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Bug #2509

[jmol] bash permission deny

bit4bit - over 4 years ago - . Updated over 4 years ago.

Status:
fixed
Priority:
bug
Assignee:
bill-auger
% Done:

0%

Description

On version: jmol-14.29.3-1

The file /usr/bin/jmol is a link to /usr/share/jmol/jmol.sh but the jmol.sh is not executable
and sagemath(https://www.parabola.nu/packages/community/x86_64/sagemath/) not execute 3d graphic
s.

$ ls -l /usr/share/jmol/jmol.sh
-rw-r--r-- 1 root root 849 feb  6  2018 /usr/share/jmol/jmol.sh

I fixed on my sistem with:

# chmod +x /usr/share/jmol/jmol.sh

I see the mode for the file on source package jmol-14.29.3-1.parabola1-any.pkg.tar.xz:

$ tar --list -f jmol-14.29.3-1.parabola1-any.pkg.tar -vvv
...
-rw-r--r-- root/root       849 2018-02-06 18:16 usr/share/jmol/jmol.sh
...

I see the arch package but that is other version (jmol 14.29.54-1) and on that package the file jmol.sh has correct execute permisions:

$ tar --list -f jmol-14.29.54-1-any.pkg.tar -vvv
-rwxr-xr-x root/root       849 2019-10-09 14:37 usr/share/jmol/jmol.sh

History

#1

Updated by bill-auger over 4 years ago

  • Status changed from unconfirmed to confirmed
  • Description updated (diff)

A+ bit4bit - excellent bug report

#2

Updated by bill-auger over 4 years ago

there is a new PKGBUILD in abslibre now that fixes this bug - i also bumped the version up to the same as arch (v14.29.54); but the patches need re-working - im putting it on hold though

 |  patching file build.xml
 |  Hunk #1 FAILED at 159.
 |  Hunk #2 FAILED at 520.
 |  Hunk #3 succeeded at 724 with fuzz 2 (offset 169 lines).
 |  Hunk #4 succeeded at 755 (offset 169 lines).
 |  Hunk #5 succeeded at 1309 (offset 146 lines).
 |  2 out of 5 hunks FAILED -- saving rejects to file build.xml.rej
 |  ==> ERROR: A failure occurred in prepare().
 |      Aborting...
==> Copying log and package files out of the chroot...
#3

Updated by bill-auger over 4 years ago

  • Assignee set to bill-auger

patches are re-worked for v14.29.54 - FTBS with java v13

classes:
    [mkdir] Created dir: /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/build/classes
    [javac] Compiling 1072 source files to /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/build/classes
    [javac] warning: [options] bootstrap class path not set in conjunction with -source 6
    [javac] error: Source option 6 is no longer supported. Use 7 or later.
    [javac] error: Target option 6 is no longer supported. Use 7 or later.

BUILD FAILED
/code/packages/abslibre/libre/jmol/src/jmol-14.29.54/build.xml:449: Compile failed; see the compiler error output for details.

FTBS with java v10, v11

/JmolAudio.java:42: error: package sun.audio does not exist
    [javac] import sun.audio.AudioData;
    [javac]                 ^
    [javac] /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/src/org/jmol/util/JmolAudio.java:43: error: package sun.audio does not exist
    [javac] import sun.audio.AudioDataStream;
    [javac]                 ^
    [javac] /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/src/org/jmol/util/JmolAudio.java:48: error: package sun.audio does not exist
    [javac]     javax.sound.sampled.LineListener.class, sun.audio.AudioData.class,
    [javac]                                                      ^
    [javac] /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/src/org/jmol/util/JmolAudio.java:49: error: package sun.audio does not exist
    [javac]     sun.audio.AudioDataStream.class })
    [javac]              ^
    [javac] /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/src/jspecview/application/AwtTreeNode.java:9: error: AwtTreeNode is not abstract and does not override abstract method children() in JSVTreeNode
    [javac] public class AwtTreeNode extends
    [javac]        ^
    [javac] /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/src/org/jmol/util/JmolAudio.java:117: error: cannot find symbol
    [javac]     AudioInputStream ais = AudioSystem.getAudioInputStream(new AudioDataStream(
    [javac]                                                                ^
    [javac]   symbol:   class AudioDataStream
    [javac]   location: class JmolAudio
    [javac] /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/src/org/jmol/util/JmolAudio.java:118: error: cannot find symbol
    [javac]         new AudioData((byte[]) data)));
    [javac]             ^
    [javac]   symbol:   class AudioData
    [javac]   location: class JmolAudio
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: /code/packages/abslibre/libre/jmol/src/jmol-14.29.54/src/org/jmol/util/BZone.java uses unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 7 errors
    [javac] 6 warnings

BUILD FAILED
/code/packages/abslibre/libre/jmol/src/jmol-14.29.54/build.xml:449: Compile failed; see the compiler error output for details.

java v8 appears to have built jmol successfully - posted BR upstream

https://sourceforge.net/p/jmol/bugs/608/

#4

Updated by bill-auger over 4 years ago

  • Status changed from confirmed to fixed

bit4bit -

jmol-14.29.54 is in the repos now - im not quite sure to expect from this program; but it launches successfully - could you try it out and let us know if it functions as expected

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