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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