Previously, I invoked runValue (strand (GRangesList)) in order to extract strand information for a GRangesList object. However, upon updating to R 3.1.2 and Bioconductor 3.0, this code no longer works:

>   refSeqDb = suppressWarnings (makeTranscriptDbFromUCSC (
    "hg19",
    tablename = "refGene"))

> head (runValue (strand (exonsBy (refSeqDb))))
IntegerList of length 6
Error in encodeString(obj) : adding class "factor" to an invalid object

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] C

attached base packages:
 [1] stats4    grid      parallel  grDevices utils     datasets  stats     graphics  methods   base     

other attached packages:
 [1] BiocInstaller_1.16.1                       BSgenome.Hsapiens.UCSC.hg19_1.3.99         BSgenome_1.34.0                            beanplot_1.2                              
 [5] IlluminaHumanMethylation450kmanifest_0.4.0 goseq_1.18.0                               geneLenDataBase_1.1.1                      BiasedUrn_1.06.1                          
 [9] GO.db_3.0.0                                seqLogo_1.32.1                             fastcluster_1.1.13                         rtracklayer_1.26.1                        
[13] minfi_1.12.0                               bumphunter_1.6.0                           locfit_1.5-9.1                             iterators_1.0.7                           
[17] foreach_1.4.2                              Biostrings_2.34.0                          XVector_0.6.0                              lattice_0.20-29                           
[21] FDb.InfiniumMethylation.hg19_2.1.999       org.Hs.eg.db_3.0.0                         RSQLite_1.0.0                              DBI_0.3.1                                 
[25] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0    GenomicFeatures_1.18.2                     AnnotationDbi_1.28.1                       Biobase_2.26.0                            
[29] GenomicRanges_1.18.1                       GenomeInfoDb_1.2.2                         IRanges_2.0.0                              S4Vectors_0.4.0                           
[33] VennDiagram_1.6.9                          RColorBrewer_1.0-5                         biomaRt_2.22.0                             BiocGenerics_0.12.0                       
[37] ggplot2_1.0.0                              reshape2_1.4                               gplots_2.14.2                              Rcpp_0.11.3                               
[41] apcluster_1.3.5                            mgcv_1.8-3                                 nlme_3.1-118                              

loaded via a namespace (and not attached):
 [1] BBmisc_1.8              BatchJobs_1.5           BiocParallel_1.0.0      GenomicAlignments_1.2.1 KernSmooth_2.23-13      MASS_7.3-35             Matrix_1.1-4           
 [8] R.methodsS3_1.6.1       RCurl_1.95-4.3          Rsamtools_1.18.1        XML_3.98-1.1            annotate_1.44.0         base64_1.1              base64enc_0.1-2        
[15] bitops_1.0-6            brew_1.0-6              caTools_1.17.1          checkmate_1.5.0         codetools_0.2-9         colorspace_1.2-4        compiler_3.1.2         
[22] digest_0.6.4            doRNG_1.6               fail_1.2                gdata_2.13.3            genefilter_1.48.1       gtable_0.1.2            gtools_3.4.1           
[29] illuminaio_0.8.0        labeling_0.3            limma_3.22.1            matrixStats_0.10.3      mclust_4.4              multtest_2.22.0         munsell_0.4.2          
[36] nor1mix_1.2-0           pkgmaker_0.22           plyr_1.8.1              preprocessCore_1.28.0   proto_0.3-10            quadprog_1.5-5          registry_0.2           
[43] reshape_0.8.5           rngtools_1.2.4          scales_0.2.4            sendmailR_1.2-1         siggenes_1.40.0         splines_3.1.2           stringr_0.6.2          
[50] survival_2.37-7         tcltk_3.1.2             tools_3.1.2             xtable_1.7-4            zlibbioc_1.12.0        

Hi Robert,

Good catch, thanks! Seems like this has been broken for a while (since BioC 2.13). Just fixed it in release (BioC 3.0) and devel (BioC 3.1). The fix is in the BiocGenerics package (version 0.12.1 in release and 0.13.1 in devel) and will propagate to our public package repositories in a couple of days. Make sure you run biocLite() with no arguments on Friday morning to get it (beside BiocGenerics, that will also update any other package that is out of sync). If you can't wait, you can grab and install the latest BiocGenerics directly from svn:

Release:

svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BiocGenerics

Devel:

svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocGenerics

Login/password: readonly/readonly

Cheers,

H.