[Debichem-devel] Bug#872418: Reproducible, forwarded

[Norwid Behrnd]

Because of recent update of Jmol in the repositories to version 16.3.55 (at
present the same release as on sourceforge) to testing (Deb 14/forky) and
backport-stable (Deb 13/trixie) I notice Jmol «works differently» depending on
the Debian release.  I know too little about Java to tell if this is relevant
/ may provide help.


1) Debian 14/forky (at present testing).  Either I unzip the .binary.zip from
[sourceforge] to then cd into the decompressed archive, and launch Jmol by
`java -jar ./Jmol.jar &` on the BASH, or I install Jmol with synaptic and
launch the viewer by `jmol` in the BASH: the program launches, the links in
the «about Jmol» widget are recognized (because the cursor changes it shape
while hovering over them), and functional (i.e., firefox starts to access the
pages\*).

This instance of Debian 14/forky/testing setup is

```bash
$ java --version
openjdk 25.0.3-ea 2026-04-21
OpenJDK Runtime Environment (build 25.0.3-ea+7-Debian-2)
OpenJDK 64-Bit Server VM (build 25.0.3-ea+7-Debian-2, mixed mode, sharing)
```

Complementary, after Jmol 16.3.55 is installed from Debian's repositories:

```bash
$ apt list --installed "*java*" "*jdk*" "*jre*" "*openjdk*"
ca-certificates-java/testing,testing,now 20260311 all [installed,automatic]
default-jre-headless/testing,now 2:1.25-77 amd64 [installed,automatic]
default-jre/testing,now 2:1.25-77 amd64 [installed]
java-common/testing,testing,now 0.77 all [installed,automatic]
javascript-common/testing,testing,stable,stable,now 12+nmu1 all
[installed,automati>
libatk-wrapper-java-jni/testing,now 0.44.0-1 amd64 [installed,automatic]
libatk-wrapper-java/testing,testing,now 0.44.0-1 all [installed,automatic]
libbeam-java/testing,testing,stable,stable,now 1.3.9-1 all
[installed,automatic]
libcommons-cli-java/testing,testing,stable,stable,now 1.6.0-1 all
[installed,automa>
libjavascriptcoregtk-4.0-18/now 2.42.5-1 amd64 [installed,local]
libjavascriptcoregtk-4.1-0/testing,now 2.50.6-1 amd64 [installed]
libjavascriptcoregtk-6.0-1/testing,now 2.50.6-1 amd64 [installed,automatic]
libjmol-java/testing,testing,now 16.3.55+dfsg-1 all [installed,automatic]
libjna-inchi-java/testing,testing,stable,stable,now 1.3.1+dfsg-1 all
[installed,aut>
libjna-java/testing,testing,now 5.18.1-1 all [installed,automatic]
libjoptsimple-java/testing,testing,stable,stable,now 5.0.4-7 all
[installed,automat>
libnaga-java/testing,testing,stable,stable,now 3.0+svn80-5 all
[installed,automatic]
openjdk-21-jre-headless/testing,now 21.0.11~8ea-1 amd64 [installed]
openjdk-25-jre-headless/testing,now 25.0.3~7ea-2 amd64 [installed,automatic]
openjdk-25-jre/testing,now 25.0.3~7ea-2 amd64 [installed,automatic]
```

2) By default, an instance of Debian 13/trixie/stable runs with openjdk-21,
and jmol's version from Debian's repositories would be 16.2.33+dfsg-1.

2a) With Jmol from sourceforge's .zip, the links on «About Jmol» are
recognized (cursor changes into the hand shape), firefox however does not
start.
2b) I then install Jmol 16.3.55 as recently backported (i.e., by `sudo apt
install -t trixie-backports jmol`) -- the viewer is functional, but on the
about page, the links don't launch firefox.
2c) Speculating openjdk-21 could interfere here, I deinstalled everything
about Jmol (from apt), openjdk and java.  This includes to deinstall
`java-common`, `ca-certificates-java`, too.  On a clean slate, I installed `apt
install openjdk-25-jdk` which came with its dependencies.  Now the links in
Jmol as provided by the .zip on sourceforge are functional.
2d) Encouraged by 2c) the installation of the backport was started again with
`sudo apt install -t trixie-backports jmol`.  The links in the Jmol's «about»
again don't launch a visible action on firefox.  However I notice during the
installation of the backport, the elder openjdk-21 was added.  Now the system
(stable + backports) reports

```bash
$ java --version
openjdk 25.0.2 2026-01-20
OpenJDK Runtime Environment (build 25.0.2+10-Debian-1deb13u2)
OpenJDK 64-Bit Server VM (build 25.0.2+10-Debian-1deb13u2, mixed mode, sharing)
$ apt list --installed "*java" "*jdk" "jre*" "openjdk*"
ca-certificates-java/stable,now 20240118 all [installed,automatic]
libatk-wrapper-java/stable,now 0.40.0-3 all [installed,automatic]
libbeam-java/stable,now 1.3.9-1 all [installed,auto-removable]
libcommons-cli-java/stable,now 1.6.0-1 all [installed,auto-removable]
libgoogle-gson-java/stable,now 2.10.1-1 all [installed]
libjmol-java/stable-backports,now 16.3.55+dfsg-1~bpo13+1 all
[installed,auto-re>
libjna-inchi-java/stable,now 1.3.1+dfsg-1 all [installed,auto-removable]
libjna-java/stable,now 5.15.0-1 all [installed,auto-removable]
libjoptsimple-java/stable,now 5.0.4-7 all [installed,auto-removable]
libnaga-java/stable,now 3.0+svn80-5 all [installed,auto-removable]
openjdk-21-jre-headless/stable,stable-security,now 21.0.10+7-1~deb13u1 amd64
[i>
openjdk-21-jre/stable,stable-security,now 21.0.10+7-1~deb13u1 amd64
[installed,>
openjdk-25-jdk-headless/stable,stable-security,now 25.0.2+10-1~deb13u2 amd64
[i>
openjdk-25-jdk/stable,stable-security,now 25.0.2+10-1~deb13u2 amd64 [installed]
openjdk-25-jre-headless/stable,stable-security,now 25.0.2+10-1~deb13u2 amd64
[i>
openjdk-25-jre/stable,stable-security,now 25.0.2+10-1~deb13u2 amd64
[installed,>
```

Best regards,
Norwid


\* <https://jmol.sourceforge.net/> eventually does not work, but this is the
same pattern as to access <https://jmol.sourceforge.net/download/> and then
click there on «Home» (top right on their site).  For <https://www.acme.com/>
I get a time out error, but this likely is beyond Jmol's influence.

[sourceforge]:
https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.3/Jmol%2016.3.55/