[Bioc-devel] Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols'

Leonardo Collado Torres lcollado at jhsph.edu
Thu May 22 20:21:12 CEST 2014


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


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)

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> 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’:


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,

Loading required package: ggplot2
Find out what's changed in ggplot2 with
news(Version == "", 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)

[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’

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