Package: Rhdf5lib

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhdf5lib

StartedAt: 2018-10-16 15:15:13 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 15:18:14 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 181.0 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhdf5lib
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Rhdf5lib’ ...
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
untarring hdf5small_cxx_1.8.19.tar.gz ...
building the szip library...
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
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-apple-darwin15.6.0
checking host system type... x86_64-apple-darwin15.6.0
checking for config x86_64-apple-darwin15.6.0... no
checking for config x86_64-apple-darwin15.6.0... no
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checking for config x86_64-darwin15.6.0... no
checking for config x86_64-apple... no
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checking for config darwin15.6.0... no
checking for config apple... no
checking for config x86_64... no
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking how to run the C preprocessor... clang -E
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... rm: conftest.dSYM: is a directory
BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
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checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... rm: conftest.dSYM: is a directory
no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang object... rm: conftest.dSYM: is a directory
ok
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checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
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checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
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checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
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checking for stdlib.h... (cached) yes
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checking if encoding enabled... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/SZconfig.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making all in src
make  all-am
/bin/sh ../libtool  --tag=CC   --mode=compile clang -DHAVE_CONFIG_H -I.     -Wall -O2 -w  -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c
libtool: compile:  clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c  -fno-common -DPIC -o rice.o
mv -f .deps/rice.Tpo .deps/rice.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile clang -DHAVE_CONFIG_H -I.     -Wall -O2 -w  -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c
libtool: compile:  clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c  -fno-common -DPIC -o sz_api.o
mv -f .deps/sz_api.Tpo .deps/sz_api.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile clang -DHAVE_CONFIG_H -I.     -Wall -O2 -w  -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c
libtool: compile:  clang -DHAVE_CONFIG_H -I. -Wall -O2 -w -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c  -fno-common -DPIC -o encoding.o
mv -f .deps/encoding.Tpo .deps/encoding.Plo
/bin/sh ../libtool  --tag=CC   --mode=link clang  -Wall -O2 -w  -version-info 2:0:0  -o libsz.la -rpath /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo  -lm
libtool: link: ar cru .libs/libsz.a  rice.o sz_api.o encoding.o
libtool: link: ranlib .libs/libsz.a
libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" )
make[1]: Nothing to be done for `all-am'.
building the hdf5 library...
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checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
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checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... i386-apple-darwin15.6.0
checking host system type... i386-apple-darwin15.6.0
checking shell variables initial values... done
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compiler 'gfortran' is GNU gfortran-6.1.0
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checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
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checking dependency style of clang... gcc3
checking if unsupported combinations of configure options are allowed... no
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checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert i386-apple-darwin15.6.0 file names to i386-apple-darwin15.6.0 format... func_convert_file_noop
checking how to convert i386-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
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checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang object... ok
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checking how to truncate binary pipes... /bin/dd bs=4096 count=1
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checking whether the clang linker (/usr/bin/ld) supports shared libraries... yes
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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 which version of public symbols to use by default... v18
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configure: creating ./config.lt
config.lt: creating libtool
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating c++/Makefile
config.status: creating c++/src/Makefile
config.status: creating c++/src/h5c++
config.status: creating src/H5config.h
config.status: executing pubconf commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.19
		  Configured on: Tue Oct 16 15:15:52 EDT 2018
		  Configured by: biocbuild@merida2.bioconductor.org
		 Configure mode: production
		    Host system: i386-apple-darwin15.6.0
	      Uname information: Darwin merida2.bioconductor.org 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11˜1/RELEASE_X86_64 x86_64
		       Byte sex: little-endian
		      Libraries: static
	     Installation point: /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib/src/hdf5/hdf5

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/local/clang4/bin/clang
                         CFLAGS: -Wall -g -O2 -w
                      H5_CFLAGS:  
                      AM_CFLAGS: 
                       CPPFLAGS: -I/Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib/src/hdf5/szip/src/
                    H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: 
               Shared C Library: no
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS: -L/Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib/src/hdf5/szip/src/.libs
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
 	 	Extra libraries: -lsz -lz -ldl -lm 
 		       Archiver: ar
 		 	 Ranlib: ranlib
 	      Debugged Packages: 
		    API Tracing: no

Languages:
----------
                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/local/clang4/bin/clang++
                      C++ Flags: 
                   H5 C++ Flags:  
                   AM C++ Flags: 
             Shared C++ Library: no
             Static C++ Library: yes

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),szip(encoder)
                            MPE: no
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
      Strict File Format Checks: no
   Optimization Instrumentation: no
for d in src  . c++; do                                \
	  if test $d != .; then                                        \
	   (cd $d && make  lib) || exit 1;            \
	  fi;                                                           \
	done
  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       H5Fint.lo
  CC       H5Faccum.lo
  CC       H5Fcwfs.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       H5FDmulti.lo
  CC       H5FDsec2.lo
  CC       H5FDspace.lo
  CC       H5FDstdio.lo
  CC       H5FL.lo
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  CC       H5FS.lo
  CC       H5FScache.lo
  CC       H5FSdbg.lo
  CC       H5FSsection.lo
  CC       H5FSstat.lo
  CC       H5FStest.lo
  CC       H5G.lo
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  CC       H5Gcache.lo
  CC       H5Gcompact.lo
  CC       H5Gdense.lo
  CC       H5Gdeprec.lo
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  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
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  CC       H5HFiter.lo
  CC       H5HFman.lo
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  CC       H5HFtest.lo
  CC       H5HFtiny.lo
  CC       H5HG.lo
  CC       H5HGcache.lo
  CC       H5HGdbg.lo
  CC       H5HGquery.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 -L/Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib/src/hdf5/szip/src/.libs |                  \
		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
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  CC       H5Pfmpl.lo
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  CC       H5Pint.lo
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  CC       H5Pocpypl.lo
  CC       H5Pstrcpl.lo
  CC       H5Ptest.lo
  CC       H5PL.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.o
  CCLD     H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib/src/hdf5/szip/src/.libs |                  \
		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       H5VM.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     libhdf5.la
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Dmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Fmpi.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDdirect.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpi.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5MFdbg.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Smpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Dmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Fmpi.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDdirect.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpi.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5FDmpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5MFdbg.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Smpio.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols
make[2]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
  CXX      H5Exception.lo
  CXX      H5IdComponent.lo
  CXX      H5DataSpace.lo
  CXX      H5PropList.lo
  CXX      H5Library.lo
  CXX      H5FaccProp.lo
  CXX      H5FcreatProp.lo
  CXX      H5LaccProp.lo
  CXX      H5DxferProp.lo
  CXX      H5DcreatProp.lo
  CXX      H5Location.lo
  CXX      H5AbstractDs.lo
  CXX      H5Attribute.lo
  CXX      H5Object.lo
  CXX      H5OcreatProp.lo
  CXX      H5DataType.lo
  CXX      H5AtomType.lo
  CXX      H5PredType.lo
  CXX      H5EnumType.lo
  CXX      H5IntType.lo
  CXX      H5FloatType.lo
  CXX      H5StrType.lo
  CXX      H5ArrayType.lo
  CXX      H5VarLenType.lo
  CXX      H5CompType.lo
  CXX      H5DataSet.lo
  CXX      H5CommonFG.lo
  CXX      H5Group.lo
  CXX      H5File.lo
  CXXLD    libhdf5_cpp.la
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include"
cp hdf5/src/*.h /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include
cp hdf5/c++/src/*.h /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include
mkdir -p "/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/"
cp hdf5/src/.libs/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/
cp hdf5/c++/src/.libs/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/
cp hdf5/szip/src/.libs/libsz.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -Ihdf5/src  -fPIC  -Wall -g -O2  -c Rhdf5lib.c -o Rhdf5lib.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 Rhdf5lib.so Rhdf5lib.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rhdf5lib)