Package Details: hdfview 3.1.0-1

Git Clone URL: https://aur.archlinux.org/hdfview.git (read-only, click to copy)
Package Base: hdfview
Description: a GUI browser for reading hdf5 files
Upstream URL: https://www.hdfgroup.org/downloads/hdfview/
Licenses: custom
Conflicts: hdfview-beta
Replaces: hdfview-beta
Submitter: eleftg
Maintainer: MartinDiehl (chrisjbillington)
Last Packager: eleftg
Votes: 6
Popularity: 0.003848
First Submitted: 2017-10-17 18:54
Last Updated: 2019-10-27 12:26

Latest Comments

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MartinDiehl commented on 2019-10-25 06:28

@eleftg: Thanks!

could be indeed related to openjdk11. I use the most recent version:

pacman -Q | grep jdk jdk-openjdk 13.u33-1 jre-openjdk 13.u33-1 jre-openjdk-headless 13.u33-1

Unfortunately, the --ignore-missing-deps option was required for me to avoid a long list of dependencies that caused trouble.

eleftg commented on 2019-10-24 23:12

Buildfile: /builder/hdfview/src/hdfview-3.1.0/build.xml
     [echo]
     [echo]      Application:      HDFView 3.1.0
     [echo]      Build File:       /builder/hdfview/src/hdfview-3.1.0/build.xml
     [echo]
     [echo]      Run by:           george
     [echo]      Build Dir:        build
     [echo]      Base Dir:         /builder/hdfview/src/hdfview-3.1.0
     [echo]      Dist Dir:         build/dist
     [echo]      Java Home:        /usr/lib/jvm/java-11-openjdk
     [echo]      Classpath:        /builder/hdfview/src/hdfview-3.1.0/lib/fits.jar:/builder/hdfview/src/hdfview-3.1.0/lib/netcdf.jar:/opt/hdf4/lib/jarhdf-4.2.14.jar:/usr/lib/jarhdf5-1.10.5.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/linux/x86_64/swt.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/common-image-3.3.2.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/common-io-3.3.2.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/common-lang-3.3.2.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/commons-logging-1.2.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/commons-logging.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/imageio-core-3.3.2.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/imageio-metadata-3.3.2.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/imageio-tiff-3.3.2.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/org.eclipse.core.commands.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/org.eclipse.equinox.common.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/org.eclipse.jface.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/org.eclipse.nebula.widgets.nattable.core.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/org.eclipse.osgi.jar:/builder/hdfview/src/hdfview-3.1.0/lib/ext/swt/org.eclipse.ui.workbench.jar:/builder/hdfview/src/hdfview-3.1.0/lib/slf4j-api-1.7.25.jar:/builder/hdfview/src/hdfview-3.1.0/lib/extra/slf4j-simple-1.7.25.jar
     [echo]      HDF libpath:      /opt/hdf4/lib,/usr/lib
     [echo]      HDF-Java version: 4.2.14:1.10.5
     [echo]      HDF4 version:     4.2.14
     [echo]      HDF5 version:     1.10.5
     [echo]      Operating System: Linux 4.19.80-1-lts amd64
     [echo]      Debug Build:      true
     [echo]
Trying to override old definition of task jlink

clean-package:

compileobj:
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/classes
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/classes/hdf
     [copy] Copying 1 file to /builder/hdfview/src/hdfview-3.1.0/build
    [javac] Compiling 1 source file to /builder/hdfview/src/hdfview-3.1.0/build/classes
    [javac] Compiling 12 source files to /builder/hdfview/src/hdfview-3.1.0/build/classes
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5CompoundDS.java uses unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
     [copy] Copying 2 files to /builder/hdfview/src/hdfview-3.1.0/build/classes

compilehdf4:
    [javac] Compiling 6 source files to /builder/hdfview/src/hdfview-3.1.0/build/classes
    [javac] Note: /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h4/H4Vdata.java uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.

compilespc:
    [javac] Compiling 8 source files to /builder/hdfview/src/hdfview-3.1.0/build/classes
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.

compilehdf5:

compile:
    [javac] Compiling 58 source files to /builder/hdfview/src/hdfview-3.1.0/build/classes
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: /builder/hdfview/src/hdfview-3.1.0/src/hdf/view/ImageView/DefaultImageView.java uses unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
     [copy] Copying 55 files to /builder/hdfview/src/hdfview-3.1.0/build/classes

objectjar:
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/jar
      [jar] Building jar: /builder/hdfview/src/hdfview-3.1.0/build/jar/hdfobject.jar

jar:
      [jar] Building jar: /builder/hdfview/src/hdfview-3.1.0/build/jar/HDFView.jar

javadoc:
  [javadoc] Generating Javadoc
  [javadoc] Javadoc execution
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/Attribute.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/CompoundDS.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/CompoundDataFormat.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/DataFormat.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/Dataset.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/Datatype.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/FileFormat.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/Group.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/HObject.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/MetaDataContainer.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/ScalarDS.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/Utils.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h4/H4Datatype.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h4/H4File.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h4/H4GRImage.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h4/H4Group.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h4/H4SDS.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h4/H4Vdata.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5CompoundDS.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5Datatype.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5File.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5Group.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5Link.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5ScalarDS.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/object/h5/H5Utils.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/view/Chart.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/view/DefaultFileFilter.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/view/HDFView.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/view/Tools.java...
  [javadoc] Loading source file /builder/hdfview/src/hdfview-3.1.0/src/hdf/view/ViewProperties.java...
  [javadoc] Constructing Javadoc information...
  [javadoc] Creating destination directory: "/builder/hdfview/src/hdfview-3.1.0/build/javadocs/"
  [javadoc] Standard Doclet version 11.0.4
  [javadoc] Building tree for all the packages and classes...
  [javadoc] Building index for all the packages and classes...
  [javadoc] Building index for all classes...
  [javadoc] Building index for all classes...

deployWindows:

deployUnix:
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/lib
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/lib/extra
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/share
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/share/samples
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/share/doc
     [copy] Copying 28 files to /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/lib
     [copy] Copying 2 files to /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/lib/extra
     [echo] Bundling JRE with jdeps and jlink...
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
    [apply] Result: 2
     [copy] Copying 1 file to /builder/hdfview/src/hdfview-3.1.0/build
   [delete] Deleting: /builder/hdfview/src/hdfview-3.1.0/build/jdeps.pre
     [echo] List of generated module dependencies: Error: unknown option: --ignore-missing-deps,Usage: jdeps <options> <path ...>],use --help for a list of possible options
     [exec] Error: Module Usage: jdeps <options> <path ...>] not found
     [exec] Result: 1
     [copy] Copying 1 file to /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0
     [copy] Copying 166 files to /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/share/doc/javadocs
     [copy] Copying 3 files to /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/share/doc
     [copy] Copying 9 files to /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/share/samples

deployMac:

deploy:

createWindowsInstaller:

createUnixInstaller:
    [mkdir] Created dir: /builder/hdfview/src/hdfview-3.1.0/build/dist
     [copy] Copying 1 file to /builder/hdfview/src/hdfview-3.1.0/build/dist

BUILD FAILED
/builder/hdfview/src/hdfview-3.1.0/build.xml:1564: /builder/hdfview/src/hdfview-3.1.0/build/HDF_Group/HDFView/3.1.0/jre does not exist.

Total time: 18 seconds
==> ERROR: A failure occurred in build().
    Aborting...

For the time being, the suggested PKGBUILD fails to build on my box (with openjdk-11). Seems to be an issue with --ignore-missing-deps. Will look into it further...

eleftg commented on 2019-10-24 13:39

Back from holidays. I am going to integrate the proposed changes as soon as I get back from work (in a matter of hours).

Thanks @MartinDiehl

chrisjbillington commented on 2019-10-24 13:35

@MartinDiehl, the AUR package has been orphaned. If you wanted to adopt it and make your proposed changes for the next version (even if you immediately orphan the package again), we would all be grateful. I am happy to test!

MartinDiehl commented on 2019-10-12 04:25

If I am in a directory called

/home/m/DAMASK/examples/SpectralMethod/Polycrystal

and execute

/opt/HDFView/3.1.0/hdfview.sh 20grains16x16x16_tensionX.hdf5

to open the file 20grains16x16x16_tensionX.hdf5 which is located in this directory, I get an empty HDFview window.

using

/opt/HDFView/3.1.0/hdfview.sh -root $PWD 20grains16x16x16_tensionX.hdf5

or

/opt/HDFView/3.1.0/hdfview.sh /home/m/DAMASK/examples/SpectralMethod/Polycrystal/20grains16x16x16_tensionX.hdf5

results in the expected behavior. So it seems that the current working directory is not taken into account when using a relative path.

chrisjbillington commented on 2019-10-10 20:14

Is the hdfview.sh issue only a problem when the filepath has spaces in it? If so, it's just that there are no quote marks around the argument passing in /usr/bin/hdfview.sh, it needs to be:

/opt/HDFView/3.0.0/hdfview.sh "$@"

This issue is present in the current version. Even if the issue you're seeing is different (sounds like it might be), the above should still be fixed.

MartinDiehl commented on 2019-10-06 18:46

Three more comments

1) It is not necessary to have a copy of the JRE (Java runtime environment). I'm not sure whether it is considered good practice, but to me it seems more Arch linux style to use the JRE provided by the system.

2) I think using hdfview instead of hdfview.sh is the better choice

3) Passing the file name to hdfview(.sh) does not work anymore. It requires to explicitly set the root dir to $PWD

Please find an updated version that solves these three issues on https://cloud.martin-diehl.net/index.php/s/CSaHLkb4PayD4NT It also includes a high-res logo (svg)

MartinDiehl commented on 2019-10-06 17:23

Hi,

I tried to update the package to 3.1 and found two issues which should probably be tackled upstream. I sent the following message to the HDF group

Dear HDF team,

I am trying to build the hdfviewer from source (this is required to package it for Arch linux, see https://aur.archlinux.org/packages/hdfview) and encountered the two issues:

1) First, recording the symlinks (line 1080ff in build.xml) requires write access to the location where the libraries are located. This is typically in /lib, so most users do not have permission to write there (for good reasons). However, simply removing recording and restoring the symlinks does not cause any harm on my system because the libraries are anyway available system wide.

2) The call to jdeps (line 899ff in build.xml) results in an extremely long list of arguments to the following call of jlink which cannot be handled (too many arguments). Since most of these dependencies are not found (and apparently not needed), adding "<arg value="--ignore-missing-deps" />" resolves this issue.

I think both issues are not very specific too my system and are relevant to other users as well. Please find attached a patched build.xml

best regards,

Martin

In the meantime, the following PKGBUILD including patch resolves the issues: https://cloud.martin-diehl.net/index.php/s/Wbs2D7KPKM7P6YD

Note that JDK 8 does not work anymore (I use 12, but probably already 9 is sufficient)

chrisjbillington commented on 2019-03-13 02:45

One of the dependencies, hdf5-java, has had a new release on the AUR, leading to failure with:

Warning! HDF5 library version mismatched error The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this application is linked. Data corruption or segmentation faults may occur if the application continues. This can happen when an application was compiled by one version of HDF5 but linked with a different version of static or shared HDF5 library.

etc etc.

Rebuilding hdfview fixes it. You might consider bumping the PKGREL to prompt users to rebuild. However, hdf5-openmpi-java on the AUR has not had a version bump yet, so you would need to do it again when that bumps. Also since hdf5 in the arch repos hasn't been updated to 1.10.5 yet, we're currently in an annoying situation where say, h5py from the repos won't work with hdf5-java from the AUR since h5py was compiled with 1.10.4. Annoying that patch releases break hdf5 applications.

greyltc commented on 2019-02-07 19:36

@eleftg Please accept my apologies for upsetting you by flagging your package. I personally prefer people to flag the packages I maintain when they believe a change needs to be made.

I know I had some rational thought in my head when I specified =11, but I can't remember it anymore! Removed.