fatal error: hdf5.h: No such file or directory, change from R devel r83603 to r83630 about hdf5r HOT 3 CLOSED

Thanks for reporting this issue. I have reproduced it on my side and am looking into it.

from hdf5r.

In the newest updates this error should be fixed. It was a misconfiguration in configure.ac that was triggered by recent versions of R-devel adding additional environment variables for the compilation.

from hdf5r.

I had the same issue, and 'fixed' (actually, skipped) it by creating a new empty conda environment with package r-hdf5r (from either conda-forge or bioconda channel). This one comes pre-compiled and with all dynamic links in place already. So, it works.

Another 'solution' I was trying was copying over files from /usr/include/hdf5/serial/* to /path/to/conda/include/` but I still got a compilation error, though it was downstream, while dynamic linking. Anyway.. I am only telling this, because it might be worth to ask ourselves, Are we facing this issue while having our 'base' conda environment active?

PS. here's a plausible solution.

from hdf5r.