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 <dtenenba@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.yin@sbgenomics.com>
> > To: "Leonardo Collado Torres" <lcollado@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
> > <lcollado@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 ‘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’
> > > >
> > >
> >
> >
> >
> > --
> > 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]]

