Google Groups no longer supports new Usenet posts or subscriptions. Historical content remains viewable.
Dismiss
Bug#853750: hdfview: HDF5 files appear empty
173 views
Skip to first unread message
Giuseppe Bilotta
Jan 31, 2017, 10:40:02 AM1/31/17
to
Package: hdfview
Version: 2.11.0+dfsg-2+b1
Severity: important
The current version of hdfview does not show the content of any of my
HDF5 files.
Downgrading to the 2.9-3+b2 version of libjhdf{4,5}-{java, jni}, which
also installs libhdf5-8 version 1.8.13+docs-15, seems to fix the issue
for me, even if hdfview is kept at the 2.11 version. This seems to
suggest that the problem lies in libjhdf rather than in hdfview itself,
and/or in the API of libhdf5 used by jhdf.
FWIW, a similar bug seems to affect also jhdf 2.9-5 as found in Ubuntu,
which is using libhdf5-10 (1.8.16), which would further support the idea
of a breaking API change between version 1.8.13 and 1.8.16 of libhdf5.
-- System Information:
Debian Release: 9.0
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.9.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages hdfview depends on:
ii default-jre 2:1.8-58
ii java-wrappers 0.1.28
ii libjgraph-java 5.12.4.2+dfsg-5
ii libjhdf4-java 2.11.0+dfsg-2+b1
ii libjhdf5-java 2.11.0+dfsg-2+b1
ii libslf4j-java 1.7.22-1
hdfview recommends no packages.
Versions of packages hdfview suggests:
ii chromium [www-browser] 55.0.2883.75-6
ii dillo [www-browser] 3.0.5-3
ii elinks [www-browser] 0.12~pre6-12
ii firefox [www-browser] 51.0-1
ii iceape [www-browser] 2.7.12-1+b1
ii konqueror [www-browser] 4:16.08.3-1
ii links2 [www-browser] 2.14-2
ii lynx [www-browser] 2.8.9dev11-1
ii netsurf-fb [www-browser] 3.6-3
ii opera [www-browser] 12.16.1860
ii surf [www-browser] 0.7-2
ii vivaldi-snapshot [www-browser] 1.7.735.11-1
ii w3m [www-browser] 0.5.3-34
-- no debconf information
Version: 2.11.0+dfsg-2+b1
Severity: important
The current version of hdfview does not show the content of any of my
HDF5 files.
Downgrading to the 2.9-3+b2 version of libjhdf{4,5}-{java, jni}, which
also installs libhdf5-8 version 1.8.13+docs-15, seems to fix the issue
for me, even if hdfview is kept at the 2.11 version. This seems to
suggest that the problem lies in libjhdf rather than in hdfview itself,
and/or in the API of libhdf5 used by jhdf.
FWIW, a similar bug seems to affect also jhdf 2.9-5 as found in Ubuntu,
which is using libhdf5-10 (1.8.16), which would further support the idea
of a breaking API change between version 1.8.13 and 1.8.16 of libhdf5.
-- System Information:
Debian Release: 9.0
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.9.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages hdfview depends on:
ii default-jre 2:1.8-58
ii java-wrappers 0.1.28
ii libjgraph-java 5.12.4.2+dfsg-5
ii libjhdf4-java 2.11.0+dfsg-2+b1
ii libjhdf5-java 2.11.0+dfsg-2+b1
ii libslf4j-java 1.7.22-1
hdfview recommends no packages.
Versions of packages hdfview suggests:
ii chromium [www-browser] 55.0.2883.75-6
ii dillo [www-browser] 3.0.5-3
ii elinks [www-browser] 0.12~pre6-12
ii firefox [www-browser] 51.0-1
ii iceape [www-browser] 2.7.12-1+b1
ii konqueror [www-browser] 4:16.08.3-1
ii links2 [www-browser] 2.14-2
ii lynx [www-browser] 2.8.9dev11-1
ii netsurf-fb [www-browser] 3.6-3
ii opera [www-browser] 12.16.1860
ii surf [www-browser] 0.7-2
ii vivaldi-snapshot [www-browser] 1.7.735.11-1
ii w3m [www-browser] 0.5.3-34
-- no debconf information
Mark Hymers
May 31, 2017, 7:10:02 AM5/31/17
to
On Tue, 31, Jan, 2017 at 04:27:12PM +0100, Giuseppe Bilotta spoke thus..
HDF5-1.10, the size of object identifiers was changed from 32- to
64-bit.
Unfortunately, by the HDF group's own admission, there is no version
of hdfview (and presumably the java libraries it comes with) which has
been updated for this. See https://support.hdfgroup.org/products/java/
Unless someone can suggest a solution, I suspect that this bug needs
to be upgraded to release-critical as it makes the package completely
useless.
Thanks,
Mark
--
Mark Hymers <mhy at debian dot org>
"Everyone is entitled to be stupid but some abuse the privilege."
Unknown
> Package: hdfview
> Version: 2.11.0+dfsg-2+b1
> Severity: important
>
> The current version of hdfview does not show the content of any of my
> HDF5 files.
>
> Downgrading to the 2.9-3+b2 version of libjhdf{4,5}-{java, jni}, which
> also installs libhdf5-8 version 1.8.13+docs-15, seems to fix the issue
> for me, even if hdfview is kept at the 2.11 version. This seems to
> suggest that the problem lies in libjhdf rather than in hdfview itself,
> and/or in the API of libhdf5 used by jhdf.
>
> FWIW, a similar bug seems to affect also jhdf 2.9-5 as found in Ubuntu,
> which is using libhdf5-10 (1.8.16), which would further support the idea
> of a breaking API change between version 1.8.13 and 1.8.16 of libhdf5.
I've been looking into this. It appears that between HDF5-1.8 and
> Version: 2.11.0+dfsg-2+b1
> Severity: important
>
> The current version of hdfview does not show the content of any of my
> HDF5 files.
>
> Downgrading to the 2.9-3+b2 version of libjhdf{4,5}-{java, jni}, which
> also installs libhdf5-8 version 1.8.13+docs-15, seems to fix the issue
> for me, even if hdfview is kept at the 2.11 version. This seems to
> suggest that the problem lies in libjhdf rather than in hdfview itself,
> and/or in the API of libhdf5 used by jhdf.
>
> FWIW, a similar bug seems to affect also jhdf 2.9-5 as found in Ubuntu,
> which is using libhdf5-10 (1.8.16), which would further support the idea
> of a breaking API change between version 1.8.13 and 1.8.16 of libhdf5.
HDF5-1.10, the size of object identifiers was changed from 32- to
64-bit.
Unfortunately, by the HDF group's own admission, there is no version
of hdfview (and presumably the java libraries it comes with) which has
been updated for this. See https://support.hdfgroup.org/products/java/
Unless someone can suggest a solution, I suspect that this bug needs
to be upgraded to release-critical as it makes the package completely
useless.
Thanks,
Mark
--
Mark Hymers <mhy at debian dot org>
"Everyone is entitled to be stupid but some abuse the privilege."
Unknown
Sergey Spiridonov
Sep 4, 2017, 8:20:03 AM9/4/17
to
Package: hdfview
Version: 2.11.0+dfsg-2+b1
Followup-For: Bug #853750
Hi! Just wonder, why the bug severity is "important" and not "grave" or
"critical". Hdfview is not working at all!
If package released in "stable" stretch, it is expected to work somehow,
isn't it?
Debian is famous for its stability, so removing non-working package is
better than keeping completely broken one... It took me some time to
realize that Debian released completely non-working package.
Removing the broken package will save time to others.
-- System Information:
Debian Release: 9.1
APT prefers stable
APT policy: (500, 'stable')
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8), LANGUAGE=en_GB:en (charmap=UTF-8)
Version: 2.11.0+dfsg-2+b1
Followup-For: Bug #853750
Hi! Just wonder, why the bug severity is "important" and not "grave" or
"critical". Hdfview is not working at all!
If package released in "stable" stretch, it is expected to work somehow,
isn't it?
Debian is famous for its stability, so removing non-working package is
better than keeping completely broken one... It took me some time to
realize that Debian released completely non-working package.
Removing the broken package will save time to others.
-- System Information:
Debian Release: 9.1
APT prefers stable
APT policy: (500, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.9.0-3-amd64 (SMP w/4 CPU cores)
Foreign Architectures: i386
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8), LANGUAGE=en_GB:en (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages hdfview depends on:
ii default-jre 2:1.8-58
ii java-wrappers 0.1.28
ii libjgraph-java 5.12.4.2+dfsg-5
ii libjhdf4-java 2.11.0+dfsg-2+b1
ii libjhdf5-java 2.11.0+dfsg-2+b1
ii libslf4j-java 1.7.22-1
hdfview recommends no packages.
Versions of packages hdfview suggests:
ii firefox-esr [www-browser] 52.3.0esr-1~deb9u1
Init: systemd (via /run/systemd/system)
Versions of packages hdfview depends on:
ii default-jre 2:1.8-58
ii java-wrappers 0.1.28
ii libjgraph-java 5.12.4.2+dfsg-5
ii libjhdf4-java 2.11.0+dfsg-2+b1
ii libjhdf5-java 2.11.0+dfsg-2+b1
ii libslf4j-java 1.7.22-1
hdfview recommends no packages.
Versions of packages hdfview suggests:
Dominique Delande
Nov 16, 2017, 7:10:04 AM11/16/17
to
Package: hdfview
Version: 2.11.0+dfsg-2+b1
Followup-For: Bug #853750
Dear all,
Version: 2.11.0+dfsg-2+b1
Followup-For: Bug #853750
I confirm that the version of hdfview shipped with stretch
(2.11.0+dfsg-2+b1) is not working at all!
Removing the broken package will save time to others.
I could not manage to build version 3.0.0 beta.
Best regards
Dominique Delande
--
Dominique Delande (Dominiqu...@lkb.upmc.fr)
Laboratoire Kastler-Brossel - Case 74 - Universite P. et M. Curie
4, place Jussieu, F-75252 Paris Cedex 05, FRANCE
Phone : +33 1 44 27 27 97 - Fax : +33 1 44 27 38 45
Acces : Tour 13, Couloir 12-13, 3eme etage - Bureau 316
PICCA Frederic-Emmanuel
Nov 16, 2017, 7:30:03 AM11/16/17
to
Just for info and as a work around, in stretch-backports there is the silx package which can be used in order to explore the hdf5 files.
the command line is
silx view.
Cheers
the command line is
silx view.
Cheers
Sébastien Villemot
Nov 16, 2017, 9:40:03 AM11/16/17
to
Control: severity -1 grave
On Thu, Nov 16, 2017 at 12:52:53PM +0100, Dominique Delande wrote:
> I confirm that the version of hdfview shipped with stretch
> (2.11.0+dfsg-2+b1) is not working at all!
> Removing the broken package will save time to others.
Bumping severity to grave, since several people report that this package is
currently unusable.
--
⢀⣴⠾⠻⢶⣦⠀ Sébastien Villemot
⣾⠁⢠⠒⠀⣿⡁ Debian Developer
⢿⡄⠘⠷⠚⠋⠀ http://sebastien.villemot.name
⠈⠳⣄⠀⠀⠀⠀ http://www.debian.org
On Thu, Nov 16, 2017 at 12:52:53PM +0100, Dominique Delande wrote:
> I confirm that the version of hdfview shipped with stretch
> (2.11.0+dfsg-2+b1) is not working at all!
> Removing the broken package will save time to others.
currently unusable.
--
⢀⣴⠾⠻⢶⣦⠀ Sébastien Villemot
⣾⠁⢠⠒⠀⣿⡁ Debian Developer
⢿⡄⠘⠷⠚⠋⠀ http://sebastien.villemot.name
⠈⠳⣄⠀⠀⠀⠀ http://www.debian.org
Chris Billington
Oct 27, 2019, 3:10:02 PM10/27/19
to
A further update, the Arch Linux AUR package is now building HDFView 3.1 successfully. I'm using it on Arch and it works. If Debian wants to replicate this for their package, see the build script here:
https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=hdfviewThe AUR package patches HDFview's build.xml file to unbundle java from the resulting package and to remove what looks like a workaround for incorrect library filenames that is not relevant on Arch. This may or may not be identical on Debian, but may be a useful starting point for anyone wanting to solve this bug.
0 new messages