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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
