Installation error using R

[timz0605]

Hello,

I am trying to use install.packages("hdf5r") on the R shell in HPC for installing the package, but I have been encountering difficulties. I was wondering if anyone could help me take a look? Thank you!

installing to /home/mjzhang/R_libs/4.0.4/00LOCK-hdf5r/00new/hdf5r/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
sh: line 1: 3314808 Aborted (core dumped) R_TESTS= '/share1/R/4.0.4/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/Rtmp1cpzIT/file328f4740e8b8be'
Warning! HDF5 library version mismatched error
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.10.4, library is 1.10.5
SUMMARY OF THE HDF5 CONFIGURATION
=================================

General Information:

               HDF5 Version: 1.10.5
              Configured on: Thu Aug 15 16:35:01 UTC 2019
              Configured by: mockbuild@
                Host system: x86_64-redhat-linux-gnu
          Uname information: Linux buildvm-16.phx2.fedoraproject.org 5.0.6-200.fc29.x86_64 #1 SMP Wed Apr 3 15:09:51 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
                   Byte sex: little-endian
         Installation point: /usr

Compiling Options:

                 Build Mode: production
          Debugging Symbols: no
                    Asserts: no
                  Profiling: no
         Optimization Level: high

Linking Options:

                  Libraries: static, shared

Statically Linked Executables:
LDFLAGS: -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fPIC -Wl,-z,now -Wl,--as-needed
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib

Languages:

                          C: yes
                 C Compiler: /usr/bin/gcc ( gcc (GCC) 8.2.1 20180905 )
                   CPPFLAGS:
                H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS:
                    C Flags: -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
                 H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O
                 AM C Flags:
           Shared C Library: yes
           Static C Library: yes


                    Fortran: yes
           Fortran Compiler: /usr/bin/gfortran ( GNU Fortran (GCC) 8.2.1 20180905 )
              Fortran Flags: -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib64/gfortran/modules
           H5 Fortran Flags:  -pedantic -Wall -Wextra -Wunderflow -Wimplicit-interface -Wsurprising -Wno-c-binding-type  -s -O2
           AM Fortran Flags:
     Shared Fortran Library: yes
     Static Fortran Library: yes

                        C++: yes
               C++ Compiler: /usr/bin/g++ ( g++ (GCC) 8.2.1 20180905 )
                  C++ Flags: -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
               H5 C++ Flags:   -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
               AM C++ Flags:
         Shared C++ Library: yes
         Static C++ Library: yes

                       Java: yes
              Java Compiler: /usr/bin/java (openjdk 1.8.0_222)

Features:

               Parallel HDF5: no

Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: 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
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Bye...
ERROR: loading failed

• removing ‘/home/mjzhang/R_libs/4.0.4/hdf5r’

The downloaded source packages are in
‘/tmp/RtmpXw2p4C/downloaded_packages’
Warning message:
In install.packages("hdf5r") :
installation of package ‘hdf5r’ had non-zero exit status

[mmokrejs]

I bet that /home/mjzhang/R_libs/4.0.4 and /share1/R/4.0.4/lib64/R do not match each other. Check for other places where you have h5cc and h5fc on your system.

See #100 and #188 for similar issues.