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grimbough / Rhdf5lib

Distribution of the HDF5 library in an R package
https://bioconductor.org/packages/Rhdf5lib/
6 stars 14 forks source link

Compilation on MacOS Catalina #23

Closed mikheyev closed 4 years ago

mikheyev commented 4 years ago

I am having some issues getting the package installed on MacOS Catalina. I tried this on a couple of different computers, but with the same result.

> BiocManager::install("Rhdf5lib")
Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'Rhdf5lib'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Rhdf5lib_1.8.0.tar.gz'
Content type 'application/x-gzip' length 9734415 bytes (9.3 MB)
==================================================
downloaded 9.3 MB

* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
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... no
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... no
configure: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: zlib.h: proceeding with the compiler's result
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-darwin19.0.0
checking host system type... x86_64-apple-darwin19.0.0
checking for config x86_64-apple-darwin19.0.0... no
checking for config x86_64-apple-darwin19.0.0... no
checking for config apple-darwin19.0.0... no
checking for config apple-darwin19.0.0... no
checking for config x86_64-darwin19.0.0... no
checking for config x86_64-darwin19.0.0... no
checking for config x86_64-apple... no
checking for config darwin19.0.0... no
checking for config darwin19.0.0... 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... 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... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin19.0.0 file names to x86_64-apple-darwin19.0.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin19.0.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
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 for ANSI C header files... no
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... darwin19.0.0 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) no
checking fcntl.h usability... yes
checking fcntl.h presence... no
configure: WARNING: fcntl.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: fcntl.h: proceeding with the compiler's result
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.     -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -w -fPIC  -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c
libtool: compile:  clang -DHAVE_CONFIG_H -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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.     -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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.     -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -w -fPIC  -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c
libtool: compile:  clang -DHAVE_CONFIG_H -I. -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -w -fPIC  -version-info 2:0:0  -o libsz.la -rpath /private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/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 '/private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libsz.la '/private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /usr/bin/install -c .libs/libsz.lai /private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libsz.a /private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: ranlib /private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
 ../bin/install-sh -c -d '/private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/include'
 /usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/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-darwin19.0.0
checking host system type... x86_64-apple-darwin19.0.0
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-darwin19.0.0... no
checking for config x86_64-apple-darwin19.0.0... no
checking for config apple-darwin19.0.0... no
checking for config apple-darwin19.0.0... no
checking for config x86_64-darwin19.0.0... no
checking for config x86_64-darwin19.0.0... no
checking for config x86_64-apple... no
checking for config darwin19.0.0... no
checking for config darwin19.0.0... no
checking for config apple... found
compiler 'gfortran' is GNU gfortran-6.1.0
checking for config ./config/site-specific/host-homologous... 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... 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... no
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... no
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
checking for quadmath.h... no
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... yes
checking if clang++ -std=gnu++11 can handle namespaces... no
checking if clang++ -std=gnu++11 can handle static cast... no
checking if clang++ -std=gnu++11 has offsetof extension... no
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-darwin19.0.0 file names to x86_64-apple-darwin19.0.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin19.0.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
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 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... darwin19.0.0 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
checking for clang++ -std=gnu++11 option to produce PIC... -fno-common -DPIC
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... darwin19.0.0 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 for ceil in -lm... yes
checking for dlopen in -ldl... (cached) yes
checking for ANSI C header files... (cached) no
checking whether time.h and sys/time.h may both be included... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... no
configure: WARNING: sys/resource.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: sys/resource.h: proceeding with the compiler's result
checking for sys/resource.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... no
configure: WARNING: sys/time.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: sys/time.h: proceeding with the compiler's result
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... no
configure: WARNING: sys/ioctl.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: sys/ioctl.h: proceeding with the compiler's result
checking for sys/ioctl.h... yes
checking for sys/stat.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... no
configure: WARNING: sys/socket.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: sys/socket.h: proceeding with the compiler's result
checking for sys/socket.h... yes
checking for sys/types.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... no
configure: WARNING: sys/file.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: sys/file.h: proceeding with the compiler's result
checking for sys/file.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking setjmp.h usability... yes
checking setjmp.h presence... no
configure: WARNING: setjmp.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: setjmp.h: proceeding with the compiler's result
checking for setjmp.h... yes
checking features.h usability... no
checking features.h presence... no
checking for features.h... no
checking dirent.h usability... yes
checking dirent.h presence... no
configure: WARNING: dirent.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: dirent.h: proceeding with the compiler's result
checking for dirent.h... yes
checking for stdint.h... (cached) yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking mach/mach_time.h usability... yes
checking mach/mach_time.h presence... no
configure: WARNING: mach/mach_time.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: mach/mach_time.h: proceeding with the compiler's result
checking for mach/mach_time.h... yes
checking io.h usability... no
checking io.h presence... no
checking for io.h... no
checking winsock2.h usability... no
checking winsock2.h presence... no
checking for winsock2.h... no
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... no
configure: WARNING: sys/timeb.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: sys/timeb.h: proceeding with the compiler's result
checking for sys/timeb.h... yes
checking for _FILE_OFFSET_BITS value needed for large files... no
checking size of int8_t... 1
checking size of uint8_t... 1
checking size of int_least8_t... 1
checking size of uint_least8_t... 1
checking size of int_fast8_t... 1
checking size of uint_fast8_t... 1
checking size of int16_t... 2
checking size of uint16_t... 2
checking size of int_least16_t... 2
checking size of uint_least16_t... 2
checking size of int_fast16_t... 2
checking size of uint_fast16_t... 2
checking size of int32_t... 4
checking size of uint32_t... 4
checking size of int_least32_t... 4
checking size of uint_least32_t... 4
checking size of int_fast32_t... 4
checking size of uint_fast32_t... 4
checking size of int64_t... 8
checking size of uint64_t... 8
checking size of int_least64_t... 8
checking size of uint_least64_t... 8
checking size of int_fast64_t... 8
checking size of uint_fast64_t... 8
checking size of size_t... 8
checking size of ssize_t... 8
checking size of ptrdiff_t... 8
checking size of off_t... 8
checking size of bool... 1
checking size of time_t... 8
checking if dev_t is scalar... yes
checking for dmalloc library... suppressed
checking zlib.h usability... yes
checking zlib.h presence... no
configure: WARNING: zlib.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: zlib.h: proceeding with the compiler's result
checking for zlib.h... yes
checking for compress2 in -lz... yes
checking for compress2... yes
checking szlib.h usability... yes
checking szlib.h presence... no
configure: WARNING: szlib.h: accepted by the compiler, rejected by the preprocessor!
configure: WARNING: szlib.h: proceeding with the compiler's result
checking for szlib.h... yes
checking for SZ_BufftoBuffCompress in -lsz... yes
checking for szlib encoder... yes
checking for thread safe support... no
checking whether CLOCK_MONOTONIC is declared... yes
checking for tm_gmtoff in struct tm... yes
checking for global timezone variable... yes
checking for st_blocks in struct stat... no
checking for _getvideoconfig... no
checking for gettextinfo... no
checking for GetConsoleScreenBufferInfo... no
checking for getpwuid... yes
checking for _scrsize... no
checking for ioctl... yes
checking for struct videoconfig... no
checking for struct text_info... no
checking for TIOCGWINSZ... yes
checking for TIOCGETD... yes
checking for library containing clock_gettime... none required
checking for alarm... yes
checking for clock_gettime... yes
checking for difftime... yes
checking for fcntl... yes
checking for flock... yes
checking for fork... yes
checking for frexpf... yes
checking for frexpl... yes
checking for gethostname... yes
checking for getrusage... yes
checking for gettimeofday... yes
checking for lstat... yes
checking for rand_r... yes
checking for random... yes
checking for setsysinfo... no
checking for signal... yes
checking for longjmp... yes
checking for setjmp... yes
checking for siglongjmp... yes
checking for sigsetjmp... yes
checking for sigprocmask... yes
checking for snprintf... yes
checking for srandom... yes
checking for strdup... yes
checking for symlink... yes
checking for system... yes
checking for strtoll... yes
checking for strtoull... yes
checking for tmpfile... yes
checking for asprintf... yes
checking for vasprintf... yes
checking for vsnprintf... yes
checking for waitpid... yes
checking for roundf... yes
checking for lroundf... yes
checking for llroundf... yes
checking for round... yes
checking for lround... yes
checking for llround... yes
checking for an ANSI C-conforming const... yes
checking if the compiler understands  __inline__... yes
checking if the compiler understands __inline... yes
checking if the compiler understands inline... yes
checking for __attribute__ extension... yes
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 enable debugging symbols... no
checking enable asserts... no
checking enable developer warnings... no
checking profiling... no
checking optimization level... high
checking for internal debug output... none
checking whether function stack tracking is enabled... no
checking for API tracing... no
checking whether a memory checking tool will be used... no
checking whether internal memory allocation sanity checking is 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 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: Sat Nov 23 19:42:35 AEDT 2019
                  Configured by: sasha@homologous
                    Host system: x86_64-apple-darwin19.0.0
              Uname information: Darwin homologous 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
                       Byte sex: little-endian
             Installation point: /private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/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/private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/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/private/var/folders/1j/lcnymnj97qzfykscmmfwzgw00000gn/T/RtmpMK9EhW/R.INSTALL14ca728a32f1/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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: -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -w -fPIC
                   H5 C++ Flags:    
                   AM C++ Flags:  -DOLD_HEADER_FILENAME -DHDF_NO_NAMESPACE -DNO_STATIC_CAST
             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
In file included from H5.c:22:
./H5private.h:848:23: error: unknown type name 'FILE'
H5_DLL int HDfprintf (FILE *stream, const char *fmt, ...);
                      ^
./H5private.h:1718:5: error: unknown type name 'FILE'
    FILE        *stream;                /* Open output stream */
    ^
./H5private.h:1723:5: error: unknown type name 'FILE'
    FILE    *trace;    /*API trace output stream  */
    ^
./H5private.h:1728:3: error: unknown type name 'FILE'
  FILE    *stream;  /*output stream  or NULL    */
  ^
./H5private.h:2649:30: error: unknown type name 'FILE'
H5_DLL herr_t H5_buffer_dump(FILE *stream, int indent, const uint8_t *buf,
                             ^
In file included from H5.c:23:
In file included from ./H5ACprivate.h:33:
In file included from ./H5Cprivate.h:35:
In file included from ./H5Fprivate.h:34:
./H5VMprivate.h:464:47: error: use of undeclared identifier 'CHAR_BIT'
    if(n >= (hsize_t)1 << ((sizeof(hsize_t) * CHAR_BIT) - 1))
                                              ^
6 errors generated.
make[2]: *** [H5.lo] Error 1
make[1]: *** [lib] Error 1
make: *** [lib] Error 1
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 "/usr/local/lib/R/3.6/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/usr/local/lib/R/3.6/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/usr/local/lib/R/3.6/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/usr/local/lib/R/3.6/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/usr/local/lib/R/3.6/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/usr/local/lib/R/3.6/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/usr/local/lib/R/3.6/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp: hdf5/src/.libs/libhdf5.a: No such file or directory
make: *** [copying] Error 1
ERROR: compilation failed for package ‘Rhdf5lib’
* removing ‘/usr/local/lib/R/3.6/site-library/Rhdf5lib’
grimbough commented 4 years ago

It seems very odd for stdio.h to be missing, which is where FILE should be declared.

I'm afraid I'm not an expert on Mac OS, but how did you install clang? Xcode, homebrew, conda? Are all the machines you tried running Catalina?

mikheyev commented 4 years ago

It is indeed very strange. I got the regular clang that you are supposed to use with R from https://cran.r-project.org/bin/macosx/tools/

Both my machines have had the exact same problem after installing Catalina, super annoying.

grimbough commented 4 years ago

There seem to be a lot of reports of Xcode using a different location after installing Catalina e.g.

As a test, can you try installing with the following command:

BiocManager::install('Rhdf5lib', configure.args = "CPPFLAGS='-I/usr/local/include'")

or possibly


BiocManager::install('Rhdf5lib', configure.args = "CPPFLAGS='-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/local/include'")
mikheyev commented 4 years ago

Thanks for the links @grimbough! I got it to work with 

BiocManager::install('Rhdf5lib', configure.args = "CPPFLAGS='-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include'"

Same as your suggestion, but without the local