Hi Tengfei and BioC-devel, ggbio 1.13.11 fails to load due to recent changes in IRanges' namespace as shown further below. Basically, some of IRanges previous code now lives in S4Vectors.
On a recent thread Hervé exposed his view on specific imports versus importing the whole package (see https://stat.ethz.ch/pipermail/bioc-devel/2014-July/005943.html and Stephanie's reply https://stat.ethz.ch/pipermail/bioc-devel/2014-July/005948.html ). I have been using specific imports because I thought it was the best practice and that it would also help me learn more about what are the functions/methods I'm relying on exactly. But as Hervé exposed, using specific imports involves a lot of maintenance overhead. That is why, in general I'll try to use general imports now. Cheers, Leo > library(ggbio) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: ggplot2 No methods found in "IRanges" for requests: Rle, substring, ifelse, as.factor Error : object ‘runValue’ is not exported by 'namespace:IRanges' Error: package or namespace load failed for ‘ggbio’ > traceback() 2: stop(gettextf("package or namespace load failed for %s", sQuote(package)), call. = FALSE, domain = NA) 1: library(ggbio) > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_1.0.0 BiocGenerics_0.11.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.27.8 BatchJobs_1.3 BBmisc_1.7 Biobase_2.25.0 BiocParallel_0.7.7 [6] biomaRt_2.21.1 Biostrings_2.33.12 bitops_1.0-6 brew_1.0-6 BSgenome_1.33.8 [11] checkmate_1.1 cluster_1.15.2 codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 [16] dichromat_2.0-0 digest_0.6.4 fail_1.2 foreach_1.4.2 Formula_1.1-2 [21] GenomeInfoDb_1.1.12 GenomicAlignments_1.1.21 GenomicFeatures_1.17.12 GenomicRanges_1.17.24 GGally_0.4.6 [26] grid_3.1.0 gridExtra_0.9.1 gtable_0.1.2 Hmisc_3.14-4 IRanges_1.99.22 [31] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-33 munsell_0.4.2 [36] plyr_1.8.1 proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 [41] reshape_0.8.5 reshape2_1.4 Rsamtools_1.17.31 RSQLite_0.11.4 rtracklayer_1.25.13 [46] S4Vectors_0.1.2 scales_0.2.4 sendmailR_1.1-2 splines_3.1.0 stats4_3.1.0 [51] stringr_0.6.2 survival_2.37-7 tools_3.1.0 XML_3.98-1.1 XVector_0.5.7 [56] zlibbioc_1.11.1 > > packageVersion("ggbio") [1] ‘1.13.11’ > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
