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)

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.

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.