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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