I think it caused by this importClassesFrom(OrganismDbi, OrganismDb)
when comment out, it has no error, I am working on it right now On Thu, May 22, 2014 at 2:21 PM, Leonardo Collado Torres <lcoll...@jhsph.edu > wrote: > Hello, > > Currently I'm unable to load ggbio 1.13.6 (BioC-devel) due to some > namespace issues. The basic error is: > > Error : object âcolsâ is not exported by 'namespace:AnnotationDbi' > Error: package or namespace load failed for âggbioâ > > 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: âBiocGenericsâ > > The following objects are masked from âpackage:parallelâ: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from âpackage:statsâ: > > xtabs > > The following objects are masked from âpackage:baseâ: > > 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 âcolsâ is not exported by 'namespace:AnnotationDbi' > Error: package or namespace load failed for âggbioâ > > 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] â3.0â > > packageVersion("ggbio") > [1] â1.13.6â > > > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML version deleted]]
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