[MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

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[MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------+-------------------------------------------------
 Reporter:  mf2k         |      Owner:
     Type:  defect       |     Status:  new
 Priority:  Normal       |  Milestone:
Component:  ports        |    Version:
 Keywords:               |       Port:  h4h5tools hdfeos5 netcdf octave-
                         |  devel py-tables ncarg
-------------------------+-------------------------------------------------
 Ports that depend on hdf5-18 should be updated and tested to work with the
 newer hdf5 port.

 See also #52289.

 ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
 || h4h5tools ||  -  ||  ||
 || hdfeos5 ||  tenomoto  ||  ||
 || netcdf ||  tenomoto  ||  ||
 || octave-devel ||  MarcusCalhoun-Lopez  ||  ||
 || py-tables ||  mamoll  ||  ||
 || ncarg ||  tenomoto  ||  ||

--
Ticket URL: <https://trac.macports.org/ticket/54101>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------
Changes (by mf2k):

 * type:  defect => enhancement


--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:1>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------
Description changed by mf2k:

Old description:

> Ports that depend on hdf5-18 should be updated and tested to work with
> the newer hdf5 port.
>
> See also #52289.
>
> ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
> || h4h5tools ||  -  ||  ||
> || hdfeos5 ||  tenomoto  ||  ||
> || netcdf ||  tenomoto  ||  ||
> || octave-devel ||  MarcusCalhoun-Lopez  ||  ||
> || py-tables ||  mamoll  ||  ||
> || ncarg ||  tenomoto  ||  ||

New description:

 Ports that depend on hdf5-18 should be updated and tested to work with the
 newer hdf5 port.

 See also #52289.

 ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
 ||h4h5tools ||-  ||  ||
 ||hdfeos5 ||tenomoto  ||  ||
 ||netcdf ||tenomoto  ||  ||
 ||octave-devel ||MarcusCalhoun-Lopez  ||  ||
 ||py-tables ||mamoll  ||  ||
 || ncarg ||tenomoto  ||  ||

--

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:2>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by mamoll):

 In [changeset:"1fa97da43102e3502c9381c05999f5bd8dceee61/macports-ports"
 1fa97da43102e3502c9381c05999f5bd8dceee61/macports-ports]:
 {{{
 #!ConfigurableCommitTicketReference repository="macports-ports"
 revision="1fa97da43102e3502c9381c05999f5bd8dceee61"
 py-tables: update to version 3.4.2, switch from hdf5-18 to hdf5 (see
 https://trac.macports.org/ticket/54101)
 }}}

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:4>
MacPorts <https://www.macports.org/>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------
Description changed by mf2k:

Old description:

> Ports that depend on hdf5-18 should be updated and tested to work with
> the newer hdf5 port.
>
> See also #52289.
>
> ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
> ||h4h5tools ||-  ||  ||
> ||hdfeos5 ||tenomoto  ||  ||
> ||netcdf ||tenomoto  ||  ||
> ||octave-devel ||MarcusCalhoun-Lopez  ||  ||
> ||py-tables ||mamoll  ||  ||
> || ncarg ||tenomoto  ||  ||

New description:

 Ports that depend on hdf5-18 should be updated and tested to work with the
 newer hdf5 port.

 See also #52289.

 ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
 ||h4h5tools ||-  ||  ||
 ||hdfeos5 ||tenomoto  ||  ||
 ||netcdf ||tenomoto  ||  ||
 ||octave-devel ||MarcusCalhoun-Lopez  ||  ||
 ||~~py-tables~~ ||~~mamoll~~  || Done ||
 || ncarg ||tenomoto  ||  ||

--

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:5>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by Dave-Allured):

 Please recall the original reasons for hdf5-18.  It is a little hard to
 tell from the original tickets (ticket:51089 etc), but this alternative
 port solved two problems:

 1.  All hdf5 versions starting with 1.10.0 (2016 March 30) could easily
 generate new hdf5 data files that were backward incompatible with all
 older, non-updated hdf5 applications.  Hdf5-18 prevented this, and wrote
 only backward compatible files.  The correct long term fix is to (a)
 insert a specific hdf5 compatibility function call into the calling
 application; then and only then, (b) upgrade to hdf5 1.10.x.  For example,
 here is a discussion and compatibility fix that was applied in Netcdf
 version 4.4.1 (2016 June 28).  The single function call to
 H5Pset_libver_bounds did the trick:

     https://github.com/Unidata/netcdf-c/issues/250 (2016 April 7)

 2.  Hdf5 versions 1.10.0 and 1.10.0-patch1 could not access network-
 mounted files from Macs.  I am told this was specifically due to new usage
 of the system flock function, and shortcomings of NFS version 3 on Macs.
 This of course would not affect any Mac users that used only local disk
 files.  Hdf5-18 avoided this problem because it never used flock.  Hdf5
 version 1.10.1 (2017 April 27) appears to fix this, using a special run-
 time environment variable.  IMO the correct upgrade path is to link only
 with hdf5 1.10.1 or later, and then remind users to use the environment
 variable when needed.  The 1.10.1 update is forthcoming in ticket:54139,
 which includes details about the environment variable setting.

 I recommend holding off on switching hdf5-18 dependencies to hdf5 until
 either (a) the format compatibility fix is inserted in the calling
 packages; or (b) there is some kind of consensus that original package
 developers and users no longer care about generating backward-incompatible
 hdf5 data files.

 Furthermore, because of (2), I recommend waiting for hdf5 1.10.1
 (ticket:54139) before switching any more hdf5-18 dependencies back to
 hdf5.

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:6>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------
Description changed by mf2k:

Old description:

> Ports that depend on hdf5-18 should be updated and tested to work with
> the newer hdf5 port.
>
> See also #52289.
>
> ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
> ||h4h5tools ||-  ||  ||
> ||hdfeos5 ||tenomoto  ||  ||
> ||netcdf ||tenomoto  ||  ||
> ||octave-devel ||MarcusCalhoun-Lopez  ||  ||
> ||~~py-tables~~ ||~~mamoll~~  || Done ||
> || ncarg ||tenomoto  ||  ||

New description:

 Ports that depend on hdf5-18 should be updated and tested to work with the
 newer hdf5 port.

 See also #52289.

 ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
 ||h4h5tools ||-  ||  ||
 ||hdfeos5 ||tenomoto  ||  ||
 ||netcdf ||tenomoto  || #54177 ||
 ||octave-devel ||MarcusCalhoun-Lopez  ||  ||
 ||~~py-tables~~ ||~~mamoll~~  || Done ||
 || ncarg ||tenomoto  ||  ||

--

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:8>
MacPorts <https://www.macports.org/>
Ports system for macOS
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by aaschwanden):

 I just re-installed macports from scratch, and only the ports I really
 need (e.g. hdf5, hdf5-18, netcdf, py27-netcdf4, gdal, ...) and I'm already
 stuck with the usual hdf5 vs hdf5-18 library mismatch, this time when
 using netCDF4python. So far I have never been able to have a working
 macports installation that has hdf5 and hdf5-18 along side. So far my only
 working solution has been to overwrite all ports that use hdf5-18 and link
 them against hdf5. Not pretty and it only worked because I haven't use py-
 tables in a while. Maybe I have to compile things from scratch again.

 Let's hope that hdf5 gets bumped up to 1.10.1 and we can get rid of
 hdf5-18 (I'd happily re-install macports again after that, well worth the
 trouble.)

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:9>
MacPorts <https://www.macports.org/>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by seanfarley):

 Now that hdf5 is 1.10.1 and that netcdf works with it, is there anything
 preventing netcdf from being updated? @tenomoto?

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:10>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by Dave-Allured):

 Replying to [comment:10 seanfarley]:

 I concur that netcdf (only) is ready to update to netcdf version 4.4.1.1
 (the latest), as well as its dependency to hdf5 1.10.1.  Ticket #54177 is
 in place for this purpose.

 Netcdf version 4.4.1.1 (and its predecessor 4.4.1) satisfied my complaint
 (1) above, backward compatible files.  Hdf5 1.10.1 itself resolves my
 complaint (2), network mounted files.

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:11>
MacPorts <https://www.macports.org/>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by seanfarley):

 Replying to [comment:11 Dave-Allured]:

 But other ports that depend on `hdf5-18` still need to put in the
 `H5Pset_libver_bounds`, correct?

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:12>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:
      Type:  enhancement                         |     Status:  new
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by Dave-Allured):

 Replying to [comment:12 seanfarley]:

 Yes indeed.  Thanks for asking.

 Each package should be individually verified to be using
 `H5Pset_libver_bounds` so as to ensure writing backward compatible files,
 unless the relevant user community does not care.  This is particularly
 important for packages like Netcdf that are commonly used for public
 distribution of large volumes of HDF5-based files.

 This should be the responsibility of the original package developers, not
 MacPorts, IMO.  See, for example, what the Netcdf developers did:

 ‚Äčhttps://github.com/Unidata/netcdf-c/issues/250 (2016 April 7)

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:13>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:  tenomoto
      Type:  enhancement                         |     Status:  assigned
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------
Changes (by mf2k):

 * cc: tenomoto (removed)
 * status:  new => assigned
 * owner:   => tenomoto


--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:14>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:  tenomoto
      Type:  enhancement                         |     Status:  assigned
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by tenomoto):

 netcdf in [6b3cb0cd3a6a8345bc91f950cf528c4801bfe7f5/macports-ports].

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:15>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:  tenomoto
      Type:  enhancement                         |     Status:  assigned
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by tenomoto):

 hdffeos5 in [259fb59a028dcbb823a616c554215e9aa0a325a4/macports-ports].

 I had problem building ncarg (and h4h5tools) with hdf5.

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Ticket URL: <https://trac.macports.org/ticket/54101#comment:16>
MacPorts <https://www.macports.org/>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:  tenomoto
      Type:  enhancement                         |     Status:  assigned
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by tenomoto):

 ncarg in [8a1abdde9a46af2b26b4f301a72394764e06a4e3/macports-ports].

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Ticket URL: <https://trac.macports.org/ticket/54101#comment:17>
MacPorts <https://www.macports.org/>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:  tenomoto
      Type:  enhancement                         |     Status:  assigned
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------

Comment (by tenomoto):

 h4h5tools builds fine with `configure.cflags-append -DH5_USE_18_API`. It
 appears that `h4toh5` sets the version to the latest.

     utils/h4toh5/h4toh5main.c:    if (H5Pset_libver_bounds(fapl_id,
 H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)

 I'll wait for a few days and commit the changes if no objections.

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:18>
MacPorts <https://www.macports.org/>
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Re: [MacPorts] #54101: Ports that depend on hdf5-18 should switch to hdf5

MacPorts
In reply to this post by MacPorts
#54101: Ports that depend on hdf5-18 should switch to hdf5
-------------------------------------------------+-------------------------
  Reporter:  mf2k                                |      Owner:  tenomoto
      Type:  enhancement                         |     Status:  assigned
  Priority:  Normal                              |  Milestone:
 Component:  ports                               |    Version:
Resolution:                                      |   Keywords:
      Port:  h4h5tools hdfeos5 netcdf octave-    |
  devel py-tables ncarg                          |
-------------------------------------------------+-------------------------
Description changed by mf2k:

Old description:

> Ports that depend on hdf5-18 should be updated and tested to work with
> the newer hdf5 port.
>
> See also #52289.
>
> ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
> ||h4h5tools ||-  ||  ||
> ||hdfeos5 ||tenomoto  ||  ||
> ||netcdf ||tenomoto  || #54177 ||
> ||octave-devel ||MarcusCalhoun-Lopez  ||  ||
> ||~~py-tables~~ ||~~mamoll~~  || Done ||
> || ncarg ||tenomoto  ||  ||

New description:

 Ports that depend on hdf5-18 should be updated and tested to work with the
 newer hdf5 port.

 See also #52289.

 ||= '''Port''' =||= '''Maintainer''' =||= '''status''' =||
 ||h4h5tools ||-  ||  ||
 ||~~hdfeos5~~ ||tenomoto  ||
 https://trac.macports.org/changeset/259fb59a028dcbb823a616c554215e9aa0a325a4
 /macports-ports ||
 ||~~netcdf~~ ||tenomoto  || #54177 ||
 ||octave-devel ||MarcusCalhoun-Lopez  ||  ||
 ||~~py-tables~~ ||mamoll  ||
 https://trac.macports.org/changeset/1fa97da43102e3502c9381c05999f5bd8dceee61
 /macports-ports ||
 ||~~ncarg~~ ||tenomoto  ||
 https://trac.macports.org/changeset/8a1abdde9a46af2b26b4f301a72394764e06a4e3
 /macports-ports ||

--

--
Ticket URL: <https://trac.macports.org/ticket/54101#comment:19>
MacPorts <https://www.macports.org/>
Ports system for macOS
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