* installing *source* package ‘hdf5lib’ ...
** this is package ‘hdf5lib’ version ‘1.14.6.4’
** package ‘hdf5lib’ successfully unpacked and MD5 sums checked
** using staged installation
--- [hdf5lib] Starting Unix configuration (STATIC) ---
--- [hdf5lib] Decompressing HDF5 and zlib tarballs...
> utils::untar('hdf5.tar.gz')
>
> utils::untar('zlib.tar.gz')
>
--- [hdf5lib] Configuring and compiling static zlib...
Building static library libz.a version 1.3.1 with clang -arch arm64.
Checking for size_t... Yes.
Checking for off64_t... No.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o adler32.o adler32.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o crc32.o crc32.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o deflate.o deflate.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o infback.o infback.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o inffast.o inffast.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o inflate.o inflate.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o inftrees.o inftrees.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o trees.o trees.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o zutil.o zutil.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o compress.o compress.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o uncompr.o uncompr.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o gzclose.o gzclose.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o gzlib.o gzlib.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o gzread.o gzread.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o gzwrite.o gzwrite.c
/usr/bin/libtool -o libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o
--- [hdf5lib] Starting HDF5 build...
--- [hdf5lib] Configuring bundled HDF5 library...
checking for a BSD-compatible install... Error in untar2(tarfile, files, list, exdir, restore_times) :
incomplete block on file
/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-darwin22.5.0
checking host system type... aarch64-apple-darwin22.5.0
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking enable warnings as errors... no
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checking for config aarch64-apple... no
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checking for config darwin22.5.0... no
checking for config apple... found
compiler 'clang -arch arm64' is clang-14.0.0
compiler '/opt/gfortran/bin/gfortran -arch arm64' is GNU gfortran-14.2.0
compiler 'clang++ -arch arm64 -std=gnu++17' is clang-14.0.0
No match to get cc_version_info for clang -arch arm64
checking for config ./config/site-specific/host-m1... 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... none
checking if unsupported combinations of configure options are allowed... yes
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checking size of unsigned... 4
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checking size of long long... 8
checking size of float... 4
checking size of double... 8
checking size of long double... 8
checking if non-standard feature support is enabled... yes
checking if _Float16 support is enabled... yes
configure: checking if _Float16 support is available
checking size of _Float16... 2
checking for clang -arch arm64 options needed to detect all undeclared functions... none needed
checking whether FLT16_EPSILON is declared... yes
checking whether FLT16_MIN is declared... yes
checking whether FLT16_MAX is declared... yes
checking whether FLT16_MIN_10_EXP is declared... yes
checking whether FLT16_MAX_10_EXP is declared... yes
checking whether FLT16_MANT_DIG is declared... yes
checking if compiler can correctly compile and run a test program which converts _Float16 to other types with casts... yes
checking if compiler can correctly compile and run a test program which converts _Float16 to other types with casts (without CFLAGS)... yes
checking if compiler can correctly convert long double values to _Float16... yes
checking if compiler can correctly convert long double values to _Float16 (without CFLAGS)... yes
checking for fabsf16... no
checking if _Float16 support is enabled... yes
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... none
checking how to run the C++ preprocessor... clang++ -arch arm64 -std=gnu++17 -E
checking if c++ interface enabled... no
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checking whether to use new references with dimension scales... no
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
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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... darwin22.5.0 dyld
checking how to hardcode library paths into programs... immediate
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checking Pthreads supports system scope... yes
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checking profiling... no
checking optimization level... high
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checking for pread... yes
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configure: creating ./config.lt
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checking that generated files are newer than configure... done
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SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.14.6
Configured on: Mon Nov 10 21:37:20 NZDT 2025
Configured by: pkgbuild@m1
Host system: aarch64-apple-darwin22.5.0
Uname information: Darwin m1 22.5.0 Darwin Kernel Version 22.5.0: Mon Apr 24 20:53:44 PDT 2023; root:xnu-8796.121.2~5/RELEASE_ARM64_T8103 arm64
Byte sex: little-endian
Installation point: /Volumes/Builds/packages/big-sur-arm64/results/4.5/hdf5lib.Rcheck/00_pkg_src/hdf5lib/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 -L/Volumes/Builds/packages/big-sur-arm64/results/4.5/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/zlib
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lpthread -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 -I/Library/Frameworks/R.framework/Resources/include -I/Volumes/Builds/packages/big-sur-arm64/results/4.5/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/zlib
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API -I/Volumes/Builds/packages/big-sur-arm64/results/4.5/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/src/H5FDsubfiling
AM_CPPFLAGS:
C Flags: -falign-functions=64 -Wall -g -O2 -fPIC -I/Volumes/Builds/packages/big-sur-arm64/results/4.5/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/zlib
H5 C Flags: -std=c99 -Wall -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wextra -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wpedantic -Wvolatile-register-var -Wno-c++-compat -Wbad-function-cast -Wimplicit-function-declaration -Wincompatible-pointer-types -Wmissing-declarations -Wpacked -Wshadow -Wswitch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat -Wno-missing-noreturn -O3
AM C Flags:
Shared C Library: no
Static C Library: yes
Fortran: no
C++: no
Java: no
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Dimension scales w/ new references: no
Build HDF5 Tests: no
Build HDF5 Tools: no
Build GIF Tools: no
Threadsafety: yes
Default API mapping: v114
With deprecated public symbols: yes
I/O filters (external): deflate(zlib)
_Float16 support: yes
Map (H5M) API: no
Direct VFD: no
Mirror VFD: no
Subfiling VFD: no
(Read-Only) S3 VFD: no
(Read-Only) HDFS VFD: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
--- [hdf5lib] Compiling HDF5 static library...
Making all in src
make all-am
CC H5.lo
H5.c:80:18: warning: format string is not a string literal [-Wformat-nonliteral]
Rvprintf(format, ap);
^~~~~~
H5.c:84:19: warning: format string is not a string literal [-Wformat-nonliteral]
REvprintf(format, ap);
^~~~~~
H5.c:88:32: warning: format string is not a string literal [-Wformat-nonliteral]
ret = vfprintf(stream, format, ap);
^~~~~~
3 warnings generated.
CC H5build_settings.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 H5Centry.lo
CC H5Cepoch.lo
CC H5Cimage.lo
CC H5Cint.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 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 H5ES.lo
CC H5ESevent.lo
CC H5ESint.lo
CC H5ESlist.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fcwfs.lo
CC H5Fdbg.lo
CC H5Fdeprec.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fint.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fspace.lo
CC H5Fsuper.lo
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FA.lo
CC H5FAcache.lo
CC H5FAdbg.lo
CC H5FAdblock.lo
CC H5FAdblkpage.lo
CC H5FAhdr.lo
CC H5FAint.lo
CC H5FAstat.lo
CC H5FAtest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDfamily.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmulti.lo
CC H5FDonion.lo
CC H5FDonion_header.lo
CC H5FDonion_history.lo
CC H5FDonion_index.lo
CC H5FDperform.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDsplitter.lo
CC H5FDstdio.lo
CC H5FDtest.lo
CC H5FDwindows.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 H5I.lo
CC H5Idbg.lo
CC H5Iint.lo
CC H5Itest.lo
CC H5L.lo
CC H5Ldeprec.lo
CC H5Lexternal.lo
CC H5Lint.lo
CC H5M.lo
CC H5MF.lo
CC H5MFaggr.lo
CC H5MFdbg.lo
CC H5MFsection.lo
CC H5MM.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 H5Ocopy_ref.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 H5Pmapl.lo
CC H5Pmcpl.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 H5Rdeprec.lo
CC H5Rint.lo
CC H5UC.lo
CC H5RS.lo
CC H5S.lo
CC H5Sall.lo
CC H5Sdbg.lo
CC H5Sdeprec.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 H5T.lo
CC H5Tarray.lo
CC H5Tbit.lo
CC H5Tcommit.lo
CC H5Tcompound.lo
CC H5Tconv.lo
CC H5Tconv_integer.lo
CC H5Tconv_float.lo
CC H5Tconv_string.lo
CC H5Tconv_bitfield.lo
CC H5Tconv_compound.lo
CC H5Tconv_reference.lo
CC H5Tconv_enum.lo
CC H5Tconv_vlen.lo
CC H5Tconv_array.lo
CC H5Tcset.lo
CC H5Tdbg.lo
CC H5Tdeprec.lo
CC H5Tenum.lo
CC H5Tfields.lo
CC H5Tfixed.lo
CC H5Tfloat.lo
CC H5Tinit_float.lo
CC H5Tnative.lo
CC H5Toffset.lo
CC H5Toh.lo
CC H5Topaque.lo
CC H5Torder.lo
CC H5Tref.lo
CC H5Tpad.lo
CC H5Tprecis.lo
CC H5Tstrpad.lo
CC H5Tvisit.lo
CC H5Tvlen.lo
CC H5TS.lo
CC H5VL.lo
CC H5VLcallback.lo
CC H5VLdyn_ops.lo
CC H5VLint.lo
CC H5VLnative.lo
CC H5VLnative_attr.lo
CC H5VLnative_blob.lo
CC H5VLnative_dataset.lo
CC H5VLnative_datatype.lo
CC H5VLnative_file.lo
CC H5VLnative_group.lo
CC H5VLnative_link.lo
CC H5VLnative_introspect.lo
CC H5VLnative_object.lo
CC H5VLnative_token.lo
CC H5VLpassthru.lo
CC H5VLtest.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
Making all in bin
Making all in utils
make[2]: Nothing to be done for `all-am'.
Making all in .
make[1]: Nothing to be done for `all-am'.
Making all in hl
Making all in src
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
make[2]: Nothing to be done for `all-am'.
--- [hdf5lib] Extracting all object files...
--- [hdf5lib] Merging all .o files into libhdf5.a...
ar: creating archive libhdf5.a
--- [hdf5lib] Stripping static library...
--- [hdf5lib] Exposing minified HDF5 headers...
--- [hdf5lib] Exposing final merged static library...
--- [hdf5lib] Cleaning up build-time directories...
--- [hdf5lib] Unix configuration complete. ---
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hdf5lib)