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
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