Question: GenomicFeatures should support old 'Db type' value
0
gravatar for matt.chambers42
2.6 years ago by
matt.chambers4210 wrote:

The customProDB package has a test txdb built in 2013. Its Db type is 'TranscriptDb'. I see newer databases have 'TxDb' instead. Unless there's some other schema difference making them incompatible, the new version should still support the older name.

I got this error when building on Travis CI:

Error: processing vignette 'customProDB.Rnw' failed with diagnostics:
chunk 10 (label = location)
Error in validObject(.Object) :
invalid class “TxDb” object: 'Db type' is not 'TxDb'




$ Rscript -e 'devtools::session_info(installed.packages()[, "Package"])'
Session info -------------------------------------------------------------------
setting value
version R version 3.4.0 (2017-04-21)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz Etc/UTC
date 2017-04-26

Packages -----------------------------------------------------------------------
package * version date source
AnnotationDbi 1.38.0 2017-04-26 cran (@1.38.0)
BH 1.62.0-1 2016-11-19 cran (@1.62.0-)
Biobase 2.36.0 2017-04-26 cran (@2.36.0)
BiocGenerics 0.22.0 2017-04-26 cran (@0.22.0)
BiocInstaller 1.26.0 2017-04-26 Bioconductor
BiocParallel 1.10.0 2017-04-26 cran (@1.10.0)
biomaRt 2.32.0 2017-04-26 cran (@2.32.0)
Biostrings 2.44.0 2017-04-26 cran (@2.44.0)
bitops 1.0-6 2013-08-17 cran (@1.0-6)
boot 1.3-19 2017-02-11 CRAN (R 3.4.0)
BSgenome 1.44.0 2017-04-26 cran (@1.44.0)
BSgenome.Hsapiens.UCSC.hg19 1.4.0 2017-04-26 cran (@1.4.0)
chron 2.3-50 2017-02-20 cran (@2.3-50)
class 7.3-14 2015-08-30 CRAN (R 3.4.0)
cluster 2.0.6 2017-03-10 CRAN (R 3.4.0)
codetools 0.2-15 2016-10-05 CRAN (R 3.4.0)
covr 2.2.2 2017-01-05 cran (@2.2.2)
crayon 1.3.2 2016-06-28 cran (@1.3.2)
curl 2.5 2017-04-14 CRAN (R 3.4.0)
data.table 1.10.4 2017-02-01 cran (@1.10.4)
DBI 0.6-1 2017-04-01 cran (@0.6-1)
DelayedArray 0.2.0 2017-04-26 cran (@0.2.0)
devtools 1.12.0 2016-12-05 CRAN (R 3.4.0)
digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
foreign 0.8-67 2016-09-13 CRAN (R 3.4.0)
futile.logger 1.4.3 2016-07-10 cran (@1.4.3)
futile.options 1.0.0 2010-04-06 cran (@1.0.0)
GenomeInfoDb 1.12.0 2017-04-26 cran (@1.12.0)
GenomeInfoDbData 0.99.0 2017-04-26 cran (@0.99.0)
GenomicAlignments 1.12.0 2017-04-26 cran (@1.12.0)
GenomicFeatures 1.28.0 2017-04-26 cran (@1.28.0)
GenomicRanges 1.28.0 2017-04-26 cran (@1.28.0)
GetoptLong 0.1.6 2017-03-07 cran (@0.1.6)
git2r 0.18.0 2017-01-01 CRAN (R 3.4.0)
GlobalOptions 0.0.11 2017-03-06 cran (@0.0.11)
gsubfn 0.6-6 2014-08-27 cran (@0.6-6)
httr 1.2.1 2016-07-03 CRAN (R 3.4.0)
IRanges 2.10.0 2017-04-26 cran (@2.10.0)
jsonlite 1.4 2017-04-08 CRAN (R 3.4.0)
KernSmooth 2.23-15 2015-06-29 CRAN (R 3.4.0)
lambda.r 1.1.9 2016-07-10 cran (@1.1.9)
lattice 0.20-35 2017-03-25 CRAN (R 3.4.0)
lazyeval 0.2.0 2016-06-12 cran (@0.2.0)
magrittr 1.5 2014-11-22 cran (@1.5)
MASS 7.3-47 2017-02-26 CRAN (R 3.4.0)
Matrix 1.2-9 2017-03-14 CRAN (R 3.4.0)
matrixStats 0.52.2 2017-04-14 cran (@0.52.2)
memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
mgcv 1.8-17 2017-02-08 CRAN (R 3.4.0)
mime 0.5 2016-07-07 CRAN (R 3.4.0)
nlme 3.1-131 2017-02-06 CRAN (R 3.4.0)
nnet 7.3-12 2016-02-02 CRAN (R 3.4.0)
openssl 0.9.6 2016-12-31 CRAN (R 3.4.0)
plogr 0.1-1 2016-09-24 cran (@0.1-1)
plyr 1.8.4 2016-06-08 cran (@1.8.4)
praise 1.0.0 2015-08-11 cran (@1.0.0)
proto 1.0.0 2016-10-29 cran (@1.0.0)
R6 2.2.0 2016-10-05 CRAN (R 3.4.0)
Rcpp 0.12.10 2017-03-19 cran (@0.12.10)
RCurl 1.95-4.8 2016-03-01 cran (@1.95-4.)
rex 1.1.1 2016-12-05 cran (@1.1.1)
rjson 0.2.15 2014-11-03 cran (@0.2.15)
RMySQL 0.10.11 2017-03-29 cran (@0.10.11)
rpart 4.1-11 2017-03-13 CRAN (R 3.4.0)
Rsamtools 1.28.0 2017-04-26 cran (@1.28.0)
RSQLite 1.1-2 2017-01-08 cran (@1.1-2)
rstudioapi 0.6 2016-06-27 CRAN (R 3.4.0)
rtracklayer 1.36.0 2017-04-26 cran (@1.36.0)
S4Vectors 0.14.0 2017-04-26 cran (@0.14.0)
snow 0.4-2 2016-10-14 cran (@0.4-2)
spatial 7.3-11 2015-08-30 CRAN (R 3.4.0)
sqldf 0.4-10 2014-11-07 cran (@0.4-10)
stringi 1.1.5 2017-04-07 cran (@1.1.5)
stringr 1.2.0 2017-02-18 cran (@1.2.0)
SummarizedExperiment 1.6.0 2017-04-26 cran (@1.6.0)
survival 2.41-3 2017-04-04 CRAN (R 3.4.0)
testthat 1.0.2 2016-04-23 cran (@1.0.2)
VariantAnnotation 1.22.0 2017-04-26 cran (@1.22.0)
whisker 0.3-2 2013-04-28 CRAN (R 3.4.0)
withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
XML 3.98-1.6 2017-03-30 cran (@3.98-1.)
XVector 0.16.0 2017-04-26 cran (@0.16.0)
zlibbioc 1.22.0 2017-04-26 cran (@1.22.0)
genomicfeatures • 584 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by matt.chambers4210
Answer: GenomicFeatures should support old 'Db type' value
1
gravatar for Hervé Pagès
2.6 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi Matt,

Not sure where you're getting this customProDB package from but if you are using R 3.4 you should be pointing your Travis CI builds to BioC 3.5. This means that you should be getting the most current version of customProDB:

http://bioconductor.org/packages/release/bioc/html/customProDB.html

customProDB has been updated to work with BioC 3.5 and it passes R CMD build and R CMD check on all platforms:

http://bioconductor.org/checkResults/release/bioc-LATEST/customProDB/

Hope this helps,

H.

ADD COMMENTlink written 2.6 years ago by Hervé Pagès ♦♦ 14k
Answer: GenomicFeatures should support old 'Db type' value
0
gravatar for matt.chambers42
2.6 years ago by
matt.chambers4210 wrote:

Ah, I see XJ updated the txdb.sqlite file a couple weeks ago and I just haven't pulled that change. But I still think it's weird for it to fail just based on the 'Db type' string. I did notice there is a slight schematic difference, the tx_type field is new. But in my mm10 UCSC txdb, it's always null. Regardless, a schema change is a valid reason to update older files.

ADD COMMENTlink written 2.6 years ago by matt.chambers4210

The Db type string indicates the class of the object returned by loadDb(). When calling loadDb() on the txdb.sqlite file located in the customProDB package you get a TxDb object, not a TranscriptDb object, so the Db type string was incorrect and needed to be updated. The reason it contained TranscriptDb is because the file was built in 2013 when the TxDb class was still named TranscriptDb. When this class was renamed TxDb 2.5 years ago, we kept backward compatibility with *.sqlite files built before this renaming for a while. However 2.5 years later it was time to move on so loadDb() now raises an error on these old objects.

Hope this makes sense,

H.

ADD REPLYlink written 2.6 years ago by Hervé Pagès ♦♦ 14k
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