[ome-users] Building openmicroscopy from source

[Roger Leigh]

Hi John,

I saw this a couple of times myself last week.  Doing a full clean and
rebuild fixed things for me.  I would suggest running "python build.py
clean" before rerunning the build to ensure you start from a clean
slate.  So long as ICE_HOME/SLICEPATH is set correctly and slice2xxx are
the ice 3.4 versions, this should work.


Regards,
Roger

On 14/04/2014 13:38, John Webber (NBI) wrote:
> Hi Roger,
>
> Thanks for the guidance below.
>
> I am, however, still experiencing the same issue!  I have amended all of my Paths, environment variables and the build.bat to now use Ice version 3.4, instead of ice version 3.5, but I am still seeing the same error:  "ome#bio-formats;5.0.1-DEV-ice34: not found".
>
> I have obtained Openmicroscopy by doing a "git clone" for branh dev_5_0 from https://github.com/openmicroscopy/git.
>
> Once I had obtained openmicroscopy, I used "git submodule update --init" to obtain bioformats.
>
> Am I getting Openmicroscopy an bioformats incorrectly?
>
> Thanks
> john
>
>
>
>
> -----Original Message-----
> From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Roger Leigh
> Sent: 09 April 2014 09:59
> To: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Building openmicroscopy from source
>
> On 09/04/2014 09:43, John Webber (NBI) wrote:
>> Hi Josh,
>>
>> Thanks for your quick response (as always!).
>>
>> I was indeed using different shells for these two parts - one a git bash shell and one a visual studios command prompt.
>>
>> As per your advice below, I have found the path for the git executable and added this to my PATH environment variable.  I now get a different, but very similar error:
>>
>>                   ::::::::::::::::::::::::::::::::::::::::::::::
>>
>>                   ::          UNRESOLVED DEPENDENCIES         ::
>>
>>                   ::::::::::::::::::::::::::::::::::::::::::::::
>>
>>                   :: ome#bio-formats;5.0.1-DEV-ice34: not found
>>
>>                   ::::::::::::::::::::::::::::::::::::::::::::::
>>
>> One interesting thing about this issue is that I am expecting to use ice 3.5.1, whereas the error above is for ice34. Do you have any pointers as to how I can correct this issue now?
>
> Dear John,
>
> There's a slight wrinkle here.  The ZeroC Ice packages for Ice 3.5.x use Python 3.3 rather than Python 2.6 or 2.7.  The Ice 3.4.x packages use Python 2.6.  Since all the OMERO python scripts are using python >= 2.6 (but not 3) this means that you can't currently use Ice 3.5 on Windows.
>
> You can use Python 2.6/2.7 on Windows if you build Ice yourself from source, then you can choose the Python version you want for IcePy to link against.  It's just the "official" ZeroC installer that forces you to use Python 3, so it's technically possible to use Ice 3.5 on Windows with OMERO, just hard in practice since most people prefer not to rebuild Ice.
>
>
> Kind regards,
> Roger
>
> --
> Dr Roger Leigh -- Open Microscopy Environment Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
> The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>


--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096