[Bioc-devel] AnnotationDbi::loadDb() now requires dbType and dbPackage?
Marc Carlson
mcarlson at fhcrc.org
Fri Oct 10 23:10:40 CEST 2014
Actually they are required in one sense. Just not required of an end
user who would be calling the function (so not for that manual page).
But they are required in a separate internal sense (which is what the
error is referring to) and that is that the database that is loaded it
must contain metadata that specifies this information. But this is
really just implementation details that only people who make such
databases ever really need to know about. The error in this case just
happens to be the 1st one that is hit when your package tried to load a
database file that was recently renamed. By the time you read this post
though, the problem caused by that test database resource being renamed
has already been fixed.
Marc
On 10/10/2014 08:28 AM, Leonardo Collado Torres wrote:
> On Fri, Oct 10, 2014 at 11:24 AM, Leonardo Collado Torres
> <lcollado at 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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