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Bug 690986 - sci-libs/armadillo[hdf5]: detection of HDF5 broken, ARMA_HDF5_INCLUDE_DIR set to NOTFOUND breaking builds.
Summary: sci-libs/armadillo[hdf5]: detection of HDF5 broken, ARMA_HDF5_INCLUDE_DIR set...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Andreas K. Hüttel
URL:
Whiteboard:
Keywords: PATCH, PullRequest
Depends on:
Blocks:
 
Reported: 2019-07-29 11:53 UTC by Jan-Matthias Braun
Modified: 2020-02-24 09:15 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
Fix HDF5 includes by forcing HDF5_INCLUDE_DIRS. Caution: also sets DETECT_HDF5, which is not strictly necessary for the problem at hand. (armadillo.patch,438 bytes, patch)
2019-07-29 11:53 UTC, Jan-Matthias Braun
Details | Diff

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Description Jan-Matthias Braun 2019-07-29 11:53:17 UTC
Created attachment 584972 [details, diff]
Fix HDF5 includes by forcing HDF5_INCLUDE_DIRS. Caution: also sets DETECT_HDF5, which is not strictly necessary for the problem at hand.

When emerging with hdf5 support, use of armadillo will result in failed compiler calls with:
    fatal error: NOTFOUND/hdf5.h: No such file or directory

It looks like HDF5 detection is broken. (Especially for the C-only component?)
The armadillo ebuild is overwriting the corresponding HDF5 variables, i.e., -DHDF5_FOUND=ON and-DHDF5_LIBRARIES="-lhdf5". But HDF5_INCLUDE_DIRS is not set.
Setting HDF5_INCLUDE_DIRS=/usr/include fixes this.

Caution: The attached patch is also setting DETECT_HDF5, which is probably not necessary, but it seems a possibility to turn detection off completely, when not using HDF5.
Comment 1 Larry the Git Cow gentoo-dev 2020-02-22 20:13:13 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b2dab37206f6a0b4f10c4386694166441831b784

commit b2dab37206f6a0b4f10c4386694166441831b784
Author:     Andreas K. Huettel <dilfridge@gentoo.org>
AuthorDate: 2020-02-22 20:12:34 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2020-02-22 20:12:34 +0000

    sci-libs/armadillo: Version bump; fix HDF5 detection
    
    Patch by Jan-Matthias Braun
    
    Closes: https://bugs.gentoo.org/690986
    Package-Manager: Portage-2.3.84, Repoman-2.3.20
    Signed-off-by: Andreas K. Huettel <dilfridge@gentoo.org>
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-libs/armadillo/Manifest                 |   1 +
 sci-libs/armadillo/armadillo-9.850.1.ebuild | 148 ++++++++++++++++++++++++++++
 2 files changed, 149 insertions(+)
Comment 2 Jan-Matthias Braun 2020-02-24 09:15:40 UTC
Thanks a lot!