Issue installing r-hdf5r via spack

[perrymil]

Hi @hhoeflin

I tried your suggestion from #164 just now, and am getting the following error.

checking for HDF5 libraries... yes (version )
checking hdf5.h usability... no
checking hdf5.h presence... no
checking for hdf5.h... no
checking for H5Fcreate in -lhdf5... no
configure: WARNING: Unable to compile HDF5 test program
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... no
Found hdf5 with version: 
configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.13 is installed
ERROR: configuration failed for package ‘hdf5r’

I tried

spack install r-hdf5r ^[email protected]+hl

I think the issue is that something about the r-hdf5r package checking for hdf5 package version isn't quite right, but I am having issues tracing down where that check occurs, and how r-hdf5r goes about it.

Found hdf5 with version:

That line without a specific version of hdf5 that it found makes me think that something about the check is the issue, rather than not actually having a working hdf5 dependency?

I am using the spack develop branch.

the spack-configure-args.txt shows:

--with-hdf5=[SystemPath]/linux-centos7-ivybridge/gcc-8.3.1/hdf5-1.10.7-lizgn5qbklotstzwn63svnzrxk7sbq3y/bin/h5pcc'

I omitted the full path as its pretty long, but I have confirmed that the h5pcc file is indeed present.

If you can assist me in determining why this error keeps occuring, I will update the spack package with the correct configuration. The default spack package doesn't include the +hl dependency for hdf5 you recommended in that previous closed issue, is that required? Below is the spec output from spack:

[email protected]%[email protected] arch=linux-centos7-ivybridge
    ^[email protected]%[email protected]~cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-centos7-ivybridge
        ^[email protected]%[email protected]~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-centos7-ivybridge
            ^[email protected]%[email protected]~symlinks+termlib abi=none arch=linux-centos7-ivybridge
                ^[email protected]%[email protected] arch=linux-centos7-ivybridge
            ^[email protected]%[email protected]~docs+systemcerts arch=linux-centos7-ivybridge
                ^[email protected]%[email protected]+cpanm+shared+threads arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected]+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected]~debug~pic+shared arch=linux-centos7-ivybridge
                        ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                            ^[email protected]%[email protected] libs=shared,static arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                        ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected]+optimize+pic+shared arch=linux-centos7-ivybridge
        ^[email protected]%[email protected]~atomics~cuda~cxx~cxx_exceptions+gpfs~internal-hwloc~java~legacylaunchers~lustre~memchecker+pmi~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ucx schedulers=slurm arch=linux-centos7-ivybridge
            ^[email protected]%[email protected]~cairo~cuda~gl~libudev+libxml2~netloc~nvml~opencl+pci~rocm+shared arch=linux-centos7-ivybridge
                ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                        ^[email protected]%[email protected]+sigsegv patches=9dc5fbd0d5cb1037ab1e6d0ecc74a30df218d0a94bdd5a02759a97f62daca573,bfdffa7c2eb01021d5849b36972c069693654ad826c1a20b53534009a4ec7a89 arch=linux-centos7-ivybridge
                            ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                ^[email protected]%[email protected]~python arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected]~pic libs=shared,static arch=linux-centos7-ivybridge
            ^[email protected]%[email protected]+openssl arch=linux-centos7-ivybridge
            ^[email protected]%[email protected] patches=4e1d78cbbb85de625bad28705e748856033eaafab92a66dffd383a3d7e00cc94,62fc8a8bf7665a60e8f4c93ebbd535647cebf74198f7afafec4c085a8825c006 arch=linux-centos7-ivybridge
                ^[email protected]%[email protected] patches=35c449281546376449766f92d49fc121ca50e330e60fefcfc9be2af3253082c2,7793209b33013dc0f81208718c68440c5aae80e7a1c4b8d336e382525af791a7,a49dd5bac3b62daa0ff688ab4d508d71dbd2f4f8d7e2a02321926346161bf3ee arch=linux-centos7-ivybridge
                ^[email protected]%[email protected] arch=linux-centos7-ivybridge
            ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                ^[email protected]%[email protected] arch=linux-centos7-ivybridge
            ^slurm@17-2-11-1%[email protected]~gtk~hdf5~hwloc~mariadb~pmix+readline~restd sysconfdir=PREFIX/etc arch=linux-centos7-ivybridge
            ^[email protected]%[email protected]~assertions~cm~cma~cuda~dc~debug~dm~gdrcopy~ib-hw-tm~java~knem~logging+mlx5-dv+optimizations~parameter_checking+pic+rc+thread_multiple+ud~xpmem cuda_arch=none arch=linux-centos7-ivybridge
                ^[email protected]%[email protected]~ipo build_type=RelWithDebInfo arch=linux-centos7-ivybridge
    ^[email protected]%[email protected]~X~external-lapack~memory_profiling~rmath arch=linux-centos7-ivybridge
        ^[email protected]%[email protected]~gssapi~ldap~libidn2~librtmp~libssh~libssh2~nghttp2 tls=openssl arch=linux-centos7-ivybridge
        ^[email protected]%[email protected] cxxstd=11 arch=linux-centos7-ivybridge
            ^[email protected]%[email protected]+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87 arch=linux-centos7-ivybridge
                ^[email protected]%[email protected]+libbsd arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                        ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-centos7-ivybridge
                    ^[email protected]%[email protected] arch=linux-centos7-ivybridge
                ^[email protected]%[email protected] patches=26f26c6f29a7ce9bf370ad3ab2610f99365b4bdd7b82e7c31df41a3370d685c0 arch=linux-centos7-ivybridge
                ^[email protected]%[email protected]+column_metadata+fts~functions~rtree arch=linux-centos7-ivybridge
                ^[email protected]%[email protected] arch=linux-centos7-ivybridge
        ^[email protected]_10%[email protected] arch=linux-centos7-ivybridge
        ^[email protected]%[email protected]~jit+multibyte arch=linux-centos7-ivybridge
    ^[email protected]%[email protected] arch=linux-centos7-ivybridge
        ^[email protected]%[email protected] arch=linux-centos7-ivybridge
    ^[email protected]%[email protected] arch=linux-centos7-ivybridge

   class RHdf5r(RPackage):
   """Interface to the 'HDF5' Binary Data Format

   'HDF5' is a data model, library and file format for storing and managing
   large amounts of data. This package provides a nearly feature complete,
   object oriented wrapper for the 'HDF5' API
   <https://support.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html> using R6
   classes. Additionally, functionality is added so that 'HDF5' objects behave
   very similar to their corresponding R counterparts."""

   homepage = "https://hhoeflin.github.io/hdf5r"
   url      = "https://cloud.r-project.org/src/contrib/hdf5r_1.2.0.tar.gz"
   list_url = "https://cloud.r-project.org/src/contrib/Archive/hdf5r"

   version('1.3.3', sha256='a0f83cbf21563e81dbd1a1bd8379623ed0c9c4df4e094c75013abfd7a5271545')
   version('1.2.0', sha256='58813e334fd3f9040038345a7186e5cb02090898883ac192477a76a5b8b4fe81')

   depends_on('[email protected]:', type=('build', 'run'))
   depends_on('r-r6', type=('build', 'run'))
   depends_on('r-bit64', type=('build', 'run'))
   depends_on('[email protected]:')

   def configure_args(self):
       if 'mpi' in self.spec:
           args = [
               '--with-hdf5={0}/h5pcc'.format(self.spec['hdf5'].prefix.bin),
           ]
       else:
           args = [
               '--with-hdf5={0}/h5cc'.format(self.spec['hdf5'].prefix.bin),
           ]
       return args

The spack package includes options for including the path to hdf5 provided h5pcc file for --with-hdf5=PATH, but something about that isn't working at the moment.

I tried with [email protected] and [email protected] just now and got the same error.

checking for HDF5 libraries... yes (version )
checking hdf5.h usability... no
checking hdf5.h presence... no
checking for hdf5.h... no
checking for H5Fcreate in -lhdf5... no
configure: WARNING: Unable to compile HDF5 test program
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... no
Found hdf5 with version: 
configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.13 is installed

[drkrynstrng]

I think the issue is that the Spack hdf5 package switched to a CMake build which does not currently include a h5cc -showconfig option, so the configure script for this packages fails. See spack/spack#27000 and spack/spack#27634.

[mladenivkovic]

It looks like the switch to the CMake build was indeed the issue.
Unfortunately the sowftware I work with relies on h5cc and h5pcc to be around and in working condition in order to check whether a working hdf5 build is present. The current spack version does not deliver that - while an h5cc executable is built, running it results in linking errors.

A workaround I've found is to revert the contents of spack/var/spack/repos/builtin/packages/hdf5 to commit 3039237a0e7cee898d85a33b13ed6d5ab712b3f3, which was the last version before the change to the CMake build.