hdf5 installation error (hdf5.h usability```no)

[marvelouscandy]

Hi,

I was trying to install hdf5r but encountered the following issue:

##########
Installing package into ‘/home/chen2627/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
Warning: Your system is mis-configured: ‘/etc/localtime’ is not a symlink
Warning: It is strongly recommended to set envionment variable TZ to ‘America/Fort_Wayne’ (or equivalent)

• installing source package ‘hdf5r’ ...
  ** using staged installation
  checking for a sed that does not truncate output... /bin/sed
  checking for gawk... gawk
  checking for grep that handles long lines and -e... /bin/grep
  checking for gcc... mpicc
  checking for C compiler default output file name... a.out
  checking whether the C compiler works... yes
  checking whether we are cross compiling... no
  checking for suffix of executables...
  checking for suffix of object files... o
  checking whether we are using the GNU C compiler... yes
  checking whether mpicc accepts -g... yes
  checking for mpicc option to accept ISO C89... none needed
  checking how to run the C preprocessor... mpicc -E
  checking for egrep... /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 h5cc... /apps/spack/bell-20231031/apps/hdf5/1.13.2-gcc-12.3.0-rvixayh/bin/h5cc
  checking for HDF5 libraries... yes (version 1.13.2)
  checking hdf5.h usability... no
  checking hdf5.h presence... yes
  configure: WARNING: hdf5.h: present but cannot be compiled
  configure: WARNING: hdf5.h: check for missing prerequisite headers?
  configure: WARNING: hdf5.h: see the Autoconf documentation
  configure: WARNING: hdf5.h: section "Present But Cannot Be Compiled"
  configure: WARNING: hdf5.h: proceeding with the preprocessor's result
  configure: WARNING: hdf5.h: in the future, the compiler will take precedence
  configure: WARNING: ## -------------------------------- ##
  configure: WARNING: ## Report this to [email protected] ##
  configure: WARNING: ## -------------------------------- ##
  checking for hdf5.h... yes
  checking for H5Fcreate in -lhdf5... no
  checking for hdf5_hl.h... no
  checking for H5LTpath_valid in -lhdf5_hl... no
  configure: WARNING: Unable to compile HDF5_HL test program
  checking for main in -lhdf5_hl... no
  checking for matching HDF5 Fortran wrapper... /apps/spack/bell-20231031/apps/hdf5/1.13.2-gcc-12.3.0-rvixayh/bin/h5fc
  Using code intended for version: 1_10_0
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  using C compiler: ‘gcc (Spack GCC) 12.3.0’
  cp 1_10_0/.c 1_10_0/.h .
  /apps/spack/bell-20231031/apps/gcc/12.3.0-gcc-4.8.5-zhxpuq3/bin/gcc -I"/apps/spack/bell-057b415/apps/r/4.4.1-gcc-12.3.0-gvpukeq/rlib/R/include" -DNDEBUG -I/apps/spack/bell-20231031/apps/hdf5/1.13.2-gcc-12.3.0-rvixayh/include -I/usr/local/include -D_HDF5_USE_1_8_12_=0 -fpic -g -O2 -c const_export.c -o const_export.o
  /apps/spack/bell-20231031/apps/gcc/12.3.0-gcc-4.8.5-zhxpuq3/bin/gcc -I"/apps/spack/bell-057b415/apps/r/4.4.1-gcc-12.3.0-gvpukeq/rlib/R/include" -DNDEBUG -I/apps/spack/bell-20231031/apps/hdf5/1.13.2-gcc-12.3.0-rvixayh/include -I/usr/local/include -D_HDF5_USE_1_8_12_=0 -fpic -g -O2 -c datatype_export.c -o datatype_export.o
  datatype_export.c: In function 'create_DT_H5D_mpio_no_collective_cause_t':
  datatype_export.c:1496:12: error: 'H5D_MPIO_FILTERS' undeclared (first use in this function); did you mean 'H5Z_MAX_NFILTERS'?
  1496 | myenum = H5D_MPIO_FILTERS;
  | ^~~~~~~~~~~~~~~~
  | H5Z_MAX_NFILTERS
  datatype_export.c:1496:12: note: each undeclared identifier is reported only once for each function it appears in
  datatype_export.c: In function 'create_DT_H5I_type_t':
  datatype_export.c:1762:12: error: 'H5I_REFERENCE' undeclared (first use in this function); did you mean 'H5T_REFERENCE'?
  1762 | myenum = H5I_REFERENCE;
  | ^~~~~~~~~~~~~
  | H5T_REFERENCE
  In file included from /usr/include/string.h:32,
  from /apps/spack/bell-057b415/apps/r/4.4.1-gcc-12.3.0-gvpukeq/rlib/R/include/R_ext/RS.h:34,
  from /apps/spack/bell-057b415/apps/r/4.4.1-gcc-12.3.0-gvpukeq/rlib/R/include/R.h:78,
  from global.h:27,
  from datatype_export.h:23,
  from datatype_export.c:20:
  datatype_export.c: In function 'create_DT_H5O_info_t':
  /apps/spack/bell-20231031/apps/hdf5/1.13.2-gcc-12.3.0-rvixayh/include/H5Tpublic.h:24:24: error: 'H5O_info2_t' has no member named 'addr'
  24 | #define HOFFSET(S, M) (offsetof(S, M))
  | ^~~~~~~~
  datatype_export.c:2523:31: note: in expansion of macro 'HOFFSET'
  2523 | H5Tinsert(dtype_id, "addr", HOFFSET(H5O_info_t, addr), h5_datatype[DT_haddr_t]);
  | ^~~~~~~
  /apps/spack/bell-20231031/apps/hdf5/1.13.2-gcc-12.3.0-rvixayh/include/H5Tpublic.h:24:24: error: 'H5O_info2_t' has no member named 'hdr'
  24 | #define HOFFSET(S, M) (offsetof(S, M))
  | ^~~~~~~~
  datatype_export.c:2531:30: note: in expansion of macro 'HOFFSET'
  2531 | H5Tinsert(dtype_id, "hdr", HOFFSET(H5O_info_t, hdr), h5_datatype[DT_H5O_hdr_info_t]);
  | ^~~~~~~
  /apps/spack/bell-20231031/apps/hdf5/1.13.2-gcc-12.3.0-rvixayh/include/H5Tpublic.h:24:24: error: 'H5O_info2_t' has no member named 'meta_size'
  24 | #define HOFFSET(S, M) (offsetof(S, M))
  | ^~~~~~~~
  datatype_export.c:2532:36: note: in expansion of macro 'HOFFSET'
  2532 | H5Tinsert(dtype_id, "meta_size", HOFFSET(H5O_info_t, meta_size), h5_datatype[DT_H5O_info_helper_t]);
  | ^~~~~~~
  make: *** [datatype_export.o] Error 1
  ERROR: compilation failed for package ‘hdf5r’
• removing ‘/home/chen2627/R/x86_64-pc-linux-gnu-library/4.4/hdf5r’
• restoring previous ‘/home/chen2627/R/x86_64-pc-linux-gnu-library/4.4/hdf5r’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmprnHnVJ/file1024047daecbe/hdf5r_0.9.7.tar.gz’ had non-zero exit status

##########
My sessionInfo is
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /apps/spack/bell-057b415/apps/openblas/0.3.27-gcc-12.3.0-lhwm4tu/lib/libopenblasp-r0.3.27.so; LAPACK version 3.12.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/Fort_Wayne
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] miniUI_0.1.1.1 dplyr_1.1.4 compiler_4.4.1 promises_1.2.0.1 tidyselect_1.2.0 Rcpp_1.0.12
[7] callr_3.7.3 later_1.3.0 fastmap_1.1.1 mime_0.12 R6_2.5.1 plyr_1.8.8
[13] generics_0.1.3 curl_5.2.3 htmlwidgets_1.6.4 tibble_3.2.1 desc_1.4.3 profvis_0.4.0
[19] shiny_1.8.1.1 pillar_1.9.0 rlang_1.1.2 utf8_1.2.3 cachem_1.0.7 httpuv_1.6.9
[25] fs_1.6.2 pkgload_1.4.0 memoise_2.0.1 cli_3.6.1 magrittr_2.0.3 ps_1.7.5
[31] processx_3.8.4 digest_0.6.37 rstudioapi_0.14 xtable_1.8-4 remotes_2.5.0 devtools_2.4.5
[37] lifecycle_1.0.3 vctrs_0.6.5 glue_1.6.2 urlchecker_1.0.1 sessioninfo_1.2.2 pkgbuild_1.4.4
[43] fansi_1.0.4 purrr_1.0.1 usethis_2.1.6 tools_4.4.1 pkgconfig_2.0.3 ellipsis_0.3.2
[49] htmltools_0.5.8.1

I have to mention that I do not have the sudo access.
I tried to indicate the h5cc library or load the hdf5 module in my system, but wasn't able to install hdf5r.

This is the command I used:
install.packages("hdf5r", configure.args="—with-hdf5=/opt/bin/anaconda3/h5cc")

Thank you very much for your help.

Best regards,