MarvinSketch bugs in 32 bit Ubuntu 15.04

Hi,
I'm running 32 bit Ubuntu 15.04 and I installed the Marvin Suite 15.5.18 sh file with bundled JRE for 32 bit Linux. The bugs mentioned have only been observed in MarvinSketch. Whenever I open the document style (File->Document Style->Settings...) window the program closes abruptly with no explanation given. Likewise changes to Preferences are not saved (i.e., those set by showing to Edit->Preferences in the GUI) or so it seems.

When I installed the Marvin Suite without bundled JRE for 32 bit Linux I could adjust document settings without a problem, but I couldn't change my Preferences as whenever I tried to open it via going to Edit->Preferences no window was opened. Likewise attempting to open up calculation windows like pK_a or logP was fruitless, without any windows being opened.

Specifications:

Processor	Intel® Core™ i5 CPU M 460 @ 2.53GHz × 4
Graphics	Intel® Ironlake Mobile x86/MMX/SSE2
RAM	3.8 GB

If you have any suggestions or queries please ask.

Thanks for your time,
Brenton

Hi Brenton,

can you please confirm whether the "~/.chemaxon" folder is exists and writable from Marvin? If it is not exists then can you please check whether your user home is writable?

I tried to install Marvin on a fresh 32-bit Ubuntu on a virtual machine, and it worked well, and I did not experienced any issues with it, so that is the one thing I can think of.

If the folder seems writable and you are still have the issue, then that may help if you start Marvin from the command line, if you installed with the default options, you can start it from a terminal with the command "~/ChemAxon/MarvinBeans/MarvinSketch". In this case, the terminal can show the exceptions that are thrown when the crash happens, if you find any, then please post them here.

Regards,
Istvan 

Here's my log file for this error. 

Hi, in this case it seems the problem occurs when a combo box component that is to choose the atom label font tries to render one of the fonts name with the font its name the component is rendering.

Can you please send me the output.txt after executing the following command in a terminal:

fc-list > output.txt

Thanks in advance!
Istvan 

Here it is. 

Thanks, this will take some time to examine, please be patient, I will try to get back to you today, but it is possible that I can only answer to you only after Monday.

Hi Brenton,

finally I was able to find out which font causes the issue, and I am able to reproduce it on my environment.

Your installation contains about a hundred more font then my installation I assume because I have just installed a system and Marvin for the test.

It turned out the problematic font is in the "ttf-unifont" package, I have to examine the exact issue with it, and check whether we can avoid this issue to happen or not.

In the mean time, you can avoid the crash by uninstalling that font package from your system.

To do so the easiest way for me is to type this into a terminal:

sudo apt-get purge ttf-unifont

I will get back to you if I have more information or a schedule for the fix to be released.

Regards,
Istvan 

Hi Brenton,

here I can present the final description of the issue you have, and our decision on it.

It seems there is a bug in Java about handling font maps, at least some developer mailing lists and some forum indicates this for me. So that the java version we bundle with Marvin is not able to handle the fonts in the ttf-unifont package.

Due to some other considerations we can not refresh the bundled java version currently, so if you need the ttf-unifont package, you can not use Marvin with the bundled Java, but have to install and set up a newer version, I tried with the 1.8.0_u45 and it works well with unifont. If you do not need the unifont package, then you can simple uninstall it, and use Marvin with the bundled Java.

Marvin with the bundled java is crashes when ttf-unifont is present in cases when the UI has to render something with that font. So Marvin will start, but the vm crashes immediatelly if the default system font is one from the unifont package, or immediatelly after the Document Style dialog is opened. when the default font does not came from the unifont package.

We were not able to get to a suitable solution to avoid this situation, and due to the fact that recent Java versions work well, and there are workarounds, we decided to close this case at this point.

Regards,
Istvan