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CHECK report for Rhdf5lib on machv2

This page was generated on 2020-10-17 11:59:24 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Rhdf5lib PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1484/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rhdf5lib 1.10.1
Mike Smith
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Rhdf5lib
Branch: RELEASE_3_11
Last Commit: 13ec08d
Last Changed Date: 2020-07-08 18:01:40 -0400 (Wed, 08 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Rhdf5lib
Version: 1.10.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhdf5lib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhdf5lib_1.10.1.tar.gz
StartedAt: 2020-10-17 04:37:14 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:37:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 32.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Rhdf5lib.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rhdf5lib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rhdf5lib_1.10.1.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhdf5lib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhdf5lib’ version ‘1.10.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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
* checking installed package size ... NOTE
  installed size is 25.2Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    lib      19.3Mb
    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 R 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 ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/libs/Rhdf5lib.so’:
  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)

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. 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib.Rcheck/00check.log’
for details.



Installation output

Rhdf5lib.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking whether C++ compiler accepts -w... yes
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++11 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 zlib.h... yes
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... no
checking openssl/evp.h presence... no
checking for openssl/evp.h... no
checking openssl/hmac.h usability... no
checking openssl/hmac.h presence... no
checking for openssl/hmac.h... no
checking openssl/sha.h usability... no
checking openssl/sha.h presence... no
checking for openssl/sha.h... no
untarring hdf5small_cxx_hl_1.10.6.tar.gz ...
building the szip library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe 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 to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking for config x86_64-apple-darwin18.7.0... no
checking for config x86_64-apple-darwin18.7.0... no
checking for config apple-darwin18.7.0... no
checking for config apple-darwin18.7.0... no
checking for config x86_64-darwin18.7.0... no
checking for config x86_64-darwin18.7.0... no
checking for config x86_64-apple... no
checking for config darwin18.7.0... no
checking for config darwin18.7.0... no
checking for config apple... no
checking for config x86_64... no
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether clang -mmacosx-version-min=10.13 understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... gcc3
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
checking how to print strings... printf
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 -mmacosx-version-min=10.13... /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... 196608
checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 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 command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 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 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 -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
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 for build mode... production
checking for math library support... no
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for error_at_line... no
checking for working memcmp... yes
checking for vprintf... yes
checking for _doprnt... no
checking for memset... yes
checking if encoding enabled... yes
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 src/SZconfig.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making all in src
make  all-am
/bin/sh ../libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.     -Wall -O2 -w -fPIC  -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -Wall -O2 -w -fPIC -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c  -fno-common -DPIC -o rice.o
mv -f .deps/rice.Tpo .deps/rice.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.     -Wall -O2 -w -fPIC  -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -Wall -O2 -w -fPIC -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c  -fno-common -DPIC -o sz_api.o
mv -f .deps/sz_api.Tpo .deps/sz_api.Plo
/bin/sh ../libtool  --tag=CC   --mode=compile clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I.     -Wall -O2 -w -fPIC  -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c
libtool: compile:  clang -mmacosx-version-min=10.13 -DHAVE_CONFIG_H -I. -Wall -O2 -w -fPIC -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c  -fno-common -DPIC -o encoding.o
mv -f .deps/encoding.Tpo .deps/encoding.Plo
/bin/sh ../libtool  --tag=CC   --mode=link clang -mmacosx-version-min=10.13  -Wall -O2 -w -fPIC  -version-info 2:0:0  -o libsz.la -rpath /Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo  -lm
libtool: link: ar cru .libs/libsz.a  rice.o sz_api.o encoding.o
libtool: link: ranlib .libs/libsz.a
libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" )
make[1]: Nothing to be done for `all-am'.
Making install in src
 ../bin/install-sh -c -d '/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libsz.la '/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /usr/bin/install -c .libs/libsz.lai /Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libsz.a /Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: ranlib /Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
 ../bin/install-sh -c -d '/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include'
 /usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
building the hdf5 library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe 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-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
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-darwin18.7.0... no
checking for config x86_64-apple-darwin18.7.0... no
checking for config apple-darwin18.7.0... no
checking for config apple-darwin18.7.0... no
checking for config x86_64-darwin18.7.0... no
checking for config x86_64-darwin18.7.0... no
checking for config x86_64-apple... no
checking for config darwin18.7.0... no
checking for config darwin18.7.0... no
checking for config apple... found
No match to get cc_version_info for clang -mmacosx-version-min=10.13
compiler 'gfortran' is GNU gfortran-8.2.0
checking for config ./config/site-specific/host-machv2.bioconductor.org... no
checking for config ./config/site-specific/host-bioconductor.org... no
checking for config ./config/site-specific/host-org... no
checking build mode... production
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether clang -mmacosx-version-min=10.13 understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang -mmacosx-version-min=10.13... gcc3
checking if unsupported combinations of configure options are allowed... no
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 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 quadmath.h usability... no
checking quadmath.h presence... no
checking for quadmath.h... no
checking maximum decimal precision for C... 21
checking if Fortran interface enabled... no
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++11 accepts -g... yes
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++11... gcc3
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++11 -E
checking if c++ interface enabled... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 needs old style header files in includes... no
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 can handle namespaces... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 can handle static cast... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 has offsetof extension... yes
checking if the high-level library is enabled... yes
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
checking for tr... /usr/bin/tr
checking if srcdir= and time commands work together... yes
checking if Java JNI interface enabled... no
checking if building tests is disabled... checking if building tools is disabled... checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang -mmacosx-version-min=10.13... /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... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 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... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 object... 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 for dlfcn.h... yes
checking for objdir... .libs
checking if clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
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 how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++11 -E
checking for ld used by clang++ -mmacosx-version-min=10.13 -std=gnu++11... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++11 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for clang++ -mmacosx-version-min=10.13 -std=gnu++11 option to produce PIC... -fno-common -DPIC
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 PIC flag -fno-common -DPIC works... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 static flag -static works... no
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 supports -c -o file.o... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++11 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
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checking for thread safe support... no
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checking how to print long long... %ld and %lu
checking enable debugging symbols... no
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checking profiling... no
checking optimization level... high
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checking for parallel support files... skipped
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checking for posix_memalign... yes
checking if the direct I/O virtual file driver (VFD) is enabled... no
checking if the Read-Only S3 virtual file driver (VFD) is enabled... no
checking for libhdfs... suppressed
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checking whether exception handling functions is checked during data conversions... yes
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checking if the machine has window style path name... no
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checking if using special algorithm to convert (unsigned) long to long double values... no
checking if correctly converting long double to (unsigned) long long values... yes
checking if correctly converting (unsigned) long long to long double values... yes
checking if the system is IBM ppc64le and cannot correctly convert some long double values... no
checking additional programs should be built... no
checking if deprecated public symbols are available... yes
checking which version of public symbols to use by default... v110
checking whether to perform strict file format checks... no
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checking whether to use pread/pwrite instead of read/write in certain VFDs... yes
checking whether to have library information embedded in the executables... yes
checking if alignment restrictions are strictly enforced... no
configure: creating ./config.lt
config.lt: creating libtool
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating bin/h5cc
config.status: creating bin/Makefile
config.status: creating c++/Makefile
config.status: creating c++/src/Makefile
config.status: creating c++/src/h5c++
config.status: creating hl/Makefile
config.status: creating hl/src/Makefile
config.status: creating hl/c++/Makefile
config.status: creating hl/c++/src/Makefile
config.status: creating src/H5config.h
config.status: executing pubconf commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing .classes commands
sed: -i may not be used with stdin
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
                   HDF5 Version: 1.10.6
                  Configured on: Fri Oct 16 16:02:29 EDT 2020
                  Configured by: biocbuild@machv2.bioconductor.org
                    Host system: x86_64-apple-darwin18.7.0
              Uname information: Darwin machv2.bioconductor.org 18.7.0 Darwin Kernel Version 18.7.0: Mon Aug 31 20:53:32 PDT 2020; root:xnu-4903.278.44~1/RELEASE_X86_64 x86_64
                       Byte sex: little-endian
             Installation point: /Users/biocbuild/bbs-3.11-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/usr/local/lib
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/lib
                Extra libraries: -lsz -lz -ldl -lm 
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /usr/bin/clang -mmacosx-version-min=10.13
                       CPPFLAGS: 
                    H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/Users/biocbuild/bbs-3.11-bioc/meat/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -Wall -g -O2 -w -fPIC
                     H5 C Flags:     
                     AM C Flags: 
               Shared C Library: no
               Static C Library: yes


                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/clang++ -mmacosx-version-min=10.13 -std=gnu++11
                      C++ Flags: -Wall -g -O2 -w -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: yes
                Build HDF5 Tools: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                      Direct VFD: no
              (Read-Only) S3 VFD: no
            (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
       Strict file format checks: no
    Optimization instrumentation: no
for d in src . c++ hl; do                                \
	  if test $d != .; then                                        \
	   (cd $d && make  lib) || exit 1;            \
	  fi;                                                           \
	done
  CC       H5.lo
  CC       H5checksum.lo
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  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
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  CC       H5ACdbg.lo
  CC       H5ACproxy_entry.lo
  CC       H5B.lo
  CC       H5Bcache.lo
  CC       H5Bdbg.lo
  CC       H5B2.lo
  CC       H5B2cache.lo
  CC       H5B2dbg.lo
  CC       H5B2hdr.lo
  CC       H5B2int.lo
  CC       H5B2internal.lo
  CC       H5B2leaf.lo
  CC       H5B2stat.lo
  CC       H5B2test.lo
  CC       H5C.lo
  CC       H5Cdbg.lo
  CC       H5Cepoch.lo
  CC       H5Cimage.lo
  CC       H5Clog.lo
  CC       H5Clog_json.lo
  CC       H5Clog_trace.lo
  CC       H5Cprefetched.lo
  CC       H5Cquery.lo
  CC       H5Ctag.lo
  CC       H5Ctest.lo
  CC       H5CS.lo
  CC       H5CX.lo
  CC       H5D.lo
  CC       H5Dbtree.lo
  CC       H5Dbtree2.lo
  CC       H5Dchunk.lo
  CC       H5Dcompact.lo
  CC       H5Dcontig.lo
  CC       H5Ddbg.lo
  CC       H5Ddeprec.lo
  CC       H5Dearray.lo
  CC       H5Defl.lo
  CC       H5Dfarray.lo
  CC       H5Dfill.lo
  CC       H5Dint.lo
  CC       H5Dio.lo
  CC       H5Dlayout.lo
  CC       H5Dnone.lo
  CC       H5Doh.lo
  CC       H5Dscatgath.lo
  CC       H5Dselect.lo
  CC       H5Dsingle.lo
  CC       H5Dtest.lo
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  CC       H5Edeprec.lo
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  CC       H5EAcache.lo
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  CC       H5EAdblkpage.lo
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  CC       H5F.lo
  CC       H5Faccum.lo
  CC       H5Fcwfs.lo
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  CC       H5Fio.lo
  CC       H5Fmount.lo
  CC       H5Fquery.lo
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  CC       H5Fspace.lo
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  CC       H5Fsuper_cache.lo
  CC       H5Ftest.lo
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  CC       H5FAhdr.lo
  CC       H5FAint.lo
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  CC       H5FAtest.lo
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  CC       H5FDfamily.lo
  CC       H5FDhdfs.lo
  CC       H5FDint.lo
  CC       H5FDlog.lo
  CC       H5FDmulti.lo
  CC       H5FDsec2.lo
  CC       H5FDspace.lo
  CC       H5FDstdio.lo
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  CC       H5FScache.lo
  CC       H5FSdbg.lo
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  CC       H5FStest.lo
  CC       H5G.lo
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  CC       H5Gdense.lo
  CC       H5Gdeprec.lo
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  CC       H5Gobj.lo
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  CC       H5Groot.lo
  CC       H5Gstab.lo
  CC       H5Gtest.lo
  CC       H5Gtraverse.lo
  CC       H5HF.lo
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  CC       H5HFdbg.lo
  CC       H5HFdblock.lo
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  CC       H5HFhuge.lo
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  CC       H5HFtest.lo
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  CC       H5HGquery.lo
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  CC       H5HLdbg.lo
  CC       H5HLint.lo
  CC       H5HLprfx.lo
  CC       H5HLdblk.lo
  CC       H5HP.lo
  CC       H5I.lo
  CC       H5Itest.lo
  CC       H5L.lo
  CC       H5Lexternal.lo
  CC       H5make_libsettings.o
  CCLD     H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/lib |                  \
		sed -e 's/-L/:/g' -e 's/ //g'`"                               \
	 ./H5make_libsettings > H5lib_settings.c  ||                               \
	    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
	    (rm -f H5lib_settings.c ; exit 1)
  CC       H5lib_settings.lo
  CC       H5MF.lo
  CC       H5MFaggr.lo
  CC       H5MFdbg.lo
  CC       H5MFsection.lo
  CC       H5MM.lo
  CC       H5MP.lo
  CC       H5MPtest.lo
  CC       H5O.lo
  CC       H5Odeprec.lo
  CC       H5Oainfo.lo
  CC       H5Oalloc.lo
  CC       H5Oattr.lo
  CC       H5Oattribute.lo
  CC       H5Obogus.lo
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  CC       H5Ocache.lo
  CC       H5Ocache_image.lo
  CC       H5Ochunk.lo
  CC       H5Ocont.lo
  CC       H5Ocopy.lo
  CC       H5Odbg.lo
  CC       H5Odrvinfo.lo
  CC       H5Odtype.lo
  CC       H5Oefl.lo
  CC       H5Ofill.lo
  CC       H5Oflush.lo
  CC       H5Ofsinfo.lo
  CC       H5Oginfo.lo
  CC       H5Oint.lo
  CC       H5Olayout.lo
  CC       H5Olinfo.lo
  CC       H5Olink.lo
  CC       H5Omessage.lo
  CC       H5Omtime.lo
  CC       H5Oname.lo
  CC       H5Onull.lo
  CC       H5Opline.lo
  CC       H5Orefcount.lo
  CC       H5Osdspace.lo
  CC       H5Oshared.lo
  CC       H5Oshmesg.lo
  CC       H5Ostab.lo
  CC       H5Otest.lo
  CC       H5Ounknown.lo
  CC       H5P.lo
  CC       H5Pacpl.lo
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  CC       H5Pdeprec.lo
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  CC       H5Pencdec.lo
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  CC       H5Pgcpl.lo
  CC       H5Pint.lo
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  CC       H5Plcpl.lo
  CC       H5Pocpl.lo
  CC       H5Pocpypl.lo
  CC       H5Pstrcpl.lo
  CC       H5Ptest.lo
  CC       H5PB.lo
  CC       H5PL.lo
  CC       H5PLint.lo
  CC       H5PLpath.lo
  CC       H5PLplugin_cache.lo
  CC       H5R.lo
  CC       H5Rint.lo
  CC       H5Rdeprec.lo
  CC       H5UC.lo
  CC       H5RS.lo
  CC       H5S.lo
  CC       H5Sall.lo
  CC       H5Sdbg.lo
  CC       H5Shyper.lo
  CC       H5Snone.lo
  CC       H5Spoint.lo
  CC       H5Sselect.lo
  CC       H5Stest.lo
  CC       H5SL.lo
  CC       H5SM.lo
  CC       H5SMbtree2.lo
  CC       H5SMcache.lo
  CC       H5SMmessage.lo
  CC       H5SMtest.lo
  CC       H5ST.lo
  CC       H5T.lo
  CC       H5Tarray.lo
  CC       H5Tbit.lo
  CC       H5Tcommit.lo
  CC       H5Tcompound.lo
  CC       H5Tconv.lo
  CC       H5Tcset.lo
  CC       H5Tdbg.lo
  CC       H5Tdeprec.lo
  CC       H5Tenum.lo
  CC       H5Tfields.lo
  CC       H5Tfixed.lo
  CC       H5Tfloat.lo
  CC       H5detect.o
  CCLD     H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/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
  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[2]: 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[2]: 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[3]: Nothing to be done for `build-lib'.
+ cd src
+ make lib
  CXX      H5PacketTable.lo
  CXXLD    libhdf5_hl_cpp.la
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_HL_INCLUDE=hdf5/hl/src
configure:    HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure:    HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/szip/src/.libs/libsz.a" "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -Ihdf5/src   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rhdf5lib.c -o Rhdf5lib.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rhdf5lib.so Rhdf5lib.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)

Tests output

Rhdf5lib.Rcheck/tests/tinytest.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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

Running test_library_version.R........    1 tests OK 
Running test_library_version.R........    2 tests OK 
[1] "All ok, 2 results"
> 
> proc.time()
   user  system elapsed 
  0.444   0.086   0.514 

Example timings

Rhdf5lib.Rcheck/Rhdf5lib-Ex.timings

nameusersystemelapsed
getHdf5Version0.0020.0030.011
pkgconfig0.0030.0010.006