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kasperdanielhansen avatar kasperdanielhansen commented on July 27, 2024

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.

brentp avatar brentp commented on July 27, 2024

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.

brentp avatar brentp commented on July 27, 2024

I mean separated by 84b6046

from minfi.

brentp avatar brentp commented on July 27, 2024

nm. must be my install. sorry for the noise.

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Janitza avatar Janitza commented on July 27, 2024

Hi, I had the same problem brentp. How did you fix it?

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