[Bioc-devel] Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols'
Leonardo Collado Torres
lcollado at jhsph.edu
Fri May 23 16:32:31 CEST 2014
Excellent, thanks! =)
On Thu, May 22, 2014 at 3:20 PM, Tengfei Yin <tengfei.yin at sbgenomics.com> wrote:
> 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 at 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 at sbgenomics.com>
>> > To: "Leonardo Collado Torres" <lcollado at jhsph.edu>
>> > Cc: bioc-devel at 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 at 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 at 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
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