[Bioc-devel] deprecated org.Hs.egCHRLOC UPDATE: the as.list() behaves differently in stable and devel configuration

[Marc Carlson]

Hi Raffaele,

This problem should be resolved in devel at this time.  Please update to 
the latest version of AnnotationDbi (1.27.14) and try again.

  Marc



On 09/23/2014 02:36 PM, calogero UNITO wrote:
> affaeleaffaeleHi Vincent,
> I have further investigated the error I have in the vignette of chimera
> devel package .
> It is related to the libraries used to access to org.Hs.eg.db in the
> devel branch.
>
> In the presence of the following libraries (stable branch):
> [1] org.Hs.eg.db_2.14.0  RSQLite_0.11.4       DBI_0.3.0
> [4] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2   Biobase_2.24.0
> [7] BiocGenerics_0.10.0  BiocInstaller_1.14.2
>
> If I extract start and end position for the chromosome location from
> org.Hs.eg:
>   >chr.tmps <- as.list(org.Hs.egCHRLOC)
>   >chr.tmpe <- as.list(org.Hs.egCHRLOCEND)
>
>   >  as.numeric(chr.tmps[1:3])
> [1] -58858172  18248755 -43248163
>   >  as.numeric(chr.tmpe[1:3])
> [1] -58864865  18258723 -43280376
>
> I get different numbers for star and end of a gene.
>
> In case I used the libraries derived from devel branch
> [1] org.Hs.eg.db_2.14.0   RSQLite_0.11.4 DBI_0.3.0
> [4] AnnotationDbi_1.27.13 GenomeInfoDb_1.1.19 IRanges_1.99.28
> [7] S4Vectors_0.2.4       Biobase_2.25.0 BiocGenerics_0.11.5
>
>   > chr.tmps <- as.list(org.Hs.egCHRLOC)
> 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.
>   > chr.tmpe <- as.list(org.Hs.egCHRLOCEND)
> 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.
>
>   >  as.numeric(chr.tmps[1:3])
> [1] -58858172  18248755 -43248163
>   > as.numeric(chr.tmpe[1:3])
> [1] -58858172  18248755 -43248163
>
> The values associated to start and end of the gene are the same.
> This is actually the reason why I get errors in the vignette of chimera
> package.
>
>
>
>
>
> R 3.1.1:
> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> locale:
> [1] C
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
>
> Then I installed the basic configuration needed to use org.Hs.eg.db in
> the actual stable release:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("org.Hs.eg.db")
> library("org.Hs.eg.db")
>
> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
>
> other attached packages:
> [1] org.Hs.eg.db_2.14.0  RSQLite_0.11.4       DBI_0.3.0
> [4] AnnotationDbi_1.26.0 GenomeInfoDb_1.0.2   Biobase_2.24.0
> [7] BiocGenerics_0.10.0  BiocInstaller_1.14.2
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.22.10 stats4_3.1.1    tools_3.1.1
>
>
>
> Then I used  the devel release packages:
>
> |library(BiocInstaller)
> useDevel()|
> library("org.Hs.eg.db")
>> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] org.Hs.eg.db_2.14.0   RSQLite_0.11.4        DBI_0.3.0
> [4] AnnotationDbi_1.27.13 GenomeInfoDb_1.1.19   IRanges_1.99.28
> [7] S4Vectors_0.2.4       Biobase_2.25.0        BiocGenerics_0.11.5
>
>
>
> 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
>>>
>>>
>>>           [[alternative HTML version deleted]]
>>>
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>