Compilation fatal error: iostream.h: No such file or directory when installing Rhdf5lib package
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charlotte ▴ 10
@bbcc9ab6
Last seen 3.3 years ago
Hong Kong

Hi I am currently trying to install Rhdf5lib on R 4.1.0 on ubuntu, but it occurs a fatal error of compilation : iostream.h: No such file or directory, I do not know how to solve it.

BiocManager::install("Rhdf5lib",force=TRUE)


#error and warning messages:
H5DataSpace.cpp:15:10: fatal error: iostream.h: No such file or directory
   15 | #include <iostream.h>
      |          ^~~~~~~~~~~~
compilation terminated.
make[3]: *** [Makefile:1035: H5DataSpace.lo] Error 1
make[3]: Leaving directory '/tmp/Rtmp3a5w9o/R.INSTALLfdf43ea004b/Rhdf5lib/src/hdf5/c++/src'
make[2]: *** [Makefile:1525: lib] Error 1
make[2]: Leaving directory '/tmp/Rtmp3a5w9o/R.INSTALLfdf43ea004b/Rhdf5lib/src/hdf5/c++/src'
make[1]: *** [Makefile:1261: lib] Error 1
make[1]: Leaving directory '/tmp/Rtmp3a5w9o/R.INSTALLfdf43ea004b/Rhdf5lib/src/hdf5/c++'
make: *** [Makefile:1100: lib] Error 1
configure: error: "Failed to compiled the HDF5 library"

I hope someone can help me and thanks a lot!
rhdf5 Rhdf5lib • 7.0k views
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It is likely that you need to install the libraries on your Ubuntu OS outside R, via:

apt-get install libhdf5-dev

Note: use sudo if required

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Thank you for your reply, but this seems to not work for me, do I need to install hdf5 on my Ubuntu?

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No you don't need to install HDF5 via Ubuntu. The Rhdf5lib package is essentially doing this, and is designed to provide a consistent version of HDF5 to R no matter what operating system someone is using.

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Mike Smith ★ 6.6k
@mike-smith
Last seen 1 day ago
EMBL Heidelberg

On my Ubuntu system the iostreams.h header is provided by the package libstdc++9-dev. However that package is a dependency of g++9 and I'm not sure if you would even get this far without having a C++ compiler installed.

I would make sure I've got some of the fundamental tools installed by running sudo apt-get install build-essential and then trying again.

If that still doesn't help then it would be helpful to see the complete output from the Rhdf5lib installation. It will print lots of information about the detected system setup, and that may help us identify why this isn't working.
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Thanks for your reply! I have installed the fundamental tools, and my g++ version is :

Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.3.0-17ubuntu1~20.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04)

I checked that I have installed libstdc++9-dev, so how to solve this problem?

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Here is the installation output(first part):

checking for x86_64-conda-linux-gnu-gcc... x86_64-conda-linux-gnu-cc
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 x86_64-conda-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-conda-linux-gnu-c++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... x86_64-conda-linux-gnu-c++ -std=gnu++14 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for zlib.h... yes
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... yes
checking openssl/evp.h presence... yes
checking for openssl/evp.h... yes
checking openssl/hmac.h usability... yes
checking openssl/hmac.h presence... yes
checking for openssl/hmac.h... yes
checking openssl/sha.h usability... yes
checking openssl/sha.h presence... 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
found  hdf5  header sources and tar archive;using what is there.
building the szip library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-conda-linux-gnu
checking host system type... x86_64-conda-linux-gnu
checking for config x86_64-conda-linux-gnu... no
checking for config x86_64-conda-linux-gnu... no
checking for config conda-linux-gnu... no
checking for config conda-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-conda... no
checking for config linux-gnu... found
compiler 'x86_64-conda-linux-gnu-cc' is GNU gcc-9.3.0
checking for x86_64-conda-linux-gnu-gcc... x86_64-conda-linux-gnu-cc
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 x86_64-conda-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking whether x86_64-conda-linux-gnu-cc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-conda-linux-gnu-cc... gcc3
checking how to run the C preprocessor... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-cpp
checking whether make sets $(MAKE)... (cached) yes
checking how to print strings... printf
checking for a sed that does not truncate output... /home/xyl/miniconda3/envs/Rbio/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 x86_64-conda-linux-gnu-cc... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld
checking if the linker (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-nm
checking the name lister (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-conda-linux-gnu file names to x86_64-conda-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-conda-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld option to reload object files... -r
checking for x86_64-conda-linux-gnu-objdump... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-conda-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-conda-linux-gnu-ar... x86_64-conda-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-conda-linux-gnu-strip... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-strip
checking for x86_64-conda-linux-gnu-ranlib... x86_64-conda-linux-gnu-ranlib
checking command to parse /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-nm output from x86_64-conda-linux-gnu-cc 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 x86_64-conda-linux-gnu-mt... no
checking for mt... mt
checking if mt is a manifest tool... no
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 x86_64-conda-linux-gnu-cc supports -fno-rtti -fno-exceptions... no
checking for x86_64-conda-linux-gnu-cc option to produce PIC... -fPIC -DPIC
checking if x86_64-conda-linux-gnu-cc PIC flag -fPIC -DPIC works... yes
checking if x86_64-conda-linux-gnu-cc static flag -static works... yes
checking if x86_64-conda-linux-gnu-cc supports -c -o file.o... yes
checking if x86_64-conda-linux-gnu-cc supports -c -o file.o... (cached) yes
checking whether the x86_64-conda-linux-gnu-cc linker (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) 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... no
checking for dlopen in -ldl... 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 for build mode... production
checking for math library support... no
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for error_at_line... yes
checking for working memcmp... yes
checking for vprintf... yes
checking for _doprnt... no
checking for memset... yes
checking if encoding enabled... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/SZconfig.h
config.status: src/SZconfig.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
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Here is the installation output(second part):

Making all in src
make[1]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
make  all-am
make[2]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
make[2]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/szip'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/szip'
Making install in src
make[1]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
make[2]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
 /usr/bin/mkdir -p '/home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libsz.la '/home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /usr/bin/install -c .libs/libsz.lai /home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libsz.a /home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: x86_64-conda-linux-gnu-ranlib /home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: finish: PATH="/home/xyl/.local/bin:/home/xyl/miniconda3/envs/Rbio/bin:/home/xyl/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.UbuntuonWindows_2004.2021.222.0_x64__79rhkp1fndgsc:/mnt/c/Rtools/bin:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Users/yage9/AppData/Local/Programs/Python/Python37/Scripts:/mnt/c/Users/yage9/AppData/Local/Programs/Python/Python37:/mnt/c/Program Files/MATLAB/R2018a/bin:/mnt/c/Program Files/Intel/WiFi/bin:/mnt/c/Program Files/Common Files/Intel/WirelessCommon:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files (x86)/NetSarang/Xftp 7:/mnt/c/Program Files (x86)/NetSarang/Xshell 7:/mnt/c/Users/yage9/AppData/Local/atom/bin:/mnt/c/Users/yage9/AppData/Local/Programs/Python/Python37/Scripts/jupyter-notebook.exe:/mnt/c/Users/yage9/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/yage9/anaconda3:/mnt/c/Users/yage9/anaconda3/Library/bin:/mnt/c/Users/yage9/anaconda3/Library/mingw-w64/bin:/mnt/c/Users/yage9/anaconda3/Scripts:/mnt/c/ProgramData/Microsoft/Windows/Start Menu/Programs/Rtools 4.0:/snap/bin:/sbin" ldconfig -n /home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/xyl/Rhdf5lib/src/hdf5/szip/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/xyl/Rhdf5lib/src/hdf5/szip/szip/include'
 /usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/home/xyl/Rhdf5lib/src/hdf5/szip/szip/include'
make[2]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/szip'
make[2]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/szip'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/szip'
make[1]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/szip'
building the hdf5 library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /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... x86_64-conda-linux-gnu
checking host system type... x86_64-conda-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 x86_64-conda-linux-gnu... no
checking for config x86_64-conda-linux-gnu... no
checking for config conda-linux-gnu... no
checking for config conda-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-conda... no
checking for config linux-gnu... found
compiler 'x86_64-conda-linux-gnu-cc' is GNU gcc-9.3.0
compiler '/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-gfortran' is GNU gfortran-9.3.0
compiler 'x86_64-conda-linux-gnu-c++ -std=gnu++14' is GNU g++-9.3.0
No match to get cc_version_info for x86_64-conda-linux-gnu-cc
No match to get cxx_version_info for x86_64-conda-linux-gnu-c++ -std=gnu++14
checking for config ./config/site-specific/host-LAPTOP-7RERCQS0... no
checking for clang sanitizer checks... checking build mode... production
checking for x86_64-conda-linux-gnu-gcc... x86_64-conda-linux-gnu-cc
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 x86_64-conda-linux-gnu-cc accepts -g... yes
checking for x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking whether x86_64-conda-linux-gnu-cc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-conda-linux-gnu-cc... gcc3
checking if unsupported combinations of configure options are allowed... no
checking how to run the C preprocessor... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-cpp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 0
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of __float128... 16
checking size of _Quad... 0
checking quadmath.h usability... yes
checking quadmath.h presence... yes
checking for quadmath.h... yes
checking maximum decimal precision for C... 33
checking if Fortran interface enabled... no
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-conda-linux-gnu-c++ -std=gnu++14 accepts -g... yes
checking dependency style of x86_64-conda-linux-gnu-c++ -std=gnu++14... gcc3
checking how to run the C++ preprocessor... x86_64-conda-linux-gnu-c++ -std=gnu++14 -E
checking if c++ interface enabled... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 needs old style header files in includes... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 can handle namespaces... no
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 can handle static cast... no
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 has offsetof extension... no
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... yes
checking if Java JNI interface enabled... no
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Entering edit mode

Here is the installation output(third part):

checking if building tests is disabled... checking if building tools is disabled... checking how to print strings... printf
checking for a sed that does not truncate output... /home/xyl/miniconda3/envs/Rbio/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by x86_64-conda-linux-gnu-cc... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld
checking if the linker (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-nm
checking the name lister (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-conda-linux-gnu file names to x86_64-conda-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-conda-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld option to reload object files... -r
checking for x86_64-conda-linux-gnu-objdump... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-objdump
checking how to recognize dependent libraries... pass_all
checking for x86_64-conda-linux-gnu-dlltool... no
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for x86_64-conda-linux-gnu-ar... x86_64-conda-linux-gnu-ar
checking for archiver @FILE support... @
checking for x86_64-conda-linux-gnu-strip... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-strip
checking for x86_64-conda-linux-gnu-ranlib... x86_64-conda-linux-gnu-ranlib
checking command to parse /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-nm output from x86_64-conda-linux-gnu-cc 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 x86_64-conda-linux-gnu-mt... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if x86_64-conda-linux-gnu-cc supports -fno-rtti -fno-exceptions... no
checking for x86_64-conda-linux-gnu-cc option to produce PIC... -fPIC -DPIC
checking if x86_64-conda-linux-gnu-cc PIC flag -fPIC -DPIC works... yes
checking if x86_64-conda-linux-gnu-cc static flag -static works... yes
checking if x86_64-conda-linux-gnu-cc supports -c -o file.o... yes
checking if x86_64-conda-linux-gnu-cc supports -c -o file.o... (cached) yes
checking whether the x86_64-conda-linux-gnu-cc linker (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) 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... no
checking for dlopen in -ldl... 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... x86_64-conda-linux-gnu-c++ -std=gnu++14 -E
checking for ld used by x86_64-conda-linux-gnu-c++ -std=gnu++14... /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64
checking if the linker (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) is GNU ld... yes
checking whether the x86_64-conda-linux-gnu-c++ -std=gnu++14 linker (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) supports shared libraries... yes
checking for x86_64-conda-linux-gnu-c++ -std=gnu++14 option to produce PIC... -fPIC -DPIC
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 static flag -static works... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 supports -c -o file.o... yes
checking if x86_64-conda-linux-gnu-c++ -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the x86_64-conda-linux-gnu-c++ -std=gnu++14 linker (/home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-ld -m elf_x86_64) 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... (cached) yes
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking for sys/stat.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/types.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking setjmp.h usability... yes
checking setjmp.h presence... yes
checking for setjmp.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking for stdint.h... (cached) yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking io.h usability... no
checking io.h presence... no
checking for io.h... no
checking winsock2.h usability... no
checking winsock2.h presence... no
checking for winsock2.h... no
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... yes
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 zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for compress2 in -lz... yes
checking for compress2... yes
checking for SZ_BufftoBuffCompress in -lsz... yes
checking szlib.h usability... yes
checking szlib.h presence... yes
checking for szlib.h... yes
checking for szlib encoder... yes
checking for thread safe support... no
checking whether CLOCK_MONOTONIC is declared... yes
ADD REPLY •
0
Entering edit mode

Here is the installation output(fourth part):

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... -lrt
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 curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... yes
checking openssl/evp.h presence... yes
checking for openssl/evp.h... yes
checking openssl/hmac.h usability... yes
checking openssl/hmac.h presence... yes
checking for openssl/hmac.h... yes
checking openssl/sha.h usability... yes
checking openssl/sha.h presence... 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: src/H5config.h is unchanged
config.status: executing pubconf commands
creating src/H5pubconf.h
src/H5pubconf.h is unchanged
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing .classes commands
ADD REPLY •
0
Entering edit mode

Here is the installation output(fourth part):

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... -lrt
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 curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... yes
checking openssl/evp.h presence... yes
checking for openssl/evp.h... yes
checking openssl/hmac.h usability... yes
checking openssl/hmac.h presence... yes
checking for openssl/hmac.h... yes
checking openssl/sha.h usability... yes
checking openssl/sha.h presence... 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: src/H5config.h is unchanged
config.status: executing pubconf commands
creating src/H5pubconf.h
src/H5pubconf.h is unchanged
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing .classes commands
ADD REPLY •
0
Entering edit mode

Here is the installation output(last part):

        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
                   HDF5 Version: 1.10.7
                  Configured on: Tue Aug  3 22:18:31 CST 2021
                  Configured by: xyl@LAPTOP-7RERCQS0
                    Host system: x86_64-conda-linux-gnu
              Uname information: Linux LAPTOP-7RERCQS0 4.4.0-19041-Microsoft #488-Microsoft Mon Sep 01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /home/xyl/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: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/xyl/miniconda3/envs/Rbio/lib -Wl,-rpath-link,/home/xyl/miniconda3/envs/Rbio/lib -L/home/xyl/miniconda3/envs/Rbio/lib
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/home/xyl/Rhdf5lib/src/hdf5/szip/szip/lib
                Extra libraries: -lcrypto -lcurl -lrt -lsz -lz -ldl -lm 
                       Archiver: x86_64-conda-linux-gnu-ar
                       AR_FLAGS: cr
                         Ranlib: x86_64-conda-linux-gnu-ranlib

Languages:
----------
                              C: yes
                     C Compiler: /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-cc
                       CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/xyl/miniconda3/envs/Rbio/include -I/home/xyl/miniconda3/envs/Rbio/include -Wl,-rpath-link,/home/xyl/miniconda3/envs/Rbio/lib
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/home/xyl/Rhdf5lib/src/hdf5/szip/szip/include
                        C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/xyl/miniconda3/envs/Rbio/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1625580192924/work=/usr/local/src/conda/r-base-4.1.0 -fdebug-prefix-map=/home/xyl/miniconda3/envs/Rbio=/usr/local/src/conda-prefix -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 -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -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 -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -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: /home/xyl/miniconda3/envs/Rbio/bin/x86_64-conda-linux-gnu-c++ -std=gnu++14
                      C++ Flags: -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/xyl/miniconda3/envs/Rbio/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1625580192924/work=/usr/local/src/conda/r-base-4.1.0 -fdebug-prefix-map=/home/xyl/miniconda3/envs/Rbio=/usr/local/src/conda-prefix -fpic
                   H5 C++ Flags:   -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -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:  -DOLD_HEADER_FILENAME -DHDF_NO_NAMESPACE -DNO_STATIC_CAST
             Shared C++ Library: no
             Static C++ Library: yes

                           Java: no


Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                Build HDF5 Tests: yes
                Build HDF5 Tools: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                      Direct VFD: no
                      Mirror VFD: no
              (Read-Only) S3 VFD: yes
            (Read-Only) HDFS VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
          Function stack tracing: no
                Use file locking: best-effort
       Strict file format checks: no
    Optimization instrumentation: no
for d in src . c++ hl; do                                \
  if test $d != .; then                                        \
   (cd $d && make  lib) || exit 1;            \
  fi;                                                           \
done
make[1]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/src'
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/xyl/miniconda3/envs/Rbio/lib -Wl,-rpath-link,/home/xyl/miniconda3/envs/Rbio/lib -L/home/xyl/miniconda3/envs/Rbio/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       H5Z.lo
  CC       H5Zszip.lo
  CCLD     libhdf5.la
make[2]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/src'
make[1]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/src'
make[1]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/c++'
make[2]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/c++'
make[2]: Nothing to be done for 'build-lib'.
make[2]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/c++'
make[2]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/c++/src'
make[3]: Entering directory '/home/xyl/Rhdf5lib/src/hdf5/c++/src'
  CXX      H5DataSpace.lo
make[3]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/c++/src'
make[2]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/c++/src'
make[1]: Leaving directory '/home/xyl/Rhdf5lib/src/hdf5/c++'
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Thanks for the extra details. It looks like your're using R installed via conda, which in turn uses compilers and libraries also installed via conda. These tend to be fairly isolated from the system libraries, so installing things via apt-get install probably has no effect on an R installed with conda.

There is presumeably a conda pacakge that provides the missing iostream.h however I don't know enough about conda to point you towards that.

However I as far as I know, the recommended way to install Bioconductor packages when you're using R installed via conda is to also install packages in the same way. Bioconda provide packages for all Bioconductor packages, with details of how to install them e.g. https://anaconda.org/bioconda/bioconductor-rhdf5lib

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Thanks for your help! I have installed this package successfully via conda, thank you so much!

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