Was there a new version of TxDb.Hsapiens.UCSC.hg19.knownGene in the last
day or two (v 2.9.2)? It looks like there are some issues with seqlevels
replacing isActiveSeq() in the new version:

> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb=TxDb.Hsapiens.UCSC.hg19.knownGene

For example, I never call isActiveSeq(), so I'm not sure where the warning
is coming in:

> seqlevels(txdb,force=TRUE) = paste0("chr",c(1:22,"X","Y","M"))
Warning message:
'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").

Other calls now throw warning flags for this:
> introns = intronsByTranscript(txdb)
Warning messages:
1: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
2: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
3: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
4: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
5: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
6: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").

Lastly, some calls work at all, and are met with an error

> utr5 = fiveUTRsByTranscript(txdb)
Error in validObject(.Object) :
  invalid class "GRanges" object: 'seqnames' contains missing values
In addition: Warning messages:
1: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
2: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
3: 'isActiveSeq' is deprecated.
Use 'seqinfo' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").

Any help would be appreciated. Below is sessionInfo() results

-Andrew


> sessionInfo()
R Under development (unstable) (2013-08-22 r63646)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices datasets  utils     methods
[8] base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
[2] GenomicFeatures_1.13.32
[3] AnnotationDbi_1.23.18
[4] Biobase_2.21.6
[5] GenomicRanges_1.13.36
[6] XVector_0.1.0
[7] IRanges_1.19.24
[8] BiocGenerics_0.7.4

loaded via a namespace (and not attached):
 [1] biomaRt_2.17.2     Biostrings_2.29.15 bitops_1.0-6
BSgenome_1.29.1
 [5] DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.13.29  RSQLite_0.11.4
 [9] rtracklayer_1.21.9 stats4_3.1.0       tools_3.1.0        XML_3.98-1.1
[13] zlibbioc_1.7.0

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