[Bioc-devel] AnnotationDbi::loadDb() now requires dbType and dbPackage?

[Leonardo Collado Torres]

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)
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