Dear Bioc gurus, Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some unit tests, which turns out to be reproducible independent of QuasR and might be related to R getting the wrong method for "[[<-".
The following works fine... library(GenomicRanges) grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)), r2=GRanges("chr2",IRanges(3,4))) grl[[1]] <- GRanges("chr1",IRanges(10,11)) ...but this produces an error: library(GenomicRanges) library(GenomicFeatures) grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)), r2=GRanges("chr2",IRanges(3,4))) grl[[1]] <- GRanges("chr1",IRanges(10,11)) #Error in as.list(x, use.names = FALSE) : # could not find function ".as.list.CompressedList" My guess is that loading the GenomicFeatures library in addition to GenomicRanges influences the methods dispatch, but with my limited understanding of R and S4 classes I was not able to narrow it further down. I noticed that I am using a slightly older version of R (r65206) compared to the build system (r65358), however I also see the error with the most recent release candidate (r65385). Michael My session info: R version 3.1.0 alpha (2014-03-17 r65206) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17 Biobase_2.23.6 [4] GenomicRanges_1.15.44 GenomeInfoDb_0.99.30 IRanges_1.21.43 [7] BiocGenerics_0.9.3 RColorBrewer_1.0-5 loaded via a namespace (and not attached): [1] BBmisc_1.5 BSgenome_1.31.13 [3] BatchJobs_1.2 BiocParallel_0.5.19 [5] Biostrings_2.31.21 DBI_0.2-7 [7] GenomicAlignments_0.99.37 RCurl_1.95-4.1 [9] RSQLite_0.11.4 Rcpp_0.11.1 [11] Rsamtools_1.15.41 XML_3.98-1.1 [13] XVector_0.3.7 biomaRt_2.19.3 [15] bitops_1.0-6 brew_1.0-6 [17] codetools_0.2-8 digest_0.6.4 [19] fail_1.2 foreach_1.4.1 [21] iterators_1.0.6 plyr_1.8.1 [23] rtracklayer_1.23.22 sendmailR_1.1-2 [25] stats4_3.1.0 stringr_0.6.2 [27] tools_3.1.0 zlibbioc_1.9.0 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel