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#1 2018-12-05 03:41:10

Copper36
Member
Registered: 2018-11-27
Posts: 7  

Can't start UGENE

Hi,
I've installed a bioinformatics suite UGENE (which I routinely use on different platforms) from one of the contrib repositories, but it fails to start with a segfault:

~$ ugene -ui
Translation not found: transl_en
/usr/lib/ugene/ugene: line 69:  7558 Segmentation fault      "$dirname/$appname" "${params[@]}"

Line 69 is the last "fi":

#!/bin/bash

appname=ugenecl

# Check if '-ui' parameter is present. 
# If it does exclude it from the list of parameters
# and use ugeneui instead of ugenecl

params=()

while [[ $# -gt 0 ]];
do
    if [ "$1" = "-ui" ]; then
        appname=ugeneui
        if `echo $DESKTOP_SESSION|grep -i kde >/dev/null 2>&1`; then
            IS_KDE=1
        fi
    else
        params+=("$1")
    fi
    shift
done

dirname=$(dirname "`readlink -f "$0"`")

tmp="${dirname#?}"

if [ "${dirname%$tmp}" != "/" ]; then
    dirname=$PWD/$dirname
fi

LD_LIBRARY_PATH=$dirname
export LD_LIBRARY_PATH

# check compatibility OS and UGENE (32-bit or 64-bit)
system_i686=false
system_x86_64=false

case "`uname -m|grep 64|wc -l|tr -d ' '`" in
0*) system_i686=true;;
1*) system_x86_64=true;;
esac

ugene_i686=false
ugene_x86_64=false

case "`file -b $dirname/$appname |cut -d "," -f1 |grep 64|wc -l|tr -d ' '`" in
0*) ugene_i686=true;;
1*) ugene_x86_64=true;;
esac

if $system_i686; then
  if $ugene_x86_64; then
    echo "Warning: You have a 32-bit operating system but you are trying to launch a 64-bit version of the UGENE package. You have to download the appropriate UGENE version instead."
  fi
else
  if $ugene_i686; then
    echo "Warning: You have a 64-bit operating system but you are trying to launch a 32-bit version of the UGENE package. You have to download the appropriate UGENE version instead."
  fi
fi

# Workaround for UGENE-4619
export QT_QPA_PLATFORMTHEME=

if [ -z $IS_KDE ]; then
    "$dirname/$appname" "${params[@]}"
else
    "$dirname/$appname" "${params[@]}" -style cleanlooks
fi

I looked at the same file in another installation and it looks the same, at least the very last lines.

Do you have any idea what the problem might be?

ASCII 64bit.

Thank you.

Last edited by Copper36 (2018-12-05 03:53:05)

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#2 2018-12-05 17:44:39

chris2be8
Member
Registered: 2018-08-11
Posts: 37  

Re: Can't start UGENE

It's probably the program invoked by the script that's causing the segfault.

Try making a copy of the script and changing line 68 to:
echo "$dirname/$appname" "${params[@]}" -style cleanlooks

Run that and it should tell you what program it's actually trying to run. Then try searching for problems with that program (start by running file against it, that will tell you what sort of program it is).

Chris

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#3 2018-12-06 02:33:26

Copper36
Member
Registered: 2018-11-27
Posts: 7  

Re: Can't start UGENE

Thank you Chris,

I am a bit puzzled with the result since I do not quite understand the syntax of the script. So I had changed the last but one line, so it looks like this:

# Workaround for UGENE-4619
export QT_QPA_PLATFORMTHEME=

if [ -z $IS_KDE ]; then
    "$dirname/$appname" "${params[@]}"
else
    echo "$dirname/$appname" "${params[@]}" -style cleanlooks
fi

The attempt to start the program results in the same error message:

~$ ugene -ui
Translation not found: transl_en
/usr/lib/ugene/ugene: line 69:  5363 Segmentation fault      "$dirname/$appname" "${params[@]}"

Running echo with the everything following it:

~$ echo "$dirname/$appname" "${params[@]}" -style cleanlooks
/ -style cleanlooks

The only thing which looks suspicious to me is that there is no "cleanlooks" theme in this installation (as well as in another Xubuntu 14.04, where UGENE however does not have problems). There is "clearlooks" instead.

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#4 2018-12-06 02:42:45

golinux
Administrator
Registered: 2016-11-25
Posts: 1,339  

Re: Can't start UGENE

Copper36 wrote:

The only thing which looks suspicious to me is that there is no "cleanlooks" theme in this installation (as well as in another Xubuntu 14.04, where UGENE however does not have problems). There is "clearlooks" instead.

I have never seen or heard of a "cleanlooks" theme.  I'm thinking it's a typo or inaccurate translation somewhere along the line.

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#5 2018-12-06 03:30:46

ralph.ronnquist
Administrator
From: Clifton Hill, Victoria, AUS
Registered: 2016-11-30
Posts: 276  

Re: Can't start UGENE

Copper36, I think it's the "then" fork that is selected, not the "else" fork. Perhaps you should add a line before the "if" saying

echo "$dirname/$appname" "${params[@]}"

which would tell which program is actually run.

It looks though like it's problem is that it cannot find the appropriate translation file(s) so that it can tell what it's problem is, so you might not gain anything more from this than knowing which program has a problem.

EDIT: there is also https://bugs.debian.org/cgi-bin/bugrepo … bug=868885 to ponder.

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#6 2018-12-06 04:19:13

Copper36
Member
Registered: 2018-11-27
Posts: 7  

Re: Can't start UGENE

Thank you Ralph,

Especially for the link to the filed bug report. If I understand everything correctly, it is dated summer 2017 (and "grave" severity), i.e. is more than a year old. So it looks like nobody really cares. I have neither expertise nor time to dig into this, so I am going to try the online installer provided by UGENE itself. My hunch is that I'll get a huge blob containing everything, but at least it might work... No offense, but don't you guys find it a bit ironic? It used to work just fine in a bunch of Debian derivatives like Xubuntus 12, 14, it works in Windows, but not in the stable Debian itself...

I'll let you know how it turns out.

Last edited by Copper36 (2018-12-06 04:21:12)

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#7 2018-12-06 17:30:35

chris2be8
Member
Registered: 2018-08-11
Posts: 37  

Re: Can't start UGENE

Try adding set-x as the second line of the script. That should produce tracing output from the script which will show what it's doing.

Chris

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#8 2018-12-08 02:56:26

Copper36
Member
Registered: 2018-11-27
Posts: 7  

Re: Can't start UGENE

Thank you guys for your assistance, really appreciate it. However, as I mentioned, I do not have that much time (and enthusiasm too, to be honest) to dig into the more-than-one-year-old bug...
UGENE offers its online installer (of the most recent version of the suite), so I gave it a shot. It took some time (mostly waiting), but it was installed without problems, and is now up and running. It's weird of course, but at least it works...
Thank you again!

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