Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:45 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 |
Package 1723/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rhdf5lib 1.27.0 (landing page) Mike Smith
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the Rhdf5lib package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: Rhdf5lib |
Version: 1.27.0 |
Command: rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhdf5lib_1.27.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rhdf5lib.buildbin-libdir |
StartedAt: 2024-08-27 01:54:51 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 01:56:39 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 108.5 seconds |
RetCode: 0 |
Status: OK |
PackageFile: Rhdf5lib_1.27.0.tgz |
PackageFileSize: 10.15 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rhdf5lib.buildbin-libdir && mkdir Rhdf5lib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rhdf5lib_1.27.0.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_1.27.0.tar.gz' >>>>>>> * installing *source* package ‘Rhdf5lib’ ... ** using staged installation checking for gcc... clang -arch arm64 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 the compiler supports GNU C... yes checking whether clang -arch arm64 accepts -g... yes checking for clang -arch arm64 option to enable C11 features... none needed checking whether the compiler supports GNU C++... yes checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed COMPILER = clang checking whether C compiler accepts -w... yes checking whether to use -Wl,-rpath setting... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for zlib.h... yes ON_BUILDER=false ON_BUILDER=true checking for curl/curl.h... yes checking for openssl/evp.h... yes checking for openssl/hmac.h... yes checking for openssl/sha.h... yes checking for curl_global_init in -lcurl... yes checking for EVP_sha256 in -lcrypto... yes S3_VFD=--enable-ros3-vfd configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ 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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib \ CC='clang -arch arm64' CXX='clang++ -arch arm64 -std=gnu++17' \ CPPFLAGS='-I/opt/R/arm64/include' \ CFLAGS='-falign-functions=64 -Wall -g -O2 -w -fPIC' \ AR='ar' RANLIB='ranlib'; \ make; \ make install checking build system type... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 checking how to print strings... printf checking for gcc... clang -arch arm64 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 -arch arm64 accepts -g... yes checking for clang -arch arm64 option to accept ISO C89... none needed checking whether clang -arch arm64 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 -arch arm64... /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... 786432 checking how to convert aarch64-apple-darwin22.6.0 file names to aarch64-apple-darwin22.6.0 format... func_convert_file_noop checking how to convert aarch64-apple-darwin22.6.0 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 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 -arch arm64 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 -arch arm64 -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 -arch arm64 supports -fno-rtti -fno-exceptions... yes checking for clang -arch arm64 option to produce PIC... -fno-common -DPIC checking if clang -arch arm64 PIC flag -fno-common -DPIC works... yes checking if clang -arch arm64 static flag -static works... no checking if clang -arch arm64 supports -c -o file.o... yes checking if clang -arch arm64 supports -c -o file.o... (cached) yes checking whether the clang -arch arm64 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.6.0 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 -arch arm64... gcc3 checking whether to enable maintainer-specific portions of Makefiles... yes checking for clang -arch arm64 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 -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c -o encode.lo ../../src/encode.c libtool: compile: clang -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c -o decode.lo ../../src/decode.c libtool: compile: clang -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -version-info 0:10:0 -no-undefined -o libaec.la -rpath /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/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 -arch arm64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o aec aec.o libaec.la libtool: link: clang -arch arm64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o aec aec.o ./.libs/libaec.a clang -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o utime utime.o libtool: link: clang -arch arm64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o utime utime.o /bin/sh ../libtool --tag=CC --mode=compile clang -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/arm64/include -fvisibility=hidden -falign-functions=64 -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 -arch arm64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -version-info 2:1:0 -no-undefined -o libsz.la -rpath /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libaec.la libsz.la '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' libtool: install: /usr/bin/install -c .libs/libaec.lai /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.la libtool: install: /usr/bin/install -c .libs/libsz.lai /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.la libtool: install: /usr/bin/install -c .libs/libaec.a /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: chmod 644 /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: ranlib /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: /usr/bin/install -c .libs/libsz.a /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: chmod 644 /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: ranlib /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a ../../config/install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c aec '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' libtool: install: /usr/bin/install -c aec /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec ../../config/install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/install -c -m 644 ../../src/libaec.h ../../src/szlib.h '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' ../../config/install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' /usr/bin/install -c -m 644 ../../src/aec.1 '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \ --enable-ros3-vfd \ --enable-sharedlib-rpath \ CC='clang -arch arm64' CXX='clang++ -arch arm64 -std=gnu++17' \ CPPFLAGS='-I/opt/R/arm64/include' \ CFLAGS='-falign-functions=64 -Wall -g -O2 -w -fPIC' \ CXXFLAGS='-w -falign-functions=64 -Wall -g -O2 -fPIC' \ AR='ar' RANLIB='ranlib' \ LDFLAGS='-L/opt/R/arm64/lib'; \ make lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free 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... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 checking shell variables initial values... done checking if basename works... yes checking if xargs works... yes checking for cached host... none checking for config aarch64-apple-darwin22.6.0... no checking for config aarch64-apple-darwin22.6.0... no checking for config apple-darwin22.6.0... no checking for config apple-darwin22.6.0... no checking for config aarch64-darwin22.6.0... no checking for config aarch64-darwin22.6.0... no checking for config aarch64-apple... no checking for config darwin22.6.0... no checking for config darwin22.6.0... no checking for config apple... found compiler 'clang -arch arm64' is clang-15.0.0 No match to get cc_version_info for clang -arch arm64 compiler 'gfortran' is GNU gfortran-12.2.0 checking for config ./config/site-specific/host-kjohnson3... no checking for clang sanitizer checks... none checking build mode... production checking for gcc... clang -arch arm64 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 the compiler supports GNU C... yes checking whether clang -arch arm64 accepts -g... yes checking for clang -arch arm64 option to enable C11 features... none needed checking whether clang -arch arm64 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 -arch arm64... gcc3 checking if unsupported combinations of configure options are allowed... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/time.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... 8 checking size of __float128... 0 checking size of _Quad... 0 checking for quadmath.h... no checking maximum decimal precision for C... 17 checking if Fortran interface enabled... no checking whether the compiler supports GNU C++... yes checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed checking dependency style of clang++ -arch arm64 -std=gnu++17... gcc3 checking how to run the C++ preprocessor... clang++ -arch arm64 -std=gnu++17 -E checking if c++ interface enabled... yes checking if clang++ -arch arm64 -std=gnu++17 needs old style header files in includes... no checking if clang++ -arch arm64 -std=gnu++17 can handle namespaces... yes checking if clang++ -arch arm64 -std=gnu++17 can handle static cast... yes checking if clang++ -arch arm64 -std=gnu++17 has offsetof extension... yes checking if the high-level library is enabled... yes checking whether make sets $(MAKE)... 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checking enable developer warnings... no checking profiling... no checking optimization level... high checking enable file locking... best-effort 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 if the Mirror virtual file driver (VFD) is enabled... no checking for curl/curl.h... yes checking for openssl/evp.h... yes checking for openssl/hmac.h... yes checking for openssl/sha.h... yes checking for curl_global_init in -lcurl... yes checking for EVP_sha256 in -lcrypto... yes checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes checking for libhdfs... suppressed checking for custom examples path definition... ${prefix}/share/hdf5_examples 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 utils/Makefile config.status: creating utils/mirror_vfd/Makefile config.status: creating bin/h5cc config.status: creating bin/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 or -i may not be used with stdin SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.10.7 Configured on: Tue Aug 27 01:55:21 EDT 2024 Configured by: biocbuild@kjohnson3 Host system: aarch64-apple-darwin22.6.0 Uname information: Darwin kjohnson3 22.6.0 Darwin Kernel Version 22.6.0: Mon Apr 22 20:51:27 PDT 2024; root:xnu-8796.141.3.705.2~1/RELEASE_ARM64_T6020 arm64 Byte sex: little-endian Installation point: /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/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: -L/opt/R/arm64/lib H5_LDFLAGS: AM_LDFLAGS: -L/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib Extra libraries: -lcrypto -lcurl -lsz -laec -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: ranlib Languages: ---------- C: yes C Compiler: /usr/bin/clang -arch arm64 CPPFLAGS: -I/opt/R/arm64/include H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpSEViSo/R.INSTALL1823146bae2ce/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include C Flags: -falign-functions=64 -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++ -arch arm64 -std=gnu++17 C++ Flags: -w -falign-functions=64 -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(no encoder) MPE: no Direct VFD: no Mirror VFD: no (Read-Only) S3 VFD: yes (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 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 H5FDhdfs.lo CC H5FDint.lo CC H5FDlog.lo CC H5FDmulti.lo CC H5FDsec2.lo CC H5FDspace.lo CC H5FDsplitter.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 -L/opt/R/arm64/lib | \ 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 -L/opt/R/arm64/lib | \ 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 CC H5FDros3.lo CC H5FDs3comms.lo CCLD libhdf5.la 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-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/*.h "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/c++/src"/*.h "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/src"/*.h "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/c++/src"/*.h "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/libhdf5.settings "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/src/.libs/libhdf5.a" "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rhdf5lib.c -o Rhdf5lib.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Rhdf5lib.so Rhdf5lib.o /Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Users/biocbuild/bbs-3.20-bioc/meat/Rhdf5lib.buildbin-libdir/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /Users/biocbuild/bbs-3.20-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-3.20-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 PATHS TO DYNAMIC LIBRARIES FOR Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so >>>>>>> >>>>>>> Paths before fix: Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so: Rhdf5lib.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/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/4.4-arm64/Resources/lib/libquadmath.0.dylib" "Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so" >>>>>>> Paths after fix: Rhdf5lib.buildbin-libdir/Rhdf5lib/libs/Rhdf5lib.so: Rhdf5lib.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)