Multiple platform build/check report for BioC 3.7 - BUILD BIN report for Rhdf5lib on merida2

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### Running command:
###
###   rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhdf5lib_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rhdf5lib.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhdf5lib.buildbin-libdir Rhdf5lib_1.2.1.tar.gz'
>>>>>>> 

* 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
checking for config apple-darwin15.6.0... no
checking for config apple-darwin15.6.0... no
checking for config x86_64-darwin15.6.0... no
checking for config x86_64-darwin15.6.0... no
checking for config x86_64-apple... no
checking for config darwin15.6.0... no
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
checking how to recognize dependent libraries... pass_all
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
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for build mode... production
checking for math library support... no
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for error_at_line... no
checking for working memcmp... yes
checking for vprintf... yes
checking for _doprnt... no
checking for memset... yes
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 /private/tmp/RtmpkKJcVg/R.INSTALL106d579d62912/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...
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 make supports nested variables... (cached) yes
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
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config i386-apple-darwin15.6.0... no
checking for config i386-apple-darwin15.6.0... no
checking for config apple-darwin15.6.0... no
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checking for config i386-darwin15.6.0... no
checking for config i386-apple... no
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checking for config darwin15.6.0... no
checking for config apple... found
compiler 'gfortran' is GNU gfortran-6.1.0
checking for config ./config/site-specific/host-merida2.bioconductor.org... no
checking for config ./config/site-specific/host-bioconductor.org... no
checking for config ./config/site-specific/host-org... 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 if unsupported combinations of configure options are allowed... no
checking if Fortran interface enabled... no
checking if Fortran 2003 interface enabled... no
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
checking dependency style of clang++... gcc3
checking how to run the C++ preprocessor... clang++ -E
checking if c++ interface enabled... yes
checking if clang++ needs old style header files in includes... no
checking if clang++ can handle namespaces... yes
checking if clang++ has offsetof extension... yes
checking if clang++ can handle static cast... yes
checking if high level library is enabled... yes
checking for perl... perl
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
checking for tr... /usr/bin/tr
checking if srcdir= and time commands work together... 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... 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
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
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
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... clang -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... clang++ -E
checking for ld used by clang++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the clang++ linker (/usr/bin/ld) supports shared libraries... yes
checking for clang++ option to produce PIC... -fno-common -DPIC
checking if clang++ PIC flag -fno-common -DPIC works... yes
checking if clang++ static flag -static works... no
checking if clang++ supports -c -o file.o... yes
checking if clang++ supports -c -o file.o... (cached) yes
checking whether the clang++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking if we should install only statically linked executables... no
checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes
checking whether make will build with undefined variables... yes
checking for production mode... production
checking for ceil in -lm... yes
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checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
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checking for SZ_BufftoBuffCompress in -lsz... yes
checking for szlib encoder... yes
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checking for library containing clock_gettime... no
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checking if the compiler understands  __inline__... yes
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checking for __func__ extension... yes
checking for __FUNCTION__ extension... yes
checking for C99 designated initialization support... yes
checking how to print long long... %ld and %lu
checking Threads support system scope... yes
checking for debug flags... none
checking whether function stack tracking is enabled... no
checking whether metadata trace file code is enabled... no
checking for API tracing... no
checking for instrumented library... no
checking whether to clear file buffers... yes
checking whether a memory checking tool will be used... no
checking for parallel support files... skipped
checking whether O_DIRECT is declared... no
checking for posix_memalign... yes
checking if the direct I/O virtual file driver (VFD) is enabled... no
checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin
checking whether exception handling functions is checked during data conversions... yes
checking whether data accuracy is guaranteed during data conversions... yes
checking if the machine has window style path name... no
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 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 if alignment restrictions are strictly enforced... no
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: Wed Oct 17 02:02:32 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: /private/tmp/RtmpkKJcVg/R.INSTALL106d579d62912/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/private/tmp/RtmpkKJcVg/R.INSTALL106d579d62912/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/private/tmp/RtmpkKJcVg/R.INSTALL106d579d62912/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
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  CC       H5Ftest.lo
  CC       H5FD.lo
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  CC       H5FDdirect.lo
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  CC       H5FDint.lo
  CC       H5FDlog.lo
  CC       H5FDmpi.lo
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  CC       H5FL.lo
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  CC       H5FSdbg.lo
  CC       H5FSsection.lo
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  CC       H5G.lo
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  CC       H5Gdense.lo
  CC       H5Gdeprec.lo
  CC       H5Gent.lo
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  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       H5HFtiny.lo
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  CC       H5HGdbg.lo
  CC       H5HGquery.lo
  CC       H5HL.lo
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  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/private/tmp/RtmpkKJcVg/R.INSTALL106d579d62912/Rhdf5lib/src/hdf5/szip/src/.libs |                  \
		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
	 ./H5make_libsettings > H5lib_settings.c  ||                               \
	    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
	    (rm -f H5lib_settings.c ; exit 1)
  CC       H5lib_settings.lo
  CC       H5MF.lo
  CC       H5MFaggr.lo
  CC       H5MFdbg.lo
  CC       H5MFsection.lo
  CC       H5MM.lo
  CC       H5MP.lo
  CC       H5MPtest.lo
  CC       H5O.lo
  CC       H5Oainfo.lo
  CC       H5Oalloc.lo
  CC       H5Oattr.lo
  CC       H5Oattribute.lo
  CC       H5Obogus.lo
  CC       H5Obtreek.lo
  CC       H5Ocache.lo
  CC       H5Ochunk.lo
  CC       H5Ocont.lo
  CC       H5Ocopy.lo
  CC       H5Odbg.lo
  CC       H5Odrvinfo.lo
  CC       H5Odtype.lo
  CC       H5Oefl.lo
  CC       H5Ofill.lo
  CC       H5Oginfo.lo
  CC       H5Olayout.lo
  CC       H5Olinfo.lo
  CC       H5Olink.lo
  CC       H5Omessage.lo
  CC       H5Omtime.lo
  CC       H5Oname.lo
  CC       H5Onull.lo
  CC       H5Opline.lo
  CC       H5Orefcount.lo
  CC       H5Osdspace.lo
  CC       H5Oshared.lo
  CC       H5Ostab.lo
  CC       H5Oshmesg.lo
  CC       H5Otest.lo
  CC       H5Ounknown.lo
  CC       H5P.lo
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  CC       H5R.lo
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  CC       H5Sall.lo
  CC       H5Sdbg.lo
  CC       H5Shyper.lo
  CC       H5Smpio.lo
  CC       H5Snone.lo
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  CC       H5SMbtree2.lo
  CC       H5SMcache.lo
  CC       H5SMmessage.lo
  CC       H5SMtest.lo
  CC       H5ST.lo
  CC       H5T.lo
  CC       H5Tarray.lo
  CC       H5Tbit.lo
  CC       H5Tcommit.lo
  CC       H5Tcompound.lo
  CC       H5Tconv.lo
  CC       H5Tcset.lo
  CC       H5Tdbg.lo
  CC       H5Tdeprec.lo
  CC       H5Tenum.lo
  CC       H5Tfields.lo
  CC       H5Tfixed.lo
  CC       H5Tfloat.lo
  CC       H5detect.o
  CCLD     H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/private/tmp/RtmpkKJcVg/R.INSTALL106d579d62912/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 "/Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include"
cp hdf5/src/*.h /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include
cp hdf5/c++/src/*.h /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/include
mkdir -p "/Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/"
cp hdf5/src/.libs/libhdf5.a /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/
cp hdf5/c++/src/.libs/libhdf5_cpp.a /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/
cp hdf5/szip/src/.libs/libsz.a /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/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 /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/libhdf5.a /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/Rhdf5lib.buildbin-libdir/Rhdf5lib/libs
** R
** inst
** 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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs//Rhdf5lib.so"
BUILD BIN report for Rhdf5lib on merida2

Summary

Command output
