############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL Rhdf5lib ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘Rhdf5lib’ ... ** using staged installation checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed COMPILER = gcc 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: ‘gcc (GCC) 10.3.1’ 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=/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib \ CC='gcc' CXX='g++ -std=gnu++17' \ CPPFLAGS='-I/usr/local/include' \ CFLAGS='-g -O2 -Wall -w -fPIC' \ AR='ar' RANLIB='ranlib'; \ make; \ make install checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... 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 gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes 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... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /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... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -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 gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so 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... /usr/bin/mkdir -p 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 gcc... gcc3 checking whether to enable maintainer-specific portions of Makefiles... yes checking for gcc 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... 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 config/config.h config.status: executing libtool commands config.status: executing depfiles commands make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' Making all in src make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -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 gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c -o encode.lo ../../src/encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c ../../src/encode.c -fPIC -DPIC -o encode.o mv -f .deps/encode.Tpo .deps/encode.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c -o encode_accessors.lo ../../src/encode_accessors.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c ../../src/encode_accessors.c -fPIC -DPIC -o encode_accessors.o mv -f .deps/encode_accessors.Tpo .deps/encode_accessors.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c -o decode.lo ../../src/decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c ../../src/decode.c -fPIC -DPIC -o decode.o mv -f .deps/decode.Tpo .deps/decode.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -fvisibility=hidden -g -O2 -Wall -w -fPIC -version-info 0:10:0 -no-undefined -o libaec.la -rpath /home/biocbuild/bbs-3.19-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 gcc -fvisibility=hidden -g -O2 -Wall -w -fPIC -o aec aec.o libaec.la libtool: link: gcc -fvisibility=hidden -g -O2 -Wall -w -fPIC -o aec aec.o ./.libs/libaec.a gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -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 gcc -fvisibility=hidden -g -O2 -Wall -w -fPIC -o utime utime.o libtool: link: gcc -fvisibility=hidden -g -O2 -Wall -w -fPIC -o utime utime.o /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c -o sz_compat.lo ../../src/sz_compat.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -w -fPIC -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c ../../src/sz_compat.c -fPIC -DPIC -o sz_compat.o mv -f .deps/sz_compat.Tpo .deps/sz_compat.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -fvisibility=hidden -g -O2 -Wall -w -fPIC -version-info 2:1:0 -no-undefined -o libsz.la -rpath /home/biocbuild/bbs-3.19-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]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' Making install in src make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.19-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 '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' libtool: install: /usr/bin/install -c .libs/libaec.lai /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.la libtool: install: /usr/bin/install -c .libs/libsz.lai /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.la libtool: install: /usr/bin/install -c .libs/libaec.a /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: chmod 644 /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: ranlib /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: /usr/bin/install -c .libs/libsz.a /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: chmod 644 /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: ranlib /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: finish: PATH="/home/biocbuild/.local/bin:/home/biocbuild/bin:/usr/local/ensembl-vep:/usr/share/Modules/bin:/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/usr/lib64/openmpi/bin:/home/biocbuild/libudunits-2/bin:/home/biocbuild/.dotnet:/home/biocbuild/openbabel-3.1.1/bin:/sbin" ldconfig -n /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c aec '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' libtool: install: /usr/bin/install -c aec /home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec /usr/bin/mkdir -p '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/install -c -m 644 ../../src/libaec.h ../../src/szlib.h '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' /usr/bin/install -c -m 644 ../../src/aec.1 '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build' cd hdf5; \ ./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \ --enable-tests=no --enable-tools=no \ --with-szlib=/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \ --enable-ros3-vfd \ --enable-sharedlib-rpath \ CC='gcc' CXX='g++ -std=gnu++17' \ CPPFLAGS='-I/usr/local/include' \ CFLAGS='-g -O2 -Wall -w -fPIC' \ CXXFLAGS='-w -g -O2 -Wall -fPIC' \ AR='ar' RANLIB='ranlib' \ LDFLAGS='-L/usr/local/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... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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-unknown-linux-gnu... no checking for config aarch64-unknown-linux-gnu... no checking for config unknown-linux-gnu... no checking for config unknown-linux-gnu... no checking for config aarch64-linux-gnu... no checking for config aarch64-linux-gnu... no checking for config aarch64-unknown... no checking for config linux-gnu... found compiler 'gcc' is GNU gcc-10.3.1 compiler 'gfortran' is GNU gfortran-10.3.1 compiler 'g++ -std=gnu++17' is GNU g++-10.3.1 checking for config ./config/site-specific/host-kunpeng2... no checking for clang sanitizer checks... checking build mode... production checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... 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... yes checking maximum decimal precision for C... 36 checking if Fortran interface enabled... no checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking dependency style of g++ -std=gnu++17... gcc3 checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking if c++ interface enabled... yes checking if g++ -std=gnu++17 needs old style header files in includes... no checking if g++ -std=gnu++17 can handle namespaces... yes checking if g++ -std=gnu++17 can handle static cast... yes checking if g++ -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 checking if srcdir= and time commands work together... no checking if Java JNI interface enabled... no checking if building tests is disabled... Building HDF5 tests is disabled checking if building tools is disabled... Building HDF5 tools is disabled 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 gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes 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... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /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... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no 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... g++ -std=gnu++17 -E checking for ld used by g++ -std=gnu++17... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ -std=gnu++17 linker (/usr/bin/ld) supports shared libraries... yes checking for g++ -std=gnu++17 option to produce PIC... -fPIC -DPIC checking if g++ -std=gnu++17 PIC flag -fPIC -DPIC works... yes checking if g++ -std=gnu++17 static flag -static works... no checking if g++ -std=gnu++17 supports -c -o file.o... yes checking if g++ -std=gnu++17 supports -c -o file.o... (cached) yes checking whether the g++ -std=gnu++17 linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if we should install only statically linked executables... no checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes checking for ceil in -lm... yes checking for dlopen in -ldl... yes checking for egrep... (cached) /usr/bin/grep -E checking for sys/resource.h... yes checking for sys/time.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/ioctl.h... yes checking for sys/stat.h... (cached) yes checking for sys/socket.h... yes checking for sys/types.h... (cached) yes checking for sys/file.h... yes checking for stddef.h... yes checking for setjmp.h... yes checking for features.h... yes checking for dirent.h... yes checking for stdint.h... (cached) yes checking for stdbool.h... yes checking for netdb.h... yes checking for netinet/in.h... yes checking for arpa/inet.h... yes checking for io.h... no checking for winsock2.h... no checking for sys/timeb.h... yes checking for _FILE_OFFSET_BITS value needed for large files... no checking size of int8_t... 1 checking size of uint8_t... 1 checking size of int_least8_t... 1 checking size of uint_least8_t... 1 checking size of int_fast8_t... 1 checking size of uint_fast8_t... 1 checking size of int16_t... 2 checking size of uint16_t... 2 checking size of int_least16_t... 2 checking size of uint_least16_t... 2 checking size of int_fast16_t... 8 checking size of uint_fast16_t... 8 checking size of int32_t... 4 checking size of uint32_t... 4 checking size of int_least32_t... 4 checking size of uint_least32_t... 4 checking size of int_fast32_t... 8 checking size of uint_fast32_t... 8 checking size of int64_t... 8 checking size of uint64_t... 8 checking size of int_least64_t... 8 checking size of uint_least64_t... 8 checking size of int_fast64_t... 8 checking size of uint_fast64_t... 8 checking size of size_t... 8 checking size of ssize_t... 8 checking size of ptrdiff_t... 8 checking size of off_t... 8 checking size of bool... 1 checking size of time_t... 8 checking if dev_t is scalar... yes checking for dmalloc library... suppressed checking for zlib.h... yes checking for compress2 in -lz... yes checking for compress2... yes configure: testing for aec and szip checking for aec_encode in -laec... yes checking for SZ_BufftoBuffCompress in -lsz... yes checking for libaec.h... yes checking for szlib.h... yes checking for szlib encoder... yes checking for thread safe support... no checking for gcc options needed to detect all undeclared functions... none needed checking whether CLOCK_MONOTONIC is declared... yes checking for tm_gmtoff in struct tm... yes checking for global timezone variable... yes checking for st_blocks in struct stat... no checking for _getvideoconfig... no checking for gettextinfo... no checking for GetConsoleScreenBufferInfo... no checking for getpwuid... yes checking for _scrsize... no checking for ioctl... yes checking for struct videoconfig... no checking for struct text_info... no checking for TIOCGWINSZ... yes checking for TIOCGETD... yes checking for library containing clock_gettime... none required checking for alarm... yes checking for clock_gettime... yes checking for difftime... yes checking for fcntl... yes checking for flock... yes checking for fork... yes checking for frexpf... yes checking for frexpl... yes checking for gethostname... yes checking for getrusage... yes checking for gettimeofday... yes checking for lstat... yes checking for rand_r... yes checking for random... yes checking for setsysinfo... no checking for signal... yes checking for longjmp... yes checking for setjmp... yes checking for siglongjmp... yes checking for sigsetjmp... no checking for sigprocmask... yes checking for snprintf... yes checking for srandom... yes checking for strdup... yes checking for symlink... yes checking for system... yes checking for strtoll... yes checking for strtoull... yes checking for tmpfile... yes checking for asprintf... yes checking for vasprintf... yes checking for vsnprintf... yes checking for waitpid... yes checking for roundf... yes checking for lroundf... yes checking for llroundf... yes checking for round... yes checking for lround... yes checking for llround... yes checking for an ANSI C-conforming const... yes checking if the compiler understands __inline__... yes checking if the compiler understands __inline... yes checking if the compiler understands inline... yes checking for __attribute__ extension... yes checking for __func__ extension... yes checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %ld and %lu checking enable debugging symbols... no checking enable asserts... no checking enable developer warnings... no checking profiling... no checking optimization level... high checking enable file locking... best-effort checking for internal debug output... none checking whether function stack tracking is enabled... no checking for API tracing... no checking whether a memory checking tool will be used... no checking whether internal memory allocation sanity checking is used... no checking for parallel support files... skipped checking whether O_DIRECT is declared... yes checking for posix_memalign... yes checking if the direct I/O virtual file driver (VFD) is enabled... no checking if the Mirror virtual file driver (VFD) is enabled... no 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 checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes checking for libhdfs... suppressed checking for custom examples path definition... ${prefix}/share/hdf5_examples checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin checking whether exception handling functions is checked during data conversions... yes checking whether data accuracy is guaranteed during data conversions... yes checking if the machine has window style path name... no checking if using special algorithm to convert long double to (unsigned) long values... no 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 checking for pread... yes checking for pwrite... yes 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 utils/Makefile config.status: creating utils/mirror_vfd/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 SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.10.7 Configured on: Wed May 8 20:03:15 UTC 2024 Configured by: biocbuild@kunpeng2 Host system: aarch64-unknown-linux-gnu Uname information: Linux kunpeng2 5.10.0-136.63.0.143.oe2203sp1.aarch64 #1 SMP Tue Feb 6 13:53:32 CST 2024 aarch64 aarch64 aarch64 GNU/Linux Byte sex: little-endian Installation point: /home/biocbuild/bbs-3.19-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/home/biocbuild/bbs-3.19-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/gcc ( gcc (GCC) 10.3.1) CPPFLAGS: -I/usr/local/include H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include C Flags: -g -O2 -Wall -w -fPIC H5 C Flags: -std=c99 -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3 -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized AM C Flags: Shared C Library: no Static C Library: yes Fortran: no C++: yes C++ Compiler: /usr/bin/g++ -std=gnu++17 ( g++ (GCC) 10.3.1) C++ Flags: -w -g -O2 -Wall -fPIC H5 C++ Flags: -Wall -Wconversion -Wctor-dtor-privacy -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3 -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow 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 make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5' for d in src . c++ hl; do \ if test $d != .; then \ (cd $d && make lib) || exit 1; \ fi; \ done make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/src' make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/src' CC H5.lo CC H5checksum.lo CC H5dbg.lo CC H5system.lo CC H5timer.lo CC H5trace.lo CC H5A.lo CC H5Abtree2.lo CC H5Adense.lo CC H5Adeprec.lo CC H5Aint.lo CC H5Atest.lo CC H5AC.lo CC H5ACdbg.lo CC H5ACproxy_entry.lo CC H5B.lo CC H5Bcache.lo CC H5Bdbg.lo CC H5B2.lo CC H5B2cache.lo CC H5B2dbg.lo CC H5B2hdr.lo CC H5B2int.lo CC H5B2internal.lo CC H5B2leaf.lo CC H5B2stat.lo CC H5B2test.lo CC H5C.lo CC H5Cdbg.lo CC 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 CC H5Dvirtual.lo CC H5E.lo CC H5Edeprec.lo CC H5Eint.lo CC H5EA.lo CC H5EAcache.lo CC H5EAdbg.lo CC H5EAdblkpage.lo CC H5EAdblock.lo CC H5EAhdr.lo CC H5EAiblock.lo CC H5EAint.lo CC H5EAsblock.lo CC H5EAstat.lo CC H5EAtest.lo CC H5F.lo CC H5Faccum.lo CC H5Fcwfs.lo CC H5Fdbg.lo CC H5Fdeprec.lo CC H5Fefc.lo CC H5Ffake.lo CC H5Fint.lo CC H5Fio.lo CC H5Fmount.lo CC H5Fquery.lo CC H5Fsfile.lo CC H5Fspace.lo CC H5Fsuper.lo CC H5Fsuper_cache.lo CC H5Ftest.lo CC H5FA.lo CC H5FAcache.lo CC H5FAdbg.lo CC H5FAdblock.lo CC H5FAdblkpage.lo CC H5FAhdr.lo CC H5FAint.lo CC H5FAstat.lo CC H5FAtest.lo CC H5FD.lo CC H5FDcore.lo CC H5FDfamily.lo CC H5FDhdfs.lo CC H5FDint.lo CC H5FDlog.lo CC H5FDmulti.lo CC H5FDsec2.lo CC H5FDspace.lo CC H5FDsplitter.lo CC H5FDstdio.lo CC H5FDtest.lo CC H5FL.lo CC H5FO.lo CC H5FS.lo CC H5FScache.lo CC H5FSdbg.lo CC H5FSint.lo CC H5FSsection.lo CC H5FSstat.lo CC H5FStest.lo CC H5G.lo CC H5Gbtree2.lo CC H5Gcache.lo CC H5Gcompact.lo CC H5Gdense.lo CC H5Gdeprec.lo CC H5Gent.lo CC H5Gint.lo CC H5Glink.lo CC H5Gloc.lo CC H5Gname.lo CC H5Gnode.lo CC H5Gobj.lo CC H5Goh.lo CC H5Groot.lo CC H5Gstab.lo CC H5Gtest.lo CC H5Gtraverse.lo CC H5HF.lo CC H5HFbtree2.lo CC H5HFcache.lo CC H5HFdbg.lo CC H5HFdblock.lo CC H5HFdtable.lo CC H5HFhdr.lo CC H5HFhuge.lo CC H5HFiblock.lo CC H5HFiter.lo CC H5HFman.lo CC H5HFsection.lo CC H5HFspace.lo CC H5HFstat.lo CC H5HFtest.lo CC H5HFtiny.lo CC H5HG.lo CC H5HGcache.lo CC H5HGdbg.lo CC H5HGquery.lo CC H5HL.lo CC H5HLcache.lo CC H5HLdbg.lo CC H5HLint.lo CC H5HLprfx.lo CC H5HLdblk.lo CC 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 $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5lib_settings.c ; exit 1) CC H5lib_settings.lo CC H5MF.lo CC H5MFaggr.lo CC H5MFdbg.lo CC H5MFsection.lo CC H5MM.lo CC H5MP.lo CC H5MPtest.lo CC H5O.lo CC H5Odeprec.lo CC H5Oainfo.lo CC H5Oalloc.lo CC H5Oattr.lo CC H5Oattribute.lo CC H5Obogus.lo CC H5Obtreek.lo CC H5Ocache.lo CC H5Ocache_image.lo CC H5Ochunk.lo CC H5Ocont.lo CC H5Ocopy.lo CC H5Odbg.lo CC H5Odrvinfo.lo CC H5Odtype.lo CC H5Oefl.lo CC H5Ofill.lo CC H5Oflush.lo CC H5Ofsinfo.lo CC H5Oginfo.lo CC H5Oint.lo CC H5Olayout.lo CC H5Olinfo.lo CC H5Olink.lo CC H5Omessage.lo CC H5Omtime.lo CC H5Oname.lo CC H5Onull.lo CC H5Opline.lo CC H5Orefcount.lo CC H5Osdspace.lo CC H5Oshared.lo CC H5Oshmesg.lo CC H5Ostab.lo CC H5Otest.lo CC H5Ounknown.lo CC H5P.lo CC H5Pacpl.lo CC H5Pdapl.lo CC H5Pdcpl.lo CC H5Pdeprec.lo CC H5Pdxpl.lo CC H5Pencdec.lo CC H5Pfapl.lo CC H5Pfcpl.lo CC H5Pfmpl.lo CC H5Pgcpl.lo CC H5Pint.lo CC H5Plapl.lo CC H5Plcpl.lo CC H5Pocpl.lo CC H5Pocpypl.lo CC H5Pstrcpl.lo CC H5Ptest.lo CC H5PB.lo CC H5PL.lo CC H5PLint.lo CC H5PLpath.lo CC H5PLplugin_cache.lo CC H5R.lo CC H5Rint.lo CC H5Rdeprec.lo CC H5UC.lo CC H5RS.lo CC H5S.lo CC H5Sall.lo CC H5Sdbg.lo CC H5Shyper.lo CC H5Snone.lo CC H5Spoint.lo CC H5Sselect.lo CC H5Stest.lo CC H5SL.lo CC H5SM.lo CC H5SMbtree2.lo CC H5SMcache.lo CC H5SMmessage.lo CC H5SMtest.lo CC H5ST.lo CC H5T.lo CC H5Tarray.lo CC H5Tbit.lo CC H5Tcommit.lo CC H5Tcompound.lo CC H5Tconv.lo CC H5Tcset.lo CC H5Tdbg.lo CC H5Tdeprec.lo CC H5Tenum.lo CC H5Tfields.lo CC H5Tfixed.lo CC H5Tfloat.lo CC H5detect.o CCLD H5detect LD_LIBRARY_PATH="$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 CC H5FDros3.lo CC H5FDs3comms.lo CCLD libhdf5.la make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/src' make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/src' make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++' make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++' + cd src + make lib make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++/src' make[4]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++/src' 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[4]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++/src' make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++/src' make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/c++' make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl' make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl' + cd src + make lib make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/src' make[4]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/src' CC H5DO.lo CC H5DS.lo CC H5IM.lo CC H5LT.lo CC H5LTanalyze.lo CC H5LTparse.lo CC H5PT.lo CC H5TB.lo CC H5LD.lo CCLD libhdf5_hl.la make[4]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/src' make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/src' + cd c++ + make lib make[3]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++' make[4]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++' make[4]: Nothing to be done for 'build-lib'. make[4]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++' + cd src + make lib make[4]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src' make[5]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src' CXX H5PacketTable.lo CXXLD libhdf5_hl_cpp.la make[5]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src' make[4]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src' make[3]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl/c++' make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5/hl' make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/Rhdf5lib/src/hdf5' mkdir -p "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/*.h "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/c++/src"/*.h "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/src"/*.h "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/c++/src"/*.h "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/libhdf5.settings "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/src/.libs/libhdf5.a" "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" -I/usr/local/include -fPIC -g -O2 -Wall -c Rhdf5lib.c -o Rhdf5lib.o gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o Rhdf5lib.so Rhdf5lib.o /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libaec.a -lz -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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)