################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL Rhdf5lib###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘Rhdf5lib’ ...** this is package ‘Rhdf5lib’ version ‘1.32.0’** using staged installationchecking for gcc... gcc -std=gnu2xchecking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether the compiler supports GNU C... yeschecking whether gcc -std=gnu2x accepts -g... yeschecking for gcc -std=gnu2x option to enable C11 features... none neededchecking whether the compiler supports GNU C++... yeschecking whether g++ -std=gnu++17 accepts -g... yeschecking for g++ -std=gnu++17 option to enable C++11 features... none neededCOMPILER = gccchecking whether C compiler accepts -w... yeschecking whether to use -Wl,-rpath setting... yeschecking for stdio.h... yeschecking for stdlib.h... yeschecking for string.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for strings.h... yeschecking for sys/stat.h... yeschecking for sys/types.h... yeschecking for unistd.h... yeschecking for zlib.h... yesON_BUILDER=falseON_BUILDER=truechecking for curl/curl.h... yeschecking for openssl/evp.h... yeschecking for openssl/hmac.h... yeschecking for openssl/sha.h... yeschecking for curl_global_init in -lcurl... yeschecking for EVP_sha256 in -lcrypto... yesS3_VFD=--enable-ros3-vfdconfigure: creating ./config.statusconfig.status: creating src/Makevars** libsusing C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’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-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib \CC='gcc -std=gnu2x' CXX='g++ -std=gnu++17' \CPPFLAGS='-I/usr/local/include' \CFLAGS='-g -O2 -Wall -Werror=format-security -w -fpic' \AR='ar' RANLIB='ranlib'; \make; \make installchecking build system type... x86_64-pc-linux-gnuchecking host system type... x86_64-pc-linux-gnuchecking how to print strings... printfchecking for gcc... gcc -std=gnu2xchecking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether we are using the GNU C compiler... yeschecking whether gcc -std=gnu2x accepts -g... yeschecking for gcc -std=gnu2x option to accept ISO C89... none neededchecking whether gcc -std=gnu2x understands -c and -o together... yeschecking for a sed that does not truncate output... /usr/bin/sedchecking for grep that handles long lines and -e... /usr/bin/grepchecking for egrep... /usr/bin/grep -Echecking for fgrep... /usr/bin/grep -Fchecking for ld used by gcc -std=gnu2x... /usr/bin/ldchecking if the linker (/usr/bin/ld) is GNU ld... yeschecking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -Bchecking the name lister (/usr/bin/nm -B) interface... BSD nmchecking whether ln -s works... yeschecking the maximum length of command line arguments... 1572864checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noopchecking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noopchecking for /usr/bin/ld option to reload object files... -rchecking for objdump... objdumpchecking how to recognize dependent libraries... pass_allchecking for dlltool... nochecking how to associate runtime and link libraries... printf %s\nchecking for archiver @FILE support... @checking for strip... stripchecking for ranlib... ranlibchecking for gawk... gawkchecking command to parse /usr/bin/nm -B output from gcc -std=gnu2x object... okchecking for sysroot... nochecking for a working dd... /usr/bin/ddchecking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1checking for mt... mtchecking if mt is a manifest tool... nochecking how to run the C preprocessor... gcc -std=gnu2x -Echecking for ANSI C header files... yeschecking for sys/types.h... yeschecking for sys/stat.h... yeschecking for stdlib.h... yeschecking for string.h... yeschecking for memory.h... yeschecking for strings.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for unistd.h... yeschecking for dlfcn.h... yeschecking for objdir... .libschecking if gcc -std=gnu2x supports -fno-rtti -fno-exceptions... yeschecking for gcc -std=gnu2x option to produce PIC... -fPIC -DPICchecking if gcc -std=gnu2x PIC flag -fPIC -DPIC works... yeschecking if gcc -std=gnu2x static flag -static works... yeschecking if gcc -std=gnu2x supports -c -o file.o... yeschecking if gcc -std=gnu2x supports -c -o file.o... (cached) yeschecking whether the gcc -std=gnu2x linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yeschecking dynamic linker characteristics... GNU/Linux ld.sochecking how to hardcode library paths into programs... immediatechecking whether stripping libraries is possible... yeschecking if libtool supports shared libraries... yeschecking whether to build shared libraries... nochecking whether to build static libraries... yeschecking whether the -Werror option is usable... yeschecking for simple visibility declarations... yeschecking for a BSD-compatible install... /usr/bin/install -cchecking whether build environment is sane... yeschecking for a thread-safe mkdir -p... /usr/bin/mkdir -pchecking whether make sets $(MAKE)... yeschecking whether make supports the include directive... yes (GNU style)checking whether make supports nested variables... yeschecking dependency style of gcc -std=gnu2x... gcc3checking whether to enable maintainer-specific portions of Makefiles... yeschecking for gcc -std=gnu2x option to accept ISO C99... none neededchecking for ANSI C header files... (cached) yeschecking whether byte ordering is bigendian... nochecking for inline... inlinechecking for int64_t... yeschecking for size_t... yeschecking for uint32_t... yeschecking for uint64_t... yeschecking for uint8_t... yeschecking for inline... (cached) inlinechecking for C/C++ restrict keyword... __restrictchecking for memset... yeschecking for strstr... yeschecking for snprintf... yeschecking whether __builtin_clzll is declared... yeschecking that generated files are newer than configure... doneconfigure: creating ./config.statusconfig.status: creating Makefileconfig.status: creating src/Makefileconfig.status: creating config/config.hconfig.status: executing libtool commandsconfig.status: executing depfiles commandsmake[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build'Making all in srcmake[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src'gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT aec.o -MD -MP -MF .deps/aec.Tpo -c -o aec.o ../../src/aec.cmv -f .deps/aec.Tpo .deps/aec.Po/bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c -o encode.lo ../../src/encode.clibtool: compile: gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c ../../src/encode.c -fPIC -DPIC -o encode.omv -f .deps/encode.Tpo .deps/encode.Plo/bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c -o encode_accessors.lo ../../src/encode_accessors.clibtool: compile: gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c ../../src/encode_accessors.c -fPIC -DPIC -o encode_accessors.omv -f .deps/encode_accessors.Tpo .deps/encode_accessors.Plo/bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c -o decode.lo ../../src/decode.clibtool: compile: gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c ../../src/decode.c -fPIC -DPIC -o decode.omv -f .deps/decode.Tpo .deps/decode.Plo/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu2x -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -version-info 0:10:0 -no-undefined -o libaec.la -rpath /home/biocbuild/bbs-3.22-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.olibtool: link: ranlib .libs/libaec.alibtool: link: ( cd ".libs" && rm -f "libaec.la" && ln -s "../libaec.la" "libaec.la" )/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu2x -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -o aec aec.o libaec.la libtool: link: gcc -std=gnu2x -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -o aec aec.o ./.libs/libaec.agcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT utime.o -MD -MP -MF .deps/utime.Tpo -c -o utime.o ../../src/utime.cmv -f .deps/utime.Tpo .deps/utime.Po/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu2x -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -o utime utime.o libtool: link: gcc -std=gnu2x -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -o utime utime.o /bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c -o sz_compat.lo ../../src/sz_compat.clibtool: compile: gcc -std=gnu2x -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/usr/local/include -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c ../../src/sz_compat.c -fPIC -DPIC -o sz_compat.omv -f .deps/sz_compat.Tpo .deps/sz_compat.Plo/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu2x -fvisibility=hidden -g -O2 -Wall -Werror=format-security -w -fpic -version-info 2:1:0 -no-undefined -o libsz.la -rpath /home/biocbuild/bbs-3.22-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.olibtool: link: ranlib .libs/libsz.alibtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" )make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src'make[2]: Entering directory '/home/biocbuild/bbs-3.22-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-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build'make[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build'make[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build'Making install in srcmake[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src'make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' /bin/bash ../libtool --mode=install /usr/bin/install -c libaec.la libsz.la '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib'libtool: install: /usr/bin/install -c .libs/libaec.lai /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.lalibtool: install: /usr/bin/install -c .libs/libsz.lai /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.lalibtool: install: /usr/bin/install -c .libs/libaec.a /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.alibtool: install: /usr/bin/install -c .libs/libsz.a /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.alibtool: install: chmod 644 /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.alibtool: install: ranlib /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.alibtool: finish: PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/sbin" ldconfig -n /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib----------------------------------------------------------------------Libraries have been installed in: /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/libIf you ever happen to want to link against installed librariesin a given directory, LIBDIR, you must either use libtool, andspecify 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 formore information, such as the ld(1) and ld.so(8) manual pages.---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c aec '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin'libtool: install: /usr/bin/install -c aec /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-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-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.22-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-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src'make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build'make[3]: Entering directory '/home/biocbuild/bbs-3.22-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-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build'make[1]: Leaving directory '/home/biocbuild/bbs-3.22-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-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \--enable-ros3-vfd \--enable-sharedlib-rpath \CC='gcc -std=gnu2x' CXX='g++ -std=gnu++17' \CPPFLAGS='-I/usr/local/include' \CFLAGS='-g -O2 -Wall -Werror=format-security -w -fpic' \CXXFLAGS='-w -g -O2 -Wall -Werror=format-security -fpic' \AR='ar' RANLIB='ranlib' \LDFLAGS='-L/usr/local/lib'; \make libchecking for a BSD-compatible install... /usr/bin/install -cchecking whether build environment is sane... yeschecking for a race-free mkdir -p... /usr/bin/mkdir -pchecking for gawk... gawkchecking whether make sets $(MAKE)... yeschecking whether make supports nested variables... yeschecking whether make supports nested variables... (cached) yeschecking whether to enable maintainer-specific portions of Makefiles... nochecking build system type... x86_64-pc-linux-gnuchecking host system type... x86_64-pc-linux-gnuchecking shell variables initial values... donechecking if basename works... yeschecking if xargs works... yeschecking for cached host... nonechecking for config x86_64-pc-linux-gnu... nochecking for config x86_64-pc-linux-gnu... nochecking for config pc-linux-gnu... nochecking for config pc-linux-gnu... nochecking for config x86_64-linux-gnu... nochecking for config x86_64-linux-gnu... nochecking for config x86_64-pc... nochecking for config linux-gnu... foundcompiler 'gcc -std=gnu2x' is GNU gcc-13.3.0compiler 'gfortran' is GNU gfortran-13.3.0compiler 'g++ -std=gnu++17' is GNU g++-13.3.0checking for config ./config/site-specific/host-nebbiolo2... nochecking for clang sanitizer checks... checking build mode... productionchecking for gcc... gcc -std=gnu2xchecking whether the C compiler works... yeschecking for C compiler default output file name... a.outchecking for suffix of executables... checking whether we are cross compiling... nochecking for suffix of object files... ochecking whether the compiler supports GNU C... yeschecking whether gcc -std=gnu2x accepts -g... yeschecking for gcc -std=gnu2x option to enable C11 features... none neededchecking whether gcc -std=gnu2x understands -c and -o together... yeschecking whether make supports the include directive... yes (GNU style)checking dependency style of gcc -std=gnu2x... gcc3checking if unsupported combinations of configure options are allowed... nochecking for stdio.h... yeschecking for stdlib.h... yeschecking for string.h... yeschecking for inttypes.h... yeschecking for stdint.h... yeschecking for strings.h... yeschecking for sys/stat.h... yeschecking for sys/types.h... yeschecking for unistd.h... yeschecking for sys/time.h... yeschecking for off_t... yeschecking for size_t... yeschecking for ssize_t... yeschecking for ptrdiff_t... yeschecking whether byte ordering is bigendian... nochecking size of char... 1checking size of short... 2checking size of int... 4checking size of unsigned... 4checking size of long... 8checking size of long long... 8checking size of __int64... 0checking size of float... 4checking size of double... 8checking size of long double... 16checking size of __float128... 16checking size of _Quad... 0checking for quadmath.h... yeschecking maximum decimal precision for C... 33checking if Fortran interface enabled... nochecking whether the compiler supports GNU C++... yeschecking whether g++ -std=gnu++17 accepts -g... yeschecking for g++ -std=gnu++17 option to enable C++11 features... none neededchecking dependency style of g++ -std=gnu++17... gcc3checking how to run the C++ preprocessor... g++ -std=gnu++17 -Echecking if c++ interface enabled... yeschecking if g++ -std=gnu++17 needs old style header files in includes... nochecking if g++ -std=gnu++17 can handle namespaces... yeschecking if g++ -std=gnu++17 can handle static cast... yeschecking if g++ -std=gnu++17 has offsetof extension... yeschecking if the high-level library is enabled... yeschecking whether make sets $(MAKE)... (cached) yeschecking for tr... /usr/bin/trchecking if srcdir= and time commands work together... yeschecking if Java JNI interface enabled... nochecking if building tests is disabled... Building HDF5 tests is disabledchecking if building tools is disabled... Building HDF5 tools is disabledchecking how to print strings... printfchecking for a sed that does not truncate output... /usr/bin/sedchecking for grep that handles long lines and -e... /usr/bin/grepchecking for egrep... /usr/bin/grep -Echecking for fgrep... /usr/bin/grep -Fchecking for ld used by gcc -std=gnu2x... /usr/bin/ldchecking if the linker (/usr/bin/ld) is GNU ld... yeschecking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -Bchecking the name lister (/usr/bin/nm -B) interface... BSD nmchecking whether ln -s works... yeschecking the maximum length of command line arguments... 1572864checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noopchecking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noopchecking for /usr/bin/ld option to reload object files... -rchecking for objdump... objdumpchecking how to recognize dependent libraries... pass_allchecking for dlltool... nochecking how to associate runtime and link libraries... printf %s\nchecking for archiver @FILE support... @checking for strip... stripchecking for ranlib... ranlibchecking command to parse /usr/bin/nm -B output from gcc -std=gnu2x object... okchecking for sysroot... nochecking for a working dd... /usr/bin/ddchecking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1checking for mt... mtchecking if mt is a manifest tool... nochecking for dlfcn.h... yeschecking for objdir... .libschecking if gcc -std=gnu2x supports -fno-rtti -fno-exceptions... yeschecking for gcc -std=gnu2x option to produce PIC... -fPIC -DPICchecking if gcc -std=gnu2x PIC flag -fPIC -DPIC works... yeschecking if gcc -std=gnu2x static flag -static works... yeschecking if gcc -std=gnu2x supports -c -o file.o... yeschecking if gcc -std=gnu2x supports -c -o file.o... (cached) yeschecking whether the gcc -std=gnu2x linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yeschecking dynamic linker characteristics... GNU/Linux ld.sochecking how to hardcode library paths into programs... immediatechecking for shl_load... nochecking for shl_load in -ldld... nochecking for dlopen... yeschecking whether a program can dlopen itself... yeschecking whether a statically linked program can dlopen itself... nochecking whether stripping libraries is possible... yeschecking if libtool supports shared libraries... yeschecking whether to build shared libraries... nochecking whether to build static libraries... yeschecking how to run the C++ preprocessor... g++ -std=gnu++17 -Echecking for ld used by g++ -std=gnu++17... /usr/bin/ld -m elf_x86_64checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yeschecking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yeschecking for g++ -std=gnu++17 option to produce PIC... -fPIC -DPICchecking if g++ -std=gnu++17 PIC flag -fPIC -DPIC works... yeschecking if g++ -std=gnu++17 static flag -static works... yeschecking if g++ -std=gnu++17 supports -c -o file.o... yeschecking if g++ -std=gnu++17 supports -c -o file.o... (cached) yeschecking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yeschecking dynamic linker characteristics... (cached) GNU/Linux ld.sochecking how to hardcode library paths into programs... immediatechecking if we should install only statically linked executables... nochecking if -Wl,-rpath should be used to link shared libs in nondefault directories... yeschecking for ceil in -lm... yeschecking for dlopen in -ldl... yeschecking for egrep... (cached) /usr/bin/grep -Echecking for sys/resource.h... yeschecking for sys/time.h... (cached) yeschecking for unistd.h... (cached) yeschecking for sys/ioctl.h... yeschecking for sys/stat.h... (cached) yeschecking for sys/socket.h... yeschecking for sys/types.h... (cached) yeschecking for sys/file.h... yeschecking for stddef.h... yeschecking for setjmp.h... yeschecking for features.h... yeschecking for dirent.h... yeschecking for stdint.h... (cached) yeschecking for stdbool.h... yeschecking for netdb.h... yeschecking for netinet/in.h... yeschecking for arpa/inet.h... yeschecking for io.h... nochecking for winsock2.h... nochecking for sys/timeb.h... yeschecking for _FILE_OFFSET_BITS value needed for large files... nochecking size of int8_t... 1checking size of uint8_t... 1checking size of int_least8_t... 1checking size of uint_least8_t... 1checking size of int_fast8_t... 1checking size of uint_fast8_t... 1checking size of int16_t... 2checking size of uint16_t... 2checking size of int_least16_t... 2checking size of uint_least16_t... 2checking size of int_fast16_t... 8checking size of uint_fast16_t... 8checking size of int32_t... 4checking size of uint32_t... 4checking size of int_least32_t... 4checking size of uint_least32_t... 4checking size of int_fast32_t... 8checking size of uint_fast32_t... 8checking size of int64_t... 8checking size of uint64_t... 8checking size of int_least64_t... 8checking size of uint_least64_t... 8checking size of int_fast64_t... 8checking size of uint_fast64_t... 8checking size of size_t... 8checking size of ssize_t... 8checking size of ptrdiff_t... 8checking size of off_t... 8checking size of bool... 1checking size of time_t... 8checking if dev_t is scalar... yeschecking for dmalloc library... suppressedchecking for zlib.h... yeschecking for compress2 in -lz... yeschecking for compress2... yesconfigure: testing for aec and szipchecking for aec_encode in -laec... yeschecking for SZ_BufftoBuffCompress in -lsz... yeschecking for libaec.h... yeschecking for szlib.h... yeschecking for szlib encoder... yeschecking for thread safe support... nochecking for gcc -std=gnu2x options needed to detect all undeclared functions... none neededchecking whether CLOCK_MONOTONIC is declared... yeschecking for tm_gmtoff in struct tm... yeschecking for global timezone variable... yeschecking for st_blocks in struct stat... nochecking for _getvideoconfig... nochecking for gettextinfo... nochecking for GetConsoleScreenBufferInfo... nochecking for getpwuid... yeschecking for _scrsize... nochecking for ioctl... yeschecking for struct videoconfig... nochecking for struct text_info... nochecking for TIOCGWINSZ... yeschecking for TIOCGETD... yeschecking for library containing clock_gettime... none requiredchecking for alarm... yeschecking for clock_gettime... yeschecking for difftime... yeschecking for fcntl... yeschecking for flock... yeschecking for fork... yeschecking for frexpf... yeschecking for frexpl... yeschecking for gethostname... yeschecking for getrusage... yeschecking for gettimeofday... yeschecking for lstat... yeschecking for rand_r... yeschecking for random... yeschecking for setsysinfo... nochecking for signal... yeschecking for longjmp... yeschecking for setjmp... yeschecking for siglongjmp... yeschecking for sigsetjmp... nochecking for sigprocmask... yeschecking for snprintf... yeschecking for srandom... yeschecking for strdup... yeschecking for symlink... yeschecking for system... yeschecking for strtoll... yeschecking for strtoull... yeschecking for tmpfile... yeschecking for asprintf... yeschecking for vasprintf... yeschecking for vsnprintf... yeschecking for waitpid... yeschecking for roundf... yeschecking for lroundf... yeschecking for llroundf... yeschecking for round... yeschecking for lround... yeschecking for llround... yeschecking for an ANSI C-conforming const... yeschecking if the compiler understands __inline__... yeschecking if the compiler understands __inline... yeschecking if the compiler understands inline... yeschecking for __attribute__ extension... yeschecking for __func__ extension... yeschecking for __FUNCTION__ extension... yeschecking for C99 designated initialization support... yeschecking how to print long long... %ld and %luchecking enable debugging symbols... nochecking enable asserts... nochecking enable developer warnings... nochecking profiling... nochecking optimization level... highchecking enable file locking... best-effortchecking for internal debug output... nonechecking whether function stack tracking is enabled... nochecking for API tracing... nochecking whether a memory checking tool will be used... nochecking whether internal memory allocation sanity checking is used... nochecking for parallel support files... skippedchecking whether O_DIRECT is declared... yeschecking for posix_memalign... yeschecking if the direct I/O virtual file driver (VFD) is enabled... nochecking if the Mirror virtual file driver (VFD) is enabled... nochecking for curl/curl.h... yeschecking for openssl/evp.h... yeschecking for openssl/hmac.h... yeschecking for openssl/sha.h... yeschecking for curl_global_init in -lcurl... yeschecking for EVP_sha256 in -lcrypto... yeschecking if the Read-Only S3 virtual file driver (VFD) is enabled... yeschecking for libhdfs... suppressedchecking for custom examples path definition... ${prefix}/share/hdf5_exampleschecking for custom plugin default path definition... /usr/local/hdf5/lib/pluginchecking whether exception handling functions is checked during data conversions... yeschecking whether data accuracy is guaranteed during data conversions... yeschecking if the machine has window style path name... nochecking if using special algorithm to convert long double to (unsigned) long values... nochecking if using special algorithm to convert (unsigned) long to long double values... nochecking if correctly converting long double to (unsigned) long long values... yeschecking if correctly converting (unsigned) long long to long double values... yeschecking if the system is IBM ppc64le and cannot correctly convert some long double values... nochecking additional programs should be built... nochecking if deprecated public symbols are available... yeschecking which version of public symbols to use by default... v110checking whether to perform strict file format checks... nochecking for pread... yeschecking for pwrite... yeschecking whether to use pread/pwrite instead of read/write in certain VFDs... yeschecking whether to have library information embedded in the executables... yeschecking if alignment restrictions are strictly enforced... noconfigure: creating ./config.ltconfig.lt: creating libtoolchecking that generated files are newer than configure... doneconfigure: creating ./config.statusconfig.status: creating src/libhdf5.settingsconfig.status: creating Makefileconfig.status: creating src/Makefileconfig.status: creating utils/Makefileconfig.status: creating utils/mirror_vfd/Makefileconfig.status: creating bin/h5ccconfig.status: creating bin/Makefileconfig.status: creating c++/Makefileconfig.status: creating c++/src/Makefileconfig.status: creating c++/src/h5c++config.status: creating hl/Makefileconfig.status: creating hl/src/Makefileconfig.status: creating hl/c++/Makefileconfig.status: creating hl/c++/src/Makefileconfig.status: creating src/H5config.hconfig.status: executing pubconf commandscreating src/H5pubconf.hPost process src/libhdf5.settingsconfig.status: executing depfiles commandsconfig.status: executing libtool commandsconfig.status: executing .classes commands SUMMARY OF THE HDF5 CONFIGURATION =================================General Information:------------------- HDF5 Version: 1.10.7 Configured on: Thu Dec 11 15:58:56 EST 2025 Configured by: biocbuild@nebbiolo2 Host system: x86_64-pc-linux-gnu Uname information: Linux nebbiolo2 6.8.0-79-generic #79-Ubuntu SMP PREEMPT_DYNAMIC Tue Aug 12 14:42:46 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Installation point: /home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hdf5Compiling Options:------------------ Build Mode: production Debugging Symbols: no Asserts: no Profiling: no Optimization Level: highLinking Options:---------------- Libraries: static Statically Linked Executables: LDFLAGS: -L/usr/local/lib H5_LDFLAGS: AM_LDFLAGS: -L/home/biocbuild/bbs-3.22-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: ranlibLanguages:---------- C: yes C Compiler: /usr/bin/gcc -std=gnu2x 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-3.22-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include C Flags: -g -O2 -Wall -Werror=format-security -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 C++ Flags: -w -g -O2 -Wall -Werror=format-security -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: noFeatures:--------- Parallel HDF5: noParallel 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: nomake[1]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5'for d in src . c++ hl; do \ if test $d != .; then \ (cd $d && make lib) || exit 1; \ fi; \donemake[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/src'make[3]: Entering directory '/home/biocbuild/bbs-3.22-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_libsettingsLD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/usr/local/lib | \sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5make_libsettings > H5lib_settings.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5lib_settings.c ; exit 1) CC H5lib_settings.lo CC H5MF.lo CC H5MFaggr.lo CC H5MFdbg.lo CC H5MFsection.lo CC H5MM.lo CC H5MP.lo CC H5MPtest.lo CC H5O.lo CC H5Odeprec.lo CC H5Oainfo.lo CC H5Oalloc.lo CC H5Oattr.lo CC H5Oattribute.lo CC H5Obogus.lo CC H5Obtreek.lo CC H5Ocache.lo CC H5Ocache_image.lo CC H5Ochunk.lo CC H5Ocont.lo CC H5Ocopy.lo CC H5Odbg.lo CC H5Odrvinfo.lo CC H5Odtype.lo CC H5Oefl.lo CC H5Ofill.lo CC H5Oflush.lo CC H5Ofsinfo.lo CC H5Oginfo.lo CC H5Oint.lo CC H5Olayout.lo CC H5Olinfo.lo CC H5Olink.lo CC H5Omessage.lo CC H5Omtime.lo CC H5Oname.lo CC H5Onull.lo CC H5Opline.lo CC H5Orefcount.lo CC H5Osdspace.lo CC H5Oshared.lo CC H5Oshmesg.lo CC H5Ostab.lo CC H5Otest.lo CC H5Ounknown.lo CC H5P.lo CC H5Pacpl.lo CC H5Pdapl.lo CC H5Pdcpl.lo CC H5Pdeprec.lo CC H5Pdxpl.lo CC H5Pencdec.lo CC H5Pfapl.lo CC H5Pfcpl.lo CC H5Pfmpl.lo CC H5Pgcpl.lo CC H5Pint.lo CC H5Plapl.lo CC H5Plcpl.lo CC H5Pocpl.lo CC H5Pocpypl.lo CC H5Pstrcpl.lo CC H5Ptest.lo CC H5PB.lo CC H5PL.lo CC H5PLint.lo CC H5PLpath.lo CC H5PLplugin_cache.lo CC H5R.lo CC H5Rint.lo CC H5Rdeprec.lo CC H5UC.lo CC H5RS.lo CC H5S.lo CC H5Sall.lo CC H5Sdbg.lo CC H5Shyper.lo CC H5Snone.lo CC H5Spoint.lo CC H5Sselect.lo CC H5Stest.lo CC H5SL.lo CC H5SM.lo CC H5SMbtree2.lo CC H5SMcache.lo CC H5SMmessage.lo CC H5SMtest.lo CC H5ST.lo CC H5T.lo CC H5Tarray.lo CC H5Tbit.lo CC H5Tcommit.lo CC H5Tcompound.lo CC H5Tconv.lo CC H5Tcset.lo CC H5Tdbg.lo CC H5Tdeprec.lo CC H5Tenum.lo CC H5Tfields.lo CC H5Tfixed.lo CC H5Tfloat.lo CC H5detect.o CCLD H5detectLD_LIBRARY_PATH="$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.lamake[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/src'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/src'make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/c++'make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/c++'make[3]: Nothing to be done for 'build-lib'.make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/c++'+ cd src+ make libmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/c++/src'make[4]: Entering directory '/home/biocbuild/bbs-3.22-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.lamake[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/c++/src'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/c++/src'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/c++'make[2]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl'make[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl'make[3]: Nothing to be done for 'build-lib'.make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl'+ cd src+ make libmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/src'make[4]: Entering directory '/home/biocbuild/bbs-3.22-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.lamake[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/src'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/src'+ cd c+++ make libmake[3]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++'make[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++'make[4]: Nothing to be done for 'build-lib'.make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++'+ cd src+ make libmake[4]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src'make[5]: Entering directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src' CXX H5PacketTable.lo CXXLD libhdf5_hl_cpp.lamake[5]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src'make[4]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++/src'make[3]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl/c++'make[2]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5/hl'make[1]: Leaving directory '/home/biocbuild/bbs-3.22-bioc/meat/Rhdf5lib/src/hdf5'mkdir -p "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"cp "hdf5/src"/*.h "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"cp "hdf5/c++/src"/*.h "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"cp "hdf5/hl/src"/*.h "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"cp "hdf5/hl/c++/src"/*.h "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"cp "hdf5/src"/libhdf5.settings "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"mkdir -p "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"cp "hdf5/src/.libs/libhdf5.a" "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Rhdf5lib.c -o Rhdf5lib.ogcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o Rhdf5lib.so Rhdf5lib.o /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libaec.a -lz -L/home/biocbuild/bbs-3.22-bioc/R/lib -lRinstalling to /home/biocbuild/bbs-3.22-bioc/R/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)