Hello, Currently I'm unable to load ggbio 1.13.6 (BioC-devel) due to some namespace issues. The basic error is:
Error : object ‘cols’ is not exported by 'namespace:AnnotationDbi' Error: package or namespace load failed for ‘ggbio’ I'm reporting this because a user reported a similar issue with a package I'm developing (see https://github.com/lcolladotor/derfinder/pull/22). Thanks, Leo The log is shown below: $ R --vanilla R version 3.1.0 (2014-04-10) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin10.8.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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 Find out what's changed in ggplot2 with news(Version == "0.9.3.1", package = "ggplot2") Error : object ‘cols’ is not exported by 'namespace:AnnotationDbi' Error: package or namespace load failed for ‘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 [8] base other attached packages: [1] ggplot2_0.9.3.1 BiocGenerics_0.11.2 loaded via a namespace (and not attached): [1] AnnotationDbi_1.27.6 BatchJobs_1.2 BBmisc_1.6 [4] Biobase_2.25.0 BiocParallel_0.7.0 biomaRt_2.21.0 [7] Biostrings_2.33.8 biovizBase_1.13.7 bitops_1.0-6 [10] brew_1.0-6 BSgenome_1.33.5 cluster_1.15.2 [13] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7 [16] dichromat_2.0-0 digest_0.6.4 fail_1.2 [19] foreach_1.4.2 Formula_1.1-1 GenomeInfoDb_1.1.5 [22] GenomicAlignments_1.1.10 GenomicFeatures_1.17.6 GenomicRanges_1.17.14 [25] graph_1.43.0 grid_3.1.0 gridExtra_0.9.1 [28] gtable_0.1.2 Hmisc_3.14-4 IRanges_1.99.13 [31] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26 [34] MASS_7.3-33 munsell_0.4.2 plyr_1.8.1 [37] proto_0.3-10 RColorBrewer_1.0-5 Rcpp_0.11.1 [40] RCurl_1.95-4.1 reshape2_1.4 Rsamtools_1.17.14 [43] RSQLite_0.11.4 rtracklayer_1.25.8 S4Vectors_0.0.6 [46] scales_0.2.4 sendmailR_1.1-2 splines_3.1.0 [49] stats4_3.1.0 stringr_0.6.2 survival_2.37-7 [52] tools_3.1.0 VariantAnnotation_1.11.5 XML_3.98-1.1 [55] XVector_0.5.6 zlibbioc_1.11.1 > source("http://bioconductor.org/biocLite.R";) Bioconductor version 3.0 (BiocInstaller 1.15.5), ?biocLite for help > biocVersion() [1] ‘3.0’ > packageVersion("ggbio") [1] ‘1.13.6’ > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
