcc -arch x86_64 -std=gnu99 -E" CXX="g++ -arch x86_64" CXXCPP="g++ -arch x86_64 -E" F77="gfortran -arch x86_64" --build="" --with-pic
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checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
checking shell variables initial values... done
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compiler 'gcc -arch x86_64 -std=gnu99' is GNU gcc-4.2.1
compiler 'gfortran' is GNU gfortran-4.2.3
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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
checking if right maximum converting floating-point to unsigned long long values... no
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
checking if using special algorithm to convert long double to (unsigned) long values... no
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: Mon Mar 25 02:11:11 PDT 2013
Configured by: biocbuild@PERCEVAL.FHCRC.ORG
Configure mode: production
Host system: i386-apple-darwin9.8.0
Uname information: Darwin PERCEVAL.FHCRC.ORG 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4˜1/RELEASE_I386 i386
Byte sex: little-endian
Libraries:
Installation point: /private/tmp/RtmpnxwCsQ/R.INSTALL11e544a27dd03/rhdf5/src/hdf5/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc -arch x86_64 -std=gnu99 ( (GCC) 4.2.1 (Apple Inc. build 5577))
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
warning: no debug symbols in executable (-arch x86_64)
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
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 .
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5A.c -o H5A.o
H5A.c: In function 'H5Aread_helper_INTEGER':
H5A.c:152: warning: unused variable 'herr'
H5A.c: In function 'H5Aread_helper_FLOAT':
H5A.c:185: warning: unused variable 'herr'
H5A.c: In function 'H5Aread_helper_STRING':
H5A.c:219: warning: unused variable 'herr'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5D.c -o H5D.o
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:108: warning: unused variable 'status'
H5D.c:105: warning: unused variable 'status'
H5D.c:120: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_FLOAT':
H5D.c:142: warning: unused variable 'status'
H5D.c:139: warning: unused variable 'status'
H5D.c:154: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_STRING':
H5D.c:184: warning: unused variable 'status'
H5D.c:181: warning: unused variable 'status'
H5D.c:189: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_ENUM':
H5D.c:222: warning: unused variable 'status'
H5D.c:233: warning: unused variable 'status'
H5D.c:230: warning: unused variable 'status'
H5D.c:247: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:298: warning: unused variable 'status'
H5D.c:295: warning: unused variable 'status'
H5D.c:320: warning: unused variable 'herr'
H5D.c: In function 'H5Dread_helper_COMPOUND':
H5D.c:352: warning: unused variable 'mem_type_id'
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:285: warning: 'arraytype' may be used uninitialized in this function
H5D.c:302: warning: 'buf' may be used uninitialized in this function
H5D.c:274: warning: 'Rval' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5F.c -o H5F.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5L.c -o H5L.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5S.c -o H5S.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5T.c -o H5T.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c H5constants.c -o H5constants.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -fasm-blocks -c HandleList.cpp -o HandleList.o
HandleList.cpp: In function 'int removeHandle(hid_t)':
HandleList.cpp:175: warning: control reaches end of non-void function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -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 3 has type 'long long unsigned int'
h5dump.c:91: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
h5dump.c:99: warning: format '%lu' expects type 'long unsigned int', but argument 3 has type 'long long unsigned int'
h5dump.c:101: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
h5dump.c: In function '_h5dump':
h5dump.c:289: warning: unused variable 'herr'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c h5ls.c -o h5ls.o
h5ls.c: In function 'opAddToLinfoList':
h5ls.c:80: warning: format '%lu' expects type 'long unsigned int', but argument 3 has type 'long long unsigned int'
h5ls.c:82: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
h5ls.c:90: warning: format '%lu' expects type 'long unsigned int', but argument 3 has type 'long long unsigned int'
h5ls.c:92: warning: format '%lu' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c h5writeDataFrame.c -o h5writeDataFrame.o
h5writeDataFrame.c: In function '_h5writeDataFrame':
h5writeDataFrame.c:8: warning: unused variable 'level'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c printdatatype.c -o printdatatype.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -g -O2 -Wall -pedantic -c wrap.c -o wrap.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.11-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x86_64
* DONE (rhdf5)
>>>>>>>
>>>>>>> FIXING LINKS FOR rhdf5.buildbin-libdir/rhdf5/libs/x86_64/rhdf5.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/x86_64/rhdf5.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/x86_64/rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/x86_64/rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/x86_64/rhdf5.so"