thanks Dan, confirmed, 1.7.2 available as source, after run
biocLite("OrganismDbi", type = "source")it works now! On Thu, May 22, 2014 at 3:12 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote: > OrganismDbi 1.7.2 (available via biocLite()) has already fixed this so you > shouldn't have to change anything. > > Dan > > > ----- Original Message ----- > > From: "Tengfei Yin" <tengfei....@sbgenomics.com> > > To: "Leonardo Collado Torres" <lcoll...@jhsph.edu> > > Cc: bioc-devel@r-project.org > > Sent: Thursday, May 22, 2014 12:10:29 PM > > Subject: Re: [Bioc-devel] Namespace issues with ggbio 1.13.6 from > AnnotationDbi 1.27.6 not exporting 'cols' > > > > 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]] > > > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > -- 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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