Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:23:36 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for Rhdf5lib on merida1


To the developers/maintainers of the Rhdf5lib package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhdf5lib.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1645/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhdf5lib 1.18.2  (landing page)
Mike Smith
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Rhdf5lib
git_branch: RELEASE_3_15
git_last_commit: d104bbf
git_last_commit_date: 2022-05-12 14:19:27 -0400 (Thu, 12 May 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rhdf5lib
Version: 1.18.2
Command: rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhdf5lib_1.18.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhdf5lib.buildbin-libdir
StartedAt: 2022-10-19 11:01:58 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 11:09:35 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 456.9 seconds
RetCode: 0
Status:   OK  
PackageFile: Rhdf5lib_1.18.2.tgz
PackageFileSize: 9.121 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhdf5lib_1.18.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhdf5lib.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rhdf5lib.buildbin-libdir Rhdf5lib_1.18.2.tar.gz'
>>>>>>> 

* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
COMPILER = clang
checking whether C compiler accepts -w... yes
checking whether to use -Wl,-rpath setting... yes
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -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... 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 zlib.h... yes
checking szlib.h usability... no
checking szlib.h presence... no
checking for szlib.h... no
checking libaec.h usability... no
checking libaec.h presence... no
checking for libaec.h... no
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... no
checking openssl/evp.h presence... no
checking for openssl/evp.h... no
checking openssl/hmac.h usability... no
checking openssl/hmac.h presence... no
checking for openssl/hmac.h... no
checking openssl/sha.h usability... no
checking openssl/sha.h presence... no
checking for openssl/sha.h... no
S3_VFD=--enable-ros3-vfd=no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gunzip -dc hdf5small_cxx_hl_1.10.7.tar.gz | tar xf -;
cd hdf5/libaec-1.0.4/build; \
	../configure --with-pic --enable-shared=no --prefix=/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib \
	CC='clang -mmacosx-version-min=10.13' CXX='clang++ -mmacosx-version-min=10.13 -std=gnu++14' \
	CPPFLAGS='-I/usr/local/include' \
	CFLAGS='-Wall -g -O2 -w -fPIC'; \
	make; \
	make install
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking how to print strings... printf
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether clang -mmacosx-version-min=10.13 understands -c and -o together... rm: conftest.dSYM: is a directory
yes
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 -mmacosx-version-min=10.13... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/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-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 file names to toolchain format... func_convert_file_noop
checking for /Library/Developer/CommandLineTools/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 ar... ar
checking for archiver @FILE support... rm: conftest.dSYM: is a directory
no
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 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 how to run the C preprocessor... clang -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
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 whether the -Werror option is usable... yes
checking for simple visibility declarations... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ../config/install-sh -c -d
checking whether make sets $(MAKE)... yes
checking whether make supports the include directive... yes (GNU style)
checking whether make supports nested variables... yes
checking dependency style of clang -mmacosx-version-min=10.13... gcc3
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C99... none needed
checking for ANSI C header files... (cached) yes
checking whether byte ordering is bigendian... no
checking for inline... inline
checking for int64_t... yes
checking for size_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for inline... (cached) inline
checking for C/C++ restrict keyword... __restrict
checking for memset... yes
checking for strstr... yes
checking for snprintf... yes
checking whether __builtin_clzll is declared... no
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 config/config.h
config.status: executing libtool commands
config.status: executing depfiles commands
Making all in src
clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT aec.o -MD -MP -MF .deps/aec.Tpo -c -o aec.o ../../src/aec.c
mv -f .deps/aec.Tpo .deps/aec.Po
/bin/sh ../libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c -o encode.lo ../../src/encode.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c ../../src/encode.c  -fno-common -DPIC -o encode.o
mv -f .deps/encode.Tpo .deps/encode.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c -o encode_accessors.lo ../../src/encode_accessors.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c ../../src/encode_accessors.c  -fno-common -DPIC -o encode_accessors.o
mv -f .deps/encode_accessors.Tpo .deps/encode_accessors.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c -o decode.lo ../../src/decode.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c ../../src/decode.c  -fno-common -DPIC -o decode.o
mv -f .deps/decode.Tpo .deps/decode.Plo
/bin/sh ../libtool  --tag=CC   --mode=link clang -mmacosx-version-min=10.13 -fvisibility=hidden -Wall -g -O2 -w -fPIC -version-info 0:10:0 -no-undefined  -o libaec.la -rpath /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib encode.lo encode_accessors.lo decode.lo  
libtool: link: ar cr .libs/libaec.a  encode.o encode_accessors.o decode.o
libtool: link: ranlib .libs/libaec.a
libtool: link: ( cd ".libs" && rm -f "libaec.la" && ln -s "../libaec.la" "libaec.la" )
/bin/sh ../libtool  --tag=CC   --mode=link clang -mmacosx-version-min=10.13 -fvisibility=hidden -Wall -g -O2 -w -fPIC   -o aec aec.o libaec.la 
libtool: link: clang -mmacosx-version-min=10.13 -fvisibility=hidden -Wall -g -O2 -w -fPIC -o aec aec.o  ./.libs/libaec.a
clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT utime.o -MD -MP -MF .deps/utime.Tpo -c -o utime.o ../../src/utime.c
mv -f .deps/utime.Tpo .deps/utime.Po
/bin/sh ../libtool  --tag=CC   --mode=link clang -mmacosx-version-min=10.13 -fvisibility=hidden -Wall -g -O2 -w -fPIC   -o utime utime.o  
libtool: link: clang -mmacosx-version-min=10.13 -fvisibility=hidden -Wall -g -O2 -w -fPIC -o utime utime.o 
/bin/sh ../libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c -o sz_compat.lo ../../src/sz_compat.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -Wall -g -O2 -w -fPIC -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c ../../src/sz_compat.c  -fno-common -DPIC -o sz_compat.o
mv -f .deps/sz_compat.Tpo .deps/sz_compat.Plo
/bin/sh ../libtool  --tag=CC   --mode=link clang -mmacosx-version-min=10.13 -fvisibility=hidden -Wall -g -O2 -w -fPIC -version-info 2:1:0 -no-undefined  -o libsz.la -rpath /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib sz_compat.lo libaec.la 
libtool: link: ar cr .libs/libsz.a  sz_compat.o
libtool: link: ranlib .libs/libsz.a
libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" )
make[2]: Nothing to be done for `all-am'.
Making install in src
 ../../config/install-sh -c -d '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libaec.la libsz.la '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib'
libtool: install: /usr/bin/install -c .libs/libaec.lai /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.la
libtool: install: /usr/bin/install -c .libs/libsz.lai /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libaec.a /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: chmod 644 /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: ranlib /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: /usr/bin/install -c .libs/libsz.a /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
libtool: install: chmod 644 /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
libtool: install: ranlib /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
 ../../config/install-sh -c -d '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c aec '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin'
libtool: install: /usr/bin/install -c aec /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec
 ../../config/install-sh -c -d '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include'
 /usr/bin/install -c -m 644 ../../src/libaec.h ../../src/szlib.h '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include'
 ../../config/install-sh -c -d '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1'
 /usr/bin/install -c -m 644 ../../src/aec.1 '/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
cd hdf5; \
	./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \
	--enable-tests=no --enable-tools=no \
	--with-szlib=/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \
	--enable-ros3-vfd=no \
	--enable-sharedlib-rpath \
	CC='clang -mmacosx-version-min=10.13' CXX='clang++ -mmacosx-version-min=10.13 -std=gnu++14' \
	CPPFLAGS='-I/usr/local/include' \
	CFLAGS='-Wall -g -O2 -w -fPIC' \
	CXXFLAGS='-w -Wall -g -O2 -fPIC'; \
	make lib
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-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
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-darwin18.7.0... no
checking for config x86_64-apple-darwin18.7.0... no
checking for config apple-darwin18.7.0... no
checking for config apple-darwin18.7.0... no
checking for config x86_64-darwin18.7.0... no
checking for config x86_64-darwin18.7.0... no
checking for config x86_64-apple... no
checking for config darwin18.7.0... no
checking for config darwin18.7.0... no
checking for config apple... found
compiler 'clang -mmacosx-version-min=10.13' is clang-11.0.0
No match to get cc_version_info for clang -mmacosx-version-min=10.13
compiler 'gfortran' is GNU gfortran-8.2.0
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 for clang sanitizer checks... none
checking build mode... production
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether clang -mmacosx-version-min=10.13 understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of clang -mmacosx-version-min=10.13... gcc3
checking if unsupported combinations of configure options are allowed... no
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -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
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checking size of char... 1
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checking size of int... 4
checking size of unsigned... 4
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checking size of long long... 8
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	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
                   HDF5 Version: 1.10.7
                  Configured on: Wed Oct 19 11:03:12 EDT 2022
                  Configured by: biocbuild@merida1.bioconductor.org
                    Host system: x86_64-apple-darwin18.7.0
              Uname information: Darwin merida1.bioconductor.org 18.7.0 Darwin Kernel Version 18.7.0: Tue Jun 22 19:37:08 PDT 2021; root:xnu-4903.278.70~1/RELEASE_X86_64 x86_64
                       Byte sex: little-endian
             Installation point: /private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/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/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib
                Extra libraries: -lsz -laec -lz -ldl -lm 
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /usr/bin/clang -mmacosx-version-min=10.13
                       CPPFLAGS: -I/usr/local/include
                    H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/private/tmp/RtmpIMCDxO/R.INSTALL15502ddca0c7/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include
                        C Flags: -Wall -g -O2 -w -fPIC
                     H5 C Flags:  -std=c99  -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wno-c++-compat -Wno-format-nonliteral -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wvolatile-register-var -Wno-self-assign-overloaded -Wno-unknown-warning-option   -Wno-missing-noreturn -O3  -Werror=bad-function-cast -Werror=implicit-function-declaration -Werror=incompatible-pointer-types -Werror=missing-declarations -Werror=packed -Werror=shadow -Werror=switch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat
                     AM C Flags: 
               Shared C Library: no
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/clang++ -mmacosx-version-min=10.13 -std=gnu++14
                      C++ Flags: -w -Wall -g -O2 -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
                Build HDF5 Tests: no
                Build HDF5 Tools: no
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                      Direct VFD: no
                      Mirror VFD: no
              (Read-Only) S3 VFD: no
            (Read-Only) HDFS 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
                Use file locking: best-effort
       Strict file format checks: no
    Optimization instrumentation: no
for d in src . c++ hl; do                                \
	  if test $d != .; then                                        \
	   (cd $d && make  lib) || exit 1;            \
	  fi;                                                           \
	done
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  CCLD     H5make_libsettings
LD_LIBRARY_PATH="$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
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  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[3]: 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[3]: 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[4]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
  CXX      H5PacketTable.lo
  CXXLD    libhdf5_hl_cpp.la
mkdir -p "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp ""hdf5/src"/"*.h "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp ""hdf5/c++/src"/"*.h "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp ""hdf5/hl/src"/"*.h "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp ""hdf5/hl/c++/src"/"*.h "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp ""hdf5/src"/"libhdf5.settings "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp ""hdf5/src/.libs/libhdf5.a"" "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp ""hdf5/c++/src/.libs/libhdf5_cpp.a"" "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp ""hdf5/hl/src/.libs/libhdf5_hl.a"" "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp ""hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a"" "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rhdf5lib.c -o Rhdf5lib.o
clang -mmacosx-version-min=10.13 -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-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libaec.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.15-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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)


>>>>>>> 
>>>>>>> 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/4.2/Resources/lib/libgcc_s.1.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so"