Hi Leo, So sorry for the late reply, I guess the problem is fixed already? I cannot see the error anymore, and thanks for the discussion!
cheers Tengfei On Wed, Jul 16, 2014 at 2:39 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > 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’ > > > -- Tengfei Yin, PhD Product Manager Seven Bridges Genomics sbgenomics.com One Broadway FL 7 Cambridge, MA 02142 (617) 866-0446 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
