H5 failing to install on CentOS 6.9 #71
Description
I am attempting to install H5 via CRAN within R and get the following messages.
- installing source package ‘h5’ ...
** package ‘h5’ successfully unpacked and MD5 sums checked
checking for h5c++... /usr/bin/h5c++
checking for ggrep... /bin/grep
checking whether /bin/grep accepts -o... yes
checking for ggrep... (cached) /bin/grep
checking whether /bin/grep accepts -o... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++0x -I/usr/include/R -DNDEBUG -I/usr/include -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c Attribute.cpp -o Attribute.o
Attribute.cpp: In function ‘Rcpp::XPtr<H5::Attribute, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer [with T = H5::Attribute], false> CreateAttribute_H5File(Rcpp::XPtr<H5::H5File, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer [with T = H5::H5File], false>, std::string, char, Rcpp::NumericVector, int)’:
Attribute.cpp:22: error: ‘class H5::H5File’ has no member named ‘createAttribute’
Attribute.cpp: In function ‘Rcpp::XPtr<H5::Attribute, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer [with T = H5::Attribute], false> OpenAttribute_H5File(Rcpp::XPtr<H5::H5File, Rcpp::PreserveStorage, Rcpp::standard_delete_finalizer [with T = H5::H5File], false>, std::string)’:
Attribute.cpp:116: error: ‘class H5::H5File’ has no member named ‘openAttribute’
make: *** [Attribute.o] Error 1
ERROR: compilation failed for package ‘h5’ - removing ‘/usr/lib64/R/library/h5’
R version 3.4.4 and hdf5-devel version 1.8.5 are installed.
Here is the output from h5cc -showconfig.
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
HDF5 Version: 1.8.5-patch1
Configured on: Thu Dec 15 23:56:42 UTC 2016
Configured by: mockbuild@buildvm-28.phx2.fedoraproject.org
Configure mode: production
Host system: x86_64-redhat-linux-gnu
Uname information: Linux buildvm-28.phx2.fedoraproject.org 4.8.12-300.fc25.x86_64 #1 SMP Fri Dec 2 17:52:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /usr
Compiling Options:
Compilation Mode: production
C Compiler: /usr/bin/gcc ( gcc (GCC) 4.4.7 20120313 )
CFLAGS: -O0 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared Libraries: yes
Static Libraries: yes
Statically Linked Executables: no
LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
Fortran: yes
Fortran Compiler: /usr/bin/gfortran ( GNU Fortran (GCC) 4.4.7 20120313 )
Fortran Flags:
H5 Fortran Flags:
AM Fortran Flags: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -I/usr/lib64/gfortran/modules
C++: yes
C++ Compiler: /usr/bin/g++ ( g++ (GCC) 4.4.7 20120313 )
C++ Flags: -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
H5 C++ Flags:
AM C++ Flags:
Features:
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
Edit: Please forgive the formating, I have yet to find a way to temporarily disable Markdown.