Comments (5)
I cannot replicate this with the release version of Bioconductor 3.0. You seem to be using Bioc devel with R-3.1.1, which is technically not recommended. Nevertheless, I don't see why it shouldn't work. I have
> sessionInfo()
R version 3.1.1 Patched (2014-10-02 r66711)
Platform: x86_64-apple-darwin13.4.0 (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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] minfiData_0.7.0
[2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
[3] IlluminaHumanMethylation450kmanifest_0.4.0
[4] minfi_1.12.0
[5] bumphunter_1.6.0
[6] locfit_1.5-9.1
[7] iterators_1.0.7
[8] foreach_1.4.2
[9] Biostrings_2.34.0
[10] XVector_0.6.0
[11] GenomicRanges_1.18.1
[12] GenomeInfoDb_1.2.0
[13] IRanges_2.0.0
[14] S4Vectors_0.4.0
[15] lattice_0.20-29
[16] Biobase_2.26.0
[17] BiocGenerics_0.12.0
loaded via a namespace (and not attached):
[1] annotate_1.44.0 AnnotationDbi_1.28.0 base64_1.1
[4] beanplot_1.2 codetools_0.2-9 DBI_0.3.1
[7] digest_0.6.4 doRNG_1.6 genefilter_1.48.1
[10] grid_3.1.1 illuminaio_0.8.0 limma_3.22.0
[13] MASS_7.3-35 matrixStats_0.10.3 mclust_4.4
[16] multtest_2.22.0 nlme_3.1-118 nor1mix_1.2-0
[19] pkgmaker_0.22 plyr_1.8.1 preprocessCore_1.28.0
[22] quadprog_1.5-5 R.methodsS3_1.6.1 RColorBrewer_1.0-5
[25] Rcpp_0.11.3 registry_0.2 reshape_0.8.5
[28] rngtools_1.2.4 RSQLite_0.11.4 siggenes_1.40.0
[31] splines_3.1.1 stringr_0.6.2 survival_2.37-7
[34] tools_3.1.1 XML_3.98-1.1 xtable_1.7-4
[37] zlibbioc_1.12.0
Perhaps transient problems with GenomicRanges
et al in devel?
from minfi.
Hmm, I was having trouble with S4Vectors so I tried to fix with newer version of bioc.
Your minfi is 1.12.0 and mine is 1.13.0 which are separated by 788b84d
from minfi.
I mean separated by 84b6046
from minfi.
nm. must be my install. sorry for the noise.
from minfi.
Hi, I had the same problem brentp. How did you fix it?
from minfi.
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from minfi.