On Fri, Oct 10, 2014 at 11:24 AM, Leonardo Collado Torres
<lcoll...@jhu.edu> wrote:
> Hi,
>
> I think that the docs for ?loadDb (AnnotationDbi) need to be updated
> as described below.
>
>
> According to ?loadDb in AnnotationDbi 1.27.19
>
> "
> dbType
> dbType - not required
>
> dbPackage
> dbPackage - not required
> "
>
> However, R CMD check for derfinder 0.99.5 and R CMD build for
> GenomicFeatures 1.17.21 are failing due to dbType not being specified.
> See
> http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder/oaxaca-checksrc.html
> and
> http://bioconductor.org/checkResults/devel/bioc-LATEST/GenomicFeatures/zin1-buildsrc.html
> So I guess that the documentation needs to be updated or something
> went wrong after GenomicFeatures 1.17.20 (with AnnotationDbi 1.17.21)
Err, I meant 1.27.19 here
> because I could get it to work then (see further below).
>
> Anyhow, I'll change the example in derfinder::makeGenomicState and
> specify dbType and dbPackage
>
>
>
>> library('GenomicFeatures')
>> samplefile <- system.file('extdata', 'UCSC_knownGene_sample.sqlite',
> + package='GenomicFeatures')
>> old <- loadDb(samplefile)
>> new <- loadDb(samplefile, dbType = 'TxDb', dbPackage = 'GenomicFeatures')
>
> ## For some reason they are not identical.
> ## My guess is that each one has a different connection, while
> everything else is the ## same.
>
>> identical(old, new)
> [1] FALSE
>
> ## However, by 'eye' they look the same
>
>> old
> TxDb object:
> | Db type: TranscriptDb
> | Supporting package: GenomicFeatures
> | Data source: UCSC
> | Genome: hg18
> | Genus and Species: Homo sapiens
> | UCSC Table: knownGene
> | Resource URL: http://genome.ucsc.edu/
> | Type of Gene ID: Entrez Gene ID
> | Full dataset: no
> | miRBase build ID: NA
> | transcript_nrow: 135
> | exon_nrow: 544
> | cds_nrow: 324
> | Db created by: GenomicFeatures package from Bioconductor
> | Creation time: 2012-04-13 14:47:54 -0700 (Fri, 13 Apr 2012)
> | GenomicFeatures version at creation time: 1.9.4
> | RSQLite version at creation time: 0.11.1
> | DBSCHEMAVERSION: 1.0
>> new
> TxDb object:
> | Db type: TranscriptDb
> | Supporting package: GenomicFeatures
> | Data source: UCSC
> | Genome: hg18
> | Genus and Species: Homo sapiens
> | UCSC Table: knownGene
> | Resource URL: http://genome.ucsc.edu/
> | Type of Gene ID: Entrez Gene ID
> | Full dataset: no
> | miRBase build ID: NA
> | transcript_nrow: 135
> | exon_nrow: 544
> | cds_nrow: 324
> | Db created by: GenomicFeatures package from Bioconductor
> | Creation time: 2012-04-13 14:47:54 -0700 (Fri, 13 Apr 2012)
> | GenomicFeatures version at creation time: 1.9.4
> | RSQLite version at creation time: 0.11.1
> | DBSCHEMAVERSION: 1.0
>
>> devtools::session_info()
> Session
> info--------------------------------------------------------------------------
> setting value
> version R version 3.1.1 (2014-07-10)
> system x86_64, darwin10.8.0
> ui AQUA
> language (EN)
> collate en_US.UTF-8
> tz America/New_York
>
> Packages------------------------------------------------------------------------------
> package * version date source
> AnnotationDbi * 1.27.19 2014-10-05 Bioconductor
> base64enc 0.1.2 2014-06-26 CRAN (R 3.1.0)
> BatchJobs 1.4 2014-09-24 CRAN (R 3.1.1)
> BBmisc 1.7 2014-06-21 CRAN (R 3.1.0)
> Biobase * 2.25.1 2014-10-09 Bioconductor
> BiocGenerics * 0.11.5 2014-09-13 Bioconductor
> BiocParallel 0.99.25 2014-10-02 Bioconductor
> biomaRt 2.21.5 2014-10-07 Bioconductor
> Biostrings 2.33.14 2014-09-09 Bioconductor
> bitops 1.0.6 2013-08-17 CRAN (R 3.1.0)
> brew 1.0.6 2011-04-13 CRAN (R 3.1.0)
> checkmate 1.4 2014-09-03 CRAN (R 3.1.1)
> codetools 0.2.9 2014-08-21 CRAN (R 3.1.1)
> DBI 0.3.1 2014-09-24 CRAN (R 3.1.1)
> devtools 1.6.1 2014-10-07 CRAN (R 3.1.1)
> digest 0.6.4 2013-12-03 CRAN (R 3.1.0)
> fail 1.2 2013-09-19 CRAN (R 3.1.0)
> foreach 1.4.2 2014-04-11 CRAN (R 3.1.0)
> futile.logger 1.3.7 2014-01-23 CRAN (R 3.1.0)
> futile.options 1.0.0 2010-04-06 CRAN (R 3.1.0)
> GenomeInfoDb * 1.1.25 2014-10-02 Bioconductor
> GenomicAlignments 1.1.30 2014-09-23 Bioconductor
> GenomicFeatures * 1.17.20 2014-10-08 Bioconductor
> GenomicRanges * 1.17.47 2014-10-09 Bioconductor
> IRanges * 1.99.31 2014-10-07 Bioconductor
> iterators 1.0.7 2014-04-11 CRAN (R 3.1.0)
> lambda.r 1.1.6 2014-01-23 CRAN (R 3.1.0)
> RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1)
> Rsamtools 1.17.34 2014-09-20 Bioconductor
> RSQLite 0.11.4 2013-05-26 CRAN (R 3.1.0)
> rstudioapi 0.1 2014-03-27 CRAN (R 3.1.0)
> rtracklayer 1.25.19 2014-10-02 Bioconductor
> S4Vectors * 0.2.5 2014-10-08 Bioconductor
> sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1)
> stringr 0.6.2 2012-12-06 CRAN (R 3.1.0)
> XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0)
> XVector 0.5.8 2014-09-07 Bioconductor
> zlibbioc 1.11.1 2014-04-19 Bioconductor
>>
>
>
> Cheers,
> Leo
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