[Bioc-devel] deprecated org.Hs.egCHRLOC

[calogero UNITO]

Hi Vincent,
sorry I only realized now that the error was below the deprecate message:

org.Hs.egCHRLOC is deprecated as the data is better accessed from
   another location. Please use an appropriate TxDb object or package for
   this kind of data.

LaTeX errors:
!pdfTeX error: /usr/bin/pdflatex (file ./coverage1.pdf): PDF inclusion: require
d page does not exist <0>
  ==> Fatal error occurred, no output PDF file produced!
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted


The error comes from LaTeX, however chimera package version 1.7.19 was 
correctly built on 2014-08-22
Since that time I did not made any changes and I do not understand where 
is the issue.
Cheers
Raf

On 23/09/14 12:41, Vincent Carey wrote:
> Of note, this is not an error and seems at this time not even to be a
> warning.
> A message is emitted indicating the deprecation, so we have a release to
> figure out how to deal with the fact that the *CHR/*CHRLOC entities will go
> away
> in the next release.
>
> There are various possible workarounds.  Some more commentary will be
> forthcoming.
>
>
> On Tue, Sep 23, 2014 at 3:52 AM, calogero UNITO <raffaele.calogero at unito.it>
> wrote:
>
>> Hi,
>> I am the maintainer of chimera package and I am getting the following
>> error in the develop version:
>>
>> org.Hs.egCHRLOC is deprecated as the data is better accessed from
>>     another location. Please use an appropriate TxDb object or package for
>>     this kind of data.
>>
>> Could please indicate me which package I should used instead of
>> org.Hs.eg.db ?
>>
>> Cheers
>> Raf
>>
>> --
>> ----------------------------------------
>> Prof. Raffaele A. Calogero
>> Bioinformatics and Genomics Unit
>> MBC Centro di Biotecnologie Molecolari
>> Via Nizza 52, Torino 10126
>> Tel.   ++39 0116706457
>> Fax    ++39 0112366457
>> Mobile ++39 3333827080
>> email: raffaele.calogero at unito.it
>>          raffaele.calogero at gmail.com
>> www:   http://www.bioinformatica.unito.it
>>
>>
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>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>


-- 
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
Via Nizza 52, Torino 10126
Tel.   ++39 0116706457
Fax    ++39 0112366457
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
        raffaele.calogero at gmail.com
www:   http://www.bioinformatica.unito.it


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