[BioC] AnnotationForge example does not work

[Marc Carlson]

I should probably say a little bit more than this.  The issue was caused 
by a change that was made after this vignette was originally written.  
An appropriate org package is really required to check (or use) any 
associated chip package that gets made.  So when the package is almost 
done, the software is trying to connect to an org package to make sure 
that the keys are present and working etc. (and then failing to find one).

The vignette should really reflect this requirement, and so I will now 
change it.

   Marc


On 11/28/2012 11:11 AM, Marc Carlson wrote:
> Thanks for finding this problem!  It shall be fixed.
>
>   Marc
>
>
> On 11/28/2012 07:38 AM, Nicos Angelopoulos (NKI Amsterdam) wrote:
>> Hi James,
>>
>> Thanks for this.
>>
>> I can confirm the call to makeDBPackage()
>> completes once 'org.Hs.eg.db' has been installed and loaded.
>>
>> SQLForge.R itself then fails on
>> file.rename(file.path(tmpout, "hcg110.db"),file.path(tmpout, "foo.db"))
>> but this is just as a matter of general info.
>> In my run there was no such file in the tmpout directory.
>> The package built correctly and I was able to load it.
>>
>> Hope the dependency to 'org.Hs.eg.db' becomes explicit both in the
>> SQLForge.pdf and the sources.
>>
>> Many thanks also to the developers and maintainers of these packages.
>>
>> Regards,
>>
>> Nicos Angelopoulos
>> ---
>> http://bioinformatics.nki.nl/~nicos/
>>
>> On Wed, 28 Nov 2012 13:55:39 +0000
>> "James F. Reid"<reidjf at gmail.com>  wrote:
>>
>>> Hi Nicos,
>>>
>>> I think installing 'org.Hs.eg.db' will solve the problem. It is a
>>> required package when you load your newly created custom annotation 
>>> package.
>>>
>>> HTH
>>> J.
>>>
>>>
>
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