* installing *source* package ‘hdf5lib’ ... ** this is package ‘hdf5lib’ version ‘1.14.6.5’ ** using staged installation --- [hdf5lib] Starting Unix configuration (STATIC) --- --- [hdf5lib] Decompressing HDF5 and zlib tarballs... R> utils::untar('hdf5.tar.gz') R> R> utils::untar('zlib.tar.gz') R> --- [hdf5lib] Configuring and compiling static zlib... Building static library libz.a version 1.3.1 with clang-19 -std=gnu23. Checking for size_t... Yes. Checking for off64_t... Yes. 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-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o adler32.o adler32.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o crc32.o crc32.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o deflate.o deflate.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o infback.o infback.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o inffast.o inffast.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o inflate.o inflate.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o inftrees.o inftrees.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o trees.o trees.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o zutil.o zutil.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o compress.o compress.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o uncompr.o uncompr.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o gzclose.o gzclose.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o gzlib.o gzlib.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o gzread.o gzread.c clang-19 -std=gnu23 -g -O3 -Wall -pedantic -fPIC -c -o gzwrite.o gzwrite.c ar rc 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... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... 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config.status: creating src/H5config.h config.status: executing pubconf commands creating src/H5pubconf.h Post process src/libhdf5.settings Post process src/H5build_settings.c config.status: executing depfiles commands config.status: executing libtool commands SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.14.6 Configured on: Mon Nov 10 20:28:33 CET 2025 Configured by: hornik@anduin3 Host system: x86_64-pc-linux-gnu Uname information: Linux anduin3 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) x86_64 GNU/Linux Byte sex: little-endian Installation point: /srv/hornik/tmp/CRAN_pretest/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: -Wl,-O1 -L/srv/hornik/tmp/CRAN_pretest/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-19 -std=gnu23 -std=gnu11 ( 19.1.7) CPPFLAGS: -I/usr/local/include -I/home/hornik/tmp/R/include -I/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/zlib H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API -I/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/src/H5FDsubfiling AM_CPPFLAGS: C Flags: -g -O3 -Wall -pedantic -fPIC 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[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/src' make all-am make[2]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/src' CC H5.lo H5.c:80:18: warning: format string is not a string literal [-Wformat-nonliteral] 80 | Rvprintf(format, ap); | ^~~~~~ H5.c:84:19: warning: format string is not a string literal [-Wformat-nonliteral] 84 | REvprintf(format, ap); | ^~~~~~ H5.c:88:32: warning: format string is not a string literal [-Wformat-nonliteral] 88 | 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 make[2]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/src' make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/src' Making all in bin make[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/bin' make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/bin' Making all in utils make[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/utils' make[2]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/utils' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/utils' make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/utils' Making all in . make[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5' make[1]: Nothing to be done for 'all-am'. make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5' Making all in hl make[1]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/hl' Making all in src make[2]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/hl/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]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/hl/src' make[2]: Entering directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/hl' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/hl' make[1]: Leaving directory '/srv/hornik/tmp/CRAN_pretest/hdf5lib.Rcheck/00_pkg_src/hdf5lib/src/hdf5/hl' --- [hdf5lib] Extracting all object files... --- [hdf5lib] Merging all .o files into libhdf5.a... ar: creating 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)