Patching hdf5small_cxx_hl_1.10.7.tar.gz for /bin/mv

[ppiecuch]

Hello Team,

When building a package under Gentoo Prefix environment (CentOS7/GCC 9.3) there is a problem with /bin/mv hardcoded into hdf5 configure:

...
creating src/H5pubconf.h
/bin/mv: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by /apps/rocs/2020.08/prefix/lib/../lib64/libpt
hread.so.0)
...

There are only two occurrences of /bin/mv in configure that should be just mv (rest is just the regular mv) - would you consider patching hdf5small_cxx_hl_1.10.7.tar.gz with that change (I have tested the package with that change and it builds fine)?

Best regards Pawel

[grimbough]

Hi @ppiecuch ,

Thanks for the report. That config script actually comes from the HDF5 library itself, but I'm happy to patch the version we're distributing.

Can you try installing the hdf5-config branch and seeing if that works on your system. You can do that with:

BiocManager::install('grimbough/Rhdf5lib', ref = 'hdf5-config')

[ppiecuch]

Thank you for trying to solve my problem. But pretty much the same result, because /bin/mv is still selected:

config.status: executing pubconf commands
/bin/mv
creating src/H5pubconf.h
mv2 one
/bin/mv: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by /apps/rocs/2020.08/prefix/lib/../lib64/libpthread.so.0)
Post process src/libhdf5.settings

I would like to replace /bin/mv with mv always (rest of the mv calls in that file is not using /bin prefix) For reference, there is ~50 mv calls in the file but only these two are /bin/mv