[Bioc-devel] AnnotationDbi::loadDb() now requires dbType and dbPackage?
Leonardo Collado Torres
lcollado at jhu.edu
Fri Oct 10 18:05:17 CEST 2014
Ahh ok! Thanks =)
On Fri, Oct 10, 2014 at 11:28 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 10/10/2014 08:24 AM, Leonardo Collado Torres 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.
>
>
> Actually, there was a missing file in GenomicFeatures, so GenomicFeatures
> (and derfinder?) was trying to access file "". This will be fixed in the
> next build, which should be available around 10am.
>
> Martin
>
>> 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)
>> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
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