NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 296 - libCg installed on system, but not accepted during Fiji.(deb) install
libCg installed on system, but not accepted during Fiji.(deb) install
Status: RESOLVED INVALID
Product: Fiji
Classification: Unclassified
Component: Debian Packages
unspecified
PC Linux
: P2 normal
Assigned To: Mark Longair
Depends on:
Blocks:
 
Reported: 2011-03-21 11:57 CDT by anamezon1972
Modified: 2011-03-22 21:36 CDT
1 user (show)

See Also:

Description anamezon1972 2011-03-21 11:57:52 CDT
libCg-2.1_October2008-1.11 already properly installed in /usr/lib/libCg.so, but during fiji_20090513_i386.deb install not accepted as libCg.so(VERSION) dependency, and if ignoring that install problem - (quite expectedly) Fiji does not launch
Comment 1 Mark Longair 2011-03-21 12:30:19 CDT
I don't think that libCg.so has anything to do with the Fiji Debian packages - at least not explicitly.  In order to help, however, I'll need much more information in this bug report.  Could you possibly add as a comment:

- The error message that you get when just running "fiji" from the command line.
- Any errors you got when installing the packages, including the command that you used to install them.

?

many thanks,
mark
Comment 2 anamezon1972 2011-03-21 15:09:39 CDT
my apologies - I should have included several clarifications and details, but I thought I had limited space to describe the bug ... anyway:

1. the binary package that I used is NOT .deb anymore, but converted to .rpm using "alien -rk --scripts" (it was converted without errors, including its scripts!); in the evening I will give the initial.deb package a try on a debian-based (LMDE) machine at home and post the results, but I don't think that conversion caused the problem I described;

2. in my particular case, when I ran into the "libCg.so(VERSION)" dependency error while installing (system-wide), I over-rode it with --no-deps (RPM) option, since I was sure libCg was installed; as a result, now I have that "libCg.so(VERSION)" (only) broken dependency reported by my GUI package manager (YaST2), so that's a problem I have to fix somehow; and I was hoping that that could be corrected in the install scripts

3. the output of running "fiji" in command prompt was:

Found that JAVA_HOME was: '/usr/lib/jvm/java-6-sun/'
Could not launch system-wide Java (No such file or directory)

so it is not libCg.so fault after all that fiji does not run; maybe I should close that particular bug report?
Comment 3 Mark Longair 2011-03-21 15:38:45 CDT
(In reply to comment #2)
> my apologies - I should have included several clarifications and details, but I
> thought I had limited space to describe the bug ... anyway:
> 
> 1. the binary package that I used is NOT .deb anymore, but converted to .rpm
> using "alien -rk --scripts" (it was converted without errors, including its
> scripts!); in the evening I will give the initial.deb package a try on a
> debian-based (LMDE) machine at home and post the results, but I don't think
> that conversion caused the problem I described;
> 
> 2. in my particular case, when I ran into the "libCg.so(VERSION)" dependency
> error while installing (system-wide), I over-rode it with --no-deps (RPM)
> option, since I was sure libCg was installed; as a result, now I have that
> "libCg.so(VERSION)" (only) broken dependency reported by my GUI package manager
> (YaST2), so that's a problem I have to fix somehow; and I was hoping that that
> could be corrected in the install scripts
> 
> 3. the output of running "fiji" in command prompt was:
> 
> Found that JAVA_HOME was: '/usr/lib/jvm/java-6-sun/'
> Could not launch system-wide Java (No such file or directory)
> 
> so it is not libCg.so fault after all that fiji does not run; maybe I should
> close that particular bug report?

I'll close it shortly, but hopefully you can fix that problem by running:

    unset JAVA_HOME

... before running fiji from the terminal.
Comment 4 anamezon1972 2011-03-22 21:04:57 CDT
Just to conclude - I installed Fiji system-wide on a Debian-based (LMDE) machine tonight using the package from the provided APT repository and there was no problem at all; the libCg.so dependency obviously is problematic only in my particular case (installing from a deb-to-rpm converted package); since I need a RPM-based system-wide Fiji install, I have to figure out a different approach (but that's more suitable for the forums, not here); once again, sorry for my initial incomplete post and for wasting your time on that issue!
Comment 5 anamezon1972 2011-03-22 21:36:31 CDT
P.S. as for unsetting JAVA_HOME, here is the outcome:

tux@AmiloV3205:~> fiji

Found that JAVA_HOME was: '/usr/lib/jvm/java-6-sun/'
Could not launch system-wide Java (No such file or directory)

tux@AmiloV3205:~> unset JAVA_HOME

tux@AmiloV3205:~> fiji

Found that JAVA_HOME was: '/usr/lib/jvm/java-6-sun/'
Could not launch system-wide Java (No such file or directory)

tux@AmiloV3205:~> env | grep JAVA

JAVA_BINDIR=/usr/lib/jvm/jre/bin
JAVA_ROOT=/usr/lib/jvm/jre

i.e. it didn't work (running it as a user); should it be done as root?