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

[Martin Morgan]

On 07/16/2014 11:39 AM, Leonardo Collado Torres 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.

That should really be a judgement call -- a nice tidy package might well import 
a very limited number of functions from a small number of packages, with the use 
of each function limited to specific and well-know locations, and with changes 
to the code being very considered -- I no longer need to import pkg::foo because 
I made a very specific change to the code. Indeed for less experienced 
developers it might be worth focusing on this as a kind of discipline -- write 
code that _is_ restricted in this way, doing a small number of tasks well rather 
than trying to do everything.

For the large and comprehensive packages Herve and others work on, this will 
certainly get tedious. For a more focused developer it is perhaps not so bad.

Martin

>
> 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’
>>
>
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