[ome-users] Bioformats java error: "illegal character: \92"

[Roger Leigh]

Just in case this is of any use to yourself or anyone else using git on
Windows:

One thing I found this morning while setting up our own Windows builds
of bioformats was that on Windows it seems that the system/global
settings (and even the registry setting from initial install of msysgit)
are not always respected.  This might be just on the inital "git clone",
where it appears to always default to using "core.autocrlf=auto".

The solution I found was to manually edit C:\Program Files
(x86)\Git\etc\gitconfig and set "core.autocrlf=input" from the default
of "auto", and this fixed things for me.


Regards,
Roger

On 16/04/2014 10:42, John Webber (NBI) wrote:
> Great - that has indeed resolved my issue - thanks.
>
>
>
> -----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: 15 April 2014 23:13
> To: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Bioformats java error: "illegal character: \92"
>
> On 15/04/2014 10:14, John Webber (NBI) wrote:
>
>> I am trying to build openmicroscopy, but am encountering an error.  I
>> see the following errors:
>>
>> D:\GitHub\openmicroscopy\components\bioformats\components\ome-xml\buil
>> d\src\ome\
>>
>> xml\meta\AggregateMetadata.java:602: error: illegal character: \92
>>
>> When I look into the java file, I see "\" characters throughout the
>> code, which are all resulting in the above error.
>>
>> As per the advice from Melisa on the following page:
>> http://www.openmicroscopy.org/community/viewtopic.php?f=6&t=7386,  I
>> have tried to configure Git to respect the repository's line endings
>> with the following commands:
>>
>> git config --global --add core.autocrlf input
>>
>> git rm --cached -r .
>> git reset --hard
>
> Maybe also do this for each of the submodules?
>
>> However, I am still seeing the same issue:  a huge number of the
>> "illegal character" errors.
>>
>> I have tried to remove these characters and re-run the build, but
>> these files are re-generated with the incorrect "\" characters.
>>
>> Please can someone give me any pointers as to what has gone wrong?
>
> This should be sufficient to fix the problem with the trailing backslashes.  Maybe also try running git config --local as well just in case the global settings are being explitly overridden?  Additionally, you could try switching branches in case the above didn't force a complete re-checkout of the sources.  Worst case, maybe re-clone the repo to be sure you're not running into any other issues with local configuration inside the existing clone.
>
> You might also wish to pick up:
>     https://github.com/openmicroscopy/bioformats/pull/1052/files
> which corrects an additional line-ending problem on Windows which you might run into /after/ getting the above problem resolved.
>
>
> 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