##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rhdf5lib.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rhdf5lib_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhdf5lib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhdf5lib’ version ‘1.29.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rhdf5lib’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
  installed size is 30.0Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    lib      23.9Mb
    libs      3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/libs/Rhdf5lib.so’:
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
  Found ‘_sprintf’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhdf5lib
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* 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=/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/Users/biocbuild/bbs-3.21-bioc/meat/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 /Users/biocbuild/bbs-3.21-bioc/meat/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 /Users/biocbuild/bbs-3.21-bioc/meat/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 '/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libaec.la libsz.la '/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib'
libtool: install: /usr/bin/install -c .libs/libaec.lai /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.la
libtool: install: /usr/bin/install -c .libs/libsz.lai /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libaec.a /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: ranlib /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: /usr/bin/install -c .libs/libsz.a /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
libtool: install: ranlib /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c aec '/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin'
libtool: install: /usr/bin/install -c aec /Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include'
 /usr/bin/install -c -m 644 ../../src/libaec.h ../../src/szlib.h '/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.21-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1'
 /usr/bin/install -c -m 644 ../../src/aec.1 '/Users/biocbuild/bbs-3.21-bioc/meat/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=/Users/biocbuild/bbs-3.21-bioc/meat/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
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configure: creating ./config.lt
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config.status: creating src/libhdf5.settings
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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 Nov 26 15:02:26 EST 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: Thu Sep  5 20:46:08 PDT 2024; root:xnu-8796.141.3.708.1~1/RELEASE_ARM64_T6020 arm64
                       Byte sex: little-endian
             Installation point: /Users/biocbuild/bbs-3.21-bioc/meat/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/Users/biocbuild/bbs-3.21-bioc/meat/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/Users/biocbuild/bbs-3.21-bioc/meat/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 $d && make  lib) || exit 1;            \
	  fi;                                                           \
	done
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LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/opt/R/arm64/lib |                  \
		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
	 ./H5make_libsettings > H5lib_settings.c  ||                               \
	    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
	    (rm -f H5lib_settings.c ; exit 1)
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  CC       H5Stest.lo
  CC       H5SL.lo
  CC       H5SM.lo
  CC       H5SMbtree2.lo
  CC       H5SMcache.lo
  CC       H5SMmessage.lo
  CC       H5SMtest.lo
  CC       H5ST.lo
  CC       H5T.lo
  CC       H5Tarray.lo
  CC       H5Tbit.lo
  CC       H5Tcommit.lo
  CC       H5Tcompound.lo
  CC       H5Tconv.lo
  CC       H5Tcset.lo
  CC       H5Tdbg.lo
  CC       H5Tdeprec.lo
  CC       H5Tenum.lo
  CC       H5Tfields.lo
  CC       H5Tfixed.lo
  CC       H5Tfloat.lo
  CC       H5detect.o
  CCLD     H5detect
LD_LIBRARY_PATH="$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 "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src"/*.h "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src"/*.h "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src"/*.h "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src"/*.h "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src"/libhdf5.settings "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/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 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libaec.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/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)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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> if ( requireNamespace("tinytest", quietly=TRUE) ) {
+   tinytest::test_package("Rhdf5lib")
+ }

test_library_version.R........    1 tests OK 
test_library_version.R........    2 tests OK 18ms

test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    0 tests    
test_link_flags.R.............    1 tests OK 
test_link_flags.R.............    2 tests OK 
test_link_flags.R.............    3 tests OK 
test_link_flags.R.............    4 tests OK 
test_link_flags.R.............    5 tests OK 
test_link_flags.R.............    6 tests OK 
test_link_flags.R.............    7 tests OK 
test_link_flags.R.............    8 tests OK 77ms
All ok, 10 results (96ms)
> 
> proc.time()
   user  system elapsed 
  0.156   0.022   0.176