Mike Smith
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rhdf5lib |
| Branch: RELEASE_3_10 |
| Last Commit: 16d91c4 |
| Last Changed Date: 2019-10-29 13:10:31 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:45:36 -0400 (Wed, 15 Apr 2020).
| Package 1430/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rhdf5lib 1.8.0 Mike Smith
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | [ OK ] | OK | OK | OK | |
| Package: Rhdf5lib |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rhdf5lib |
| StartedAt: 2020-04-14 18:05:17 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 18:09:28 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 251.3 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/3.6/Resources/library’
* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
'config' variable 'F77' is deprecated
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++ -std=gnu++11 accepts -g... yes
checking whether C++ compiler accepts -w... yes
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
untarring hdf5small_cxx_hl_1.10.5.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 -fPIC -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 -fPIC -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 -fPIC -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 -fPIC -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 -fPIC -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 -fPIC -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 -fPIC -version-info 2:0:0 -o libsz.la -rpath /Users/biocbuild/bbs-3.10-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'.
Making install in src
../bin/install-sh -c -d '/Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib'
/bin/sh ../libtool --mode=install /usr/bin/install -c libsz.la '/Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /usr/bin/install -c .libs/libsz.lai /Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libsz.a /Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: ranlib /Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
../bin/install-sh -c -d '/Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include'
/usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-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... x86_64-apple-darwin15.6.0
checking host system type... x86_64-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 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
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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... found
compiler 'gfortran' is GNU gfortran-6.1.0
checking for config ./config/site-specific/host-merida1.bioconductor.org... no
checking for config ./config/site-specific/host-bioconductor.org... no
checking for config ./config/site-specific/host-org... no
checking build mode... production
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 how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 0
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of __float128... 0
checking size of _Quad... 0
checking quadmath.h usability... no
checking quadmath.h presence... no
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checking maximum decimal precision for C... 21
checking if Fortran interface enabled... no
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
checking dependency style of clang++ -std=gnu++11... gcc3
checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
checking if c++ interface enabled... yes
checking if clang++ -std=gnu++11 needs old style header files in includes... no
checking if clang++ -std=gnu++11 can handle namespaces... yes
checking if clang++ -std=gnu++11 can handle static cast... yes
checking if clang++ -std=gnu++11 has offsetof extension... yes
checking if the high-level library is enabled... yes
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 if Java JNI interface enabled... no
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
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 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... 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
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checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... 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++ -std=gnu++11 -E
checking for ld used by clang++ -std=gnu++11... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the clang++ -std=gnu++11 linker (/usr/bin/ld) supports shared libraries... yes
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checking if clang++ -std=gnu++11 PIC flag -fno-common -DPIC works... yes
checking if clang++ -std=gnu++11 static flag -static works... no
checking if clang++ -std=gnu++11 supports -c -o file.o... yes
checking if clang++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the clang++ -std=gnu++11 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
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checking if correctly converting long double to (unsigned) long long values... yes
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checking if the system is IBM ppc64le and cannot correctly convert some long double values... no
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... v110
checking whether to perform strict file format checks... no
checking for pread... yes
checking for pwrite... yes
checking whether to use pread/pwrite instead of read/write in certain VFDs... yes
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 hl/Makefile
config.status: creating hl/src/Makefile
config.status: creating hl/c++/Makefile
config.status: creating hl/c++/src/Makefile
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
config.status: executing .classes commands
sed: -i may not be used with stdin
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.5
Configured on: Tue Apr 14 18:05:58 EDT 2020
Configured by: biocbuild@merida1.bioconductor.org
Host system: x86_64-apple-darwin15.6.0
Uname information: Darwin merida1.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
Installation point: /Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/hdf5
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static
Statically Linked Executables:
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS: -L/Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /usr/local/clang7/bin/clang
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/Users/biocbuild/bbs-3.10-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include
C Flags: -Wall -g -O2 -w -fPIC
H5 C Flags:
AM C Flags:
Shared C Library: no
Static C Library: yes
Fortran: no
C++: yes
C++ Compiler: /usr/local/clang7/bin/clang++ -std=gnu++11
C++ Flags: -Wall -g -O2 -w -fPIC
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: no
Static C++ Library: yes
Java: no
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Threadsafety: no
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE: no
Direct VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
for d in src . c++ hl; 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 H5ACdbg.lo
CC H5ACproxy_entry.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 H5B2internal.lo
CC H5B2leaf.lo
CC H5B2stat.lo
CC H5B2test.lo
CC H5C.lo
CC H5Cdbg.lo
CC H5Cepoch.lo
CC H5Cimage.lo
CC H5Clog.lo
CC H5Clog_json.lo
CC H5Clog_trace.lo
CC H5Cprefetched.lo
CC H5Cquery.lo
CC H5Ctag.lo
CC H5Ctest.lo
CC H5CS.lo
CC H5CX.lo
CC H5D.lo
CC H5Dbtree.lo
CC H5Dbtree2.lo
CC H5Dchunk.lo
CC H5Dcompact.lo
CC H5Dcontig.lo
CC H5Ddbg.lo
CC H5Ddeprec.lo
CC H5Dearray.lo
CC H5Defl.lo
CC H5Dfarray.lo
CC H5Dfill.lo
CC H5Dint.lo
CC H5Dio.lo
CC H5Dlayout.lo
CC H5Dnone.lo
CC H5Doh.lo
CC H5Dscatgath.lo
CC H5Dselect.lo
CC H5Dsingle.lo
CC H5Dtest.lo
CC H5Dvirtual.lo
CC H5E.lo
CC H5Edeprec.lo
CC H5Eint.lo
CC H5EA.lo
CC H5EAcache.lo
CC H5EAdbg.lo
CC H5EAdblkpage.lo
CC H5EAdblock.lo
CC H5EAhdr.lo
CC H5EAiblock.lo
CC H5EAint.lo
CC H5EAsblock.lo
CC H5EAstat.lo
CC H5EAtest.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fcwfs.lo
CC H5Fdbg.lo
CC H5Fdeprec.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fint.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fspace.lo
CC H5Fsuper.lo
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FA.lo
CC H5FAcache.lo
CC H5FAdbg.lo
CC H5FAdblock.lo
CC H5FAdblkpage.lo
CC H5FAhdr.lo
CC H5FAint.lo
CC H5FAstat.lo
CC H5FAtest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDfamily.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmulti.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDstdio.lo
CC H5FDtest.lo
CC H5FL.lo
CC H5FO.lo
CC H5FS.lo
CC H5FScache.lo
CC H5FSdbg.lo
CC H5FSint.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 H5HGquery.lo
CC H5HL.lo
CC H5HLcache.lo
CC H5HLdbg.lo
CC H5HLint.lo
CC H5HLprfx.lo
CC H5HLdblk.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 $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5lib_settings.c ; exit 1)
CC H5lib_settings.lo
CC H5MF.lo
CC H5MFaggr.lo
CC H5MFdbg.lo
CC H5MFsection.lo
CC H5MM.lo
CC H5MP.lo
CC H5MPtest.lo
CC H5O.lo
CC H5Odeprec.lo
CC H5Oainfo.lo
CC H5Oalloc.lo
CC H5Oattr.lo
CC H5Oattribute.lo
CC H5Obogus.lo
CC H5Obtreek.lo
CC H5Ocache.lo
CC H5Ocache_image.lo
CC H5Ochunk.lo
CC H5Ocont.lo
CC H5Ocopy.lo
CC H5Odbg.lo
CC H5Odrvinfo.lo
CC H5Odtype.lo
CC H5Oefl.lo
CC H5Ofill.lo
CC H5Oflush.lo
CC H5Ofsinfo.lo
CC H5Oginfo.lo
CC H5Oint.lo
CC H5Olayout.lo
CC H5Olinfo.lo
CC H5Olink.lo
CC H5Omessage.lo
CC H5Omtime.lo
CC H5Oname.lo
CC H5Onull.lo
CC H5Opline.lo
CC H5Orefcount.lo
CC H5Osdspace.lo
CC H5Oshared.lo
CC H5Oshmesg.lo
CC H5Ostab.lo
CC H5Otest.lo
CC H5Ounknown.lo
CC H5P.lo
CC H5Pacpl.lo
CC H5Pdapl.lo
CC H5Pdcpl.lo
CC H5Pdeprec.lo
CC H5Pdxpl.lo
CC H5Pencdec.lo
CC H5Pfapl.lo
CC H5Pfcpl.lo
CC H5Pfmpl.lo
CC H5Pgcpl.lo
CC H5Pint.lo
CC H5Plapl.lo
CC H5Plcpl.lo
CC H5Pocpl.lo
CC H5Pocpypl.lo
CC H5Pstrcpl.lo
CC H5Ptest.lo
CC H5PB.lo
CC H5PL.lo
CC H5PLint.lo
CC H5PLpath.lo
CC H5PLplugin_cache.lo
CC H5R.lo
CC H5Rint.lo
CC H5Rdeprec.lo
CC H5UC.lo
CC H5RS.lo
CC H5S.lo
CC H5Sall.lo
CC H5Sdbg.lo
CC H5Shyper.lo
CC H5Snone.lo
CC H5Spoint.lo
CC H5Sselect.lo
CC H5Stest.lo
CC H5SL.lo
CC H5SM.lo
CC H5SMbtree2.lo
CC H5SMcache.lo
CC H5SMmessage.lo
CC H5SMtest.lo
CC H5ST.lo
CC H5T.lo
CC H5Tarray.lo
CC H5Tbit.lo
CC H5Tcommit.lo
CC H5Tcompound.lo
CC H5Tconv.lo
CC H5Tcset.lo
CC H5Tdbg.lo
CC H5Tdeprec.lo
CC H5Tenum.lo
CC H5Tfields.lo
CC H5Tfixed.lo
CC H5Tfloat.lo
CC H5detect.o
CCLD H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
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 H5Zscaleoffset.lo
CC H5Zszip.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(H5Obogus.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(H5Obogus.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 H5LcreatProp.lo
CXX H5LaccProp.lo
CXX H5DaccProp.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
make[2]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
CC H5DO.lo
CC H5DS.lo
CC H5IM.lo
CC H5LT.lo
CC H5LTanalyze.lo
CC H5LTparse.lo
CC H5PT.lo
CC H5TB.lo
CC H5LD.lo
CCLD libhdf5_hl.la
+ cd c++
+ make lib
make[3]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
CXX H5PacketTable.lo
CXXLD libhdf5_hl_cpp.la
configure: HDF5_INCLUDE=hdf5/src
configure: HDF5_CXX_INCLUDE=hdf5/c++/src
configure: HDF5_HL_INCLUDE=hdf5/hl/src
configure: HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure: HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure: HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure: HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure: HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure: SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: ZLIB_HOME=yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/szip/src/.libs/libsz.a" "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -Ihdf5/src -Iyes/include -Lyes/lib -fPIC -Wall -g -O2 -c Rhdf5lib.c -o Rhdf5lib.o
clang-7: warning: argument unused during compilation: '-Lyes/lib' [-Wunused-command-line-argument]
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/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-Rhdf5lib/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rhdf5lib)