On 06/20/2016 09:22 PM, Leonardo Collado Torres wrote:
I was going to say that for the tutorial users it might be easier to
use devtools::install_github('Bioconductor-mirror/GenomicRanges')
FWIW biocLite("Bioconductor-mirror/GenomicRanges") invokes
install_github(). Martin
rather than svn.
However, from
https://github.com/Bioconductor-mirror/GenomicRanges/blob/master/DESCRIPTION#L13
you can see that it's outdated.
On Mon, Jun 20, 2016 at 6:45 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
Hi Pete,
Because of various issues with the builds, some recent changes to
some core packages have not been able to propagate. So for example
the version of GenomicRanges currently available via biocLite() is
1.25.4, which is lagging behind the version that is in svn (1.25.8).
I think this could be what is causing the problem you're reporting
(which I cannot reproduce).
For now the workaround it to install (or re-install) the latest versions
of S4Vectors, IRanges, GenomicRanges, and SummarizedExperiment directly
from svn.
Sorry for the inconvenience,
H.
On 06/20/2016 11:38 AM, Peter Hickey wrote:
I think this is a recent break. I'm mostly concerned because I need to
use this "broken" functionality in a tutorial for BioC2016 this week
and it would require changes to package internals, not the vignette,
in order to fix this at my end.
library(SummarizedExperiment)
se <- SummarizedExperiment(rowRanges = GRanges(1, IRanges(1, 10)))
granges(se)
# Error in granges(se) :
# could not find symbol "use.names" in environment of the generic
function
# This still works
rowRanges(se)
Perhaps we should be using rowRanges() rather than granges() but this
is breaking a few things in minfi and bsseq. I've noticed this on
granges,RangedSummarizedExperiment-method, but it may affect other
methods (haven't tested).
Cheers,
Pete
sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SummarizedExperiment_1.3.5 Biobase_2.33.0
[3] GenomicRanges_1.25.4 GenomeInfoDb_1.9.1
[5] IRanges_2.7.6 S4Vectors_0.11.5
[7] BiocGenerics_0.19.1 repete_0.0.0.9004
[9] devtools_1.11.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.5 codetools_0.2-14 digest_0.6.9 withr_1.0.1
[5] plyr_1.8.4 magrittr_1.5 scales_0.4.0 zlibbioc_1.19.0
[9] stringi_1.1.1 XVector_0.13.2 pryr_0.1.2 tools_3.3.0
[13] stringr_1.0.0 munsell_0.4.3 colorspace_1.2-6 memoise_1.0.0
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
