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This page was generated on 2024-03-02 11:37:50 -0500 (Sat, 02 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1743/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhdf5lib 1.24.2  (landing page)
Mike Smith
Snapshot Date: 2024-03-01 14:05:09 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/Rhdf5lib
git_branch: RELEASE_3_18
git_last_commit: f4cab37
git_last_commit_date: 2024-02-07 04:27:56 -0500 (Wed, 07 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for Rhdf5lib on lconway


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.

raw results


Summary

Package: Rhdf5lib
Version: 1.24.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhdf5lib
StartedAt: 2024-03-01 15:04:02 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 15:10:57 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 415.3 seconds
RetCode: 0
Status:   OK  

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
checking for gcc... clang -arch x86_64
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 x86_64 accepts -g... yes
checking for clang -arch x86_64 option to enable C11 features... none needed
checking whether the compiler supports GNU C++... yes
checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
checking for clang++ -arch x86_64 -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 14.0.0 (clang-1400.0.29.202)’
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-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/Users/biocbuild/bbs-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib \
	CC='clang -arch x86_64' CXX='clang++ -arch x86_64 -std=gnu++17' \
	CPPFLAGS='-I/opt/R/x86_64/include' \
	CFLAGS='-falign-functions=64 -Wall -g -O2 -w -fPIC' \
	AR='ar' RANLIB='ranlib'; \
	make; \
	make install
checking build system type... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking how to print strings... printf
checking for gcc... clang -arch x86_64
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 x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking whether clang -arch x86_64 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 x86_64... /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 x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin21.6.0 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 x86_64 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 x86_64 -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 x86_64 supports -fno-rtti -fno-exceptions... yes
checking for clang -arch x86_64 option to produce PIC... -fno-common -DPIC
checking if clang -arch x86_64 PIC flag -fno-common -DPIC works... yes
checking if clang -arch x86_64 static flag -static works... no
checking if clang -arch x86_64 supports -c -o file.o... yes
checking if clang -arch x86_64 supports -c -o file.o... (cached) yes
checking whether the clang -arch x86_64 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin21.6.0 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 x86_64... gcc3
checking whether to enable maintainer-specific portions of Makefiles... yes
checking for clang -arch x86_64 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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -version-info 0:10:0 -no-undefined  -o libaec.la -rpath /Users/biocbuild/bbs-3.18-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 x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC   -o aec aec.o libaec.la 
libtool: link: clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o aec aec.o  ./.libs/libaec.a
clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC   -o utime utime.o  
libtool: link: clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o utime utime.o 
/bin/sh ../libtool  --tag=CC   --mode=compile clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config  -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/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 x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -version-info 2:1:0 -no-undefined  -o libsz.la -rpath /Users/biocbuild/bbs-3.18-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-3.18-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-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib'
libtool: install: /usr/bin/install -c .libs/libaec.lai /Users/biocbuild/bbs-3.18-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-3.18-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-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a
libtool: install: ranlib /Users/biocbuild/bbs-3.18-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-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
libtool: install: ranlib /Users/biocbuild/bbs-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.18-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-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin'
libtool: install: /usr/bin/install -c aec /Users/biocbuild/bbs-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.18-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-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include'
 ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.18-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-3.18-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-3.18-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \
	--enable-ros3-vfd \
	--enable-sharedlib-rpath \
	CC='clang -arch x86_64' CXX='clang++ -arch x86_64 -std=gnu++17' \
	CPPFLAGS='-I/opt/R/x86_64/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/x86_64/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... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-apple-darwin21.6.0... no
checking for config x86_64-apple-darwin21.6.0... no
checking for config apple-darwin21.6.0... no
checking for config apple-darwin21.6.0... no
checking for config x86_64-darwin21.6.0... no
checking for config x86_64-darwin21.6.0... no
checking for config x86_64-apple... no
checking for config darwin21.6.0... no
checking for config darwin21.6.0... no
checking for config apple... found
compiler 'clang -arch x86_64' is clang-14.0.0
No match to get cc_version_info for clang -arch x86_64
compiler 'gfortran' is GNU gfortran-12.2.0
checking for config ./config/site-specific/host-lconway... no
checking for clang sanitizer checks... none
checking build mode... production
checking for gcc... clang -arch x86_64
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 x86_64 accepts -g... yes
checking for clang -arch x86_64 option to enable C11 features... none needed
checking whether clang -arch x86_64 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 x86_64... 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... 16
checking size of __float128... 0
checking size of _Quad... 0
checking for quadmath.h... no
checking maximum decimal precision for C... 21
checking if Fortran interface enabled... no
checking whether the compiler supports GNU C++... yes
checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
checking for clang++ -arch x86_64 -std=gnu++17 option to enable C++11 features... none needed
checking dependency style of clang++ -arch x86_64 -std=gnu++17... gcc3
checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++17 -E
checking if c++ interface enabled... yes
checking if clang++ -arch x86_64 -std=gnu++17 needs old style header files in includes... no
checking if clang++ -arch x86_64 -std=gnu++17 can handle namespaces... yes
checking if clang++ -arch x86_64 -std=gnu++17 can handle static cast... yes
checking if clang++ -arch x86_64 -std=gnu++17 has offsetof extension... yes
checking if the high-level library is enabled... yes
checking whether make sets $(MAKE)... (cached) yes
checking for tr... /usr/bin/tr
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configure: testing for aec and szip
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checking if correctly converting long double to (unsigned) long long values... yes
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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: Fri Mar  1 15:06:20 EST 2024
                  Configured by: biocbuild@lconway
                    Host system: x86_64-apple-darwin21.6.0
              Uname information: Darwin lconway 21.6.0 Darwin Kernel Version 21.6.0: Wed Oct  4 23:55:28 PDT 2023; root:xnu-8020.240.18.704.15~1/RELEASE_X86_64 x86_64
                       Byte sex: little-endian
             Installation point: /Users/biocbuild/bbs-3.18-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/x86_64/lib
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/Users/biocbuild/bbs-3.18-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 x86_64
                       CPPFLAGS: -I/opt/R/x86_64/include
                    H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/Users/biocbuild/bbs-3.18-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 x86_64 -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(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 $d && make  lib) || exit 1;            \
	  fi;                                                           \
	done
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  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/opt/R/x86_64/lib |                  \
		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
	 ./H5make_libsettings > H5lib_settings.c  ||                               \
	    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
	    (rm -f H5lib_settings.c ; exit 1)
  CC       H5lib_settings.lo
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  CC       H5detect.o
  CCLD     H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/opt/R/x86_64/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
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols
make[3]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
  CXX      H5Exception.lo
  CXX      H5IdComponent.lo
  CXX      H5DataSpace.lo
  CXX      H5PropList.lo
  CXX      H5Library.lo
  CXX      H5FaccProp.lo
  CXX      H5FcreatProp.lo
  CXX      H5LcreatProp.lo
  CXX      H5LaccProp.lo
  CXX      H5DaccProp.lo
  CXX      H5DxferProp.lo
  CXX      H5DcreatProp.lo
  CXX      H5Location.lo
  CXX      H5AbstractDs.lo
  CXX      H5Attribute.lo
  CXX      H5Object.lo
  CXX      H5OcreatProp.lo
  CXX      H5DataType.lo
  CXX      H5AtomType.lo
  CXX      H5PredType.lo
  CXX      H5EnumType.lo
  CXX      H5IntType.lo
  CXX      H5FloatType.lo
  CXX      H5StrType.lo
  CXX      H5ArrayType.lo
  CXX      H5VarLenType.lo
  CXX      H5CompType.lo
  CXX      H5DataSet.lo
  CXX      H5CommonFG.lo
  CXX      H5Group.lo
  CXX      H5File.lo
  CXXLD    libhdf5_cpp.la
make[3]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
  CC       H5DO.lo
  CC       H5DS.lo
  CC       H5IM.lo
  CC       H5LT.lo
  CC       H5LTanalyze.lo
  CC       H5LTparse.lo
  CC       H5PT.lo
  CC       H5TB.lo
  CC       H5LD.lo
  CCLD     libhdf5_hl.la
+ cd c++
+ make lib
make[4]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
  CXX      H5PacketTable.lo
  CXXLD    libhdf5_hl_cpp.la
mkdir -p "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src"/libhdf5.settings "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Rhdf5lib.c -o Rhdf5lib.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Rhdf5lib.so Rhdf5lib.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/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/4.3-x86_64/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)