[Bioc-devel] ggbio 1.13.11 fails to load due to namespace change in IRanges

[Tengfei Yin]

Hi Leo,

So sorry for the late reply, I guess the problem is fixed already? I cannot
see the error anymore, and thanks for the discussion!

cheers

Tengfei


On Wed, Jul 16, 2014 at 2:39 PM, Leonardo Collado Torres <lcollado at jhu.edu>
wrote:

> Hi Tengfei and BioC-devel,
>
> ggbio 1.13.11 fails to load due to recent changes in IRanges'
> namespace as shown further below. Basically, some of IRanges previous
> code now lives in S4Vectors.
>
> On a recent thread Hervé exposed his view on specific imports versus
> importing the whole package (see
> https://stat.ethz.ch/pipermail/bioc-devel/2014-July/005943.html and
> Stephanie's reply
> https://stat.ethz.ch/pipermail/bioc-devel/2014-July/005948.html ).
>
> I have been using specific imports because I thought it was the best
> practice and that it would also help me learn more about what are the
> functions/methods I'm relying on exactly. But as Hervé exposed, using
> specific imports involves a lot of maintenance overhead. That is why,
> in general I'll try to use general imports now.
>
> Cheers,
> Leo
>
>
>
> > 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
> No methods found in "IRanges" for requests: Rle, substring, ifelse,
> as.factor
> Error : object ‘runValue’ is not exported by 'namespace:IRanges'
> Error: package or namespace load failed for ‘ggbio’
> > traceback()
> 2: stop(gettextf("package or namespace load failed for %s",
> sQuote(package)),
>        call. = FALSE, domain = NA)
> 1: library(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   base
>
> other attached packages:
> [1] ggplot2_1.0.0       BiocGenerics_0.11.3
>
> loaded via a namespace (and not attached):
>  [1] AnnotationDbi_1.27.8     BatchJobs_1.3            BBmisc_1.7
>          Biobase_2.25.0           BiocParallel_0.7.7
>  [6] biomaRt_2.21.1           Biostrings_2.33.12       bitops_1.0-6
>          brew_1.0-6               BSgenome_1.33.8
> [11] checkmate_1.1            cluster_1.15.2           codetools_0.2-8
>          colorspace_1.2-4         DBI_0.2-7
> [16] dichromat_2.0-0          digest_0.6.4             fail_1.2
>          foreach_1.4.2            Formula_1.1-2
> [21] GenomeInfoDb_1.1.12      GenomicAlignments_1.1.21
> GenomicFeatures_1.17.12  GenomicRanges_1.17.24    GGally_0.4.6
> [26] grid_3.1.0               gridExtra_0.9.1          gtable_0.1.2
>          Hmisc_3.14-4             IRanges_1.99.22
> [31] iterators_1.0.7          lattice_0.20-29
> latticeExtra_0.6-26      MASS_7.3-33              munsell_0.4.2
> [36] plyr_1.8.1               proto_0.3-10
> RColorBrewer_1.0-5       Rcpp_0.11.2              RCurl_1.95-4.1
> [41] reshape_0.8.5            reshape2_1.4
> Rsamtools_1.17.31        RSQLite_0.11.4           rtracklayer_1.25.13
> [46] S4Vectors_0.1.2          scales_0.2.4             sendmailR_1.1-2
>          splines_3.1.0            stats4_3.1.0
> [51] stringr_0.6.2            survival_2.37-7          tools_3.1.0
>          XML_3.98-1.1             XVector_0.5.7
> [56] zlibbioc_1.11.1
> >
> > packageVersion("ggbio")
> [1] ‘1.13.11’
> >
>



-- 
Tengfei Yin, PhD
Product Manager
Seven Bridges Genomics
sbgenomics.com
One Broadway FL 7
Cambridge, MA 02142
(617) 866-0446

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