[Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’

[Michael Love]

Any ideas about this: I'm still seeing this warning on my machine,
although I've supposedly updated to the latest devel for all my
packages.

> biocVersion()
[1] ‘3.3’

> biocLite(character())
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.2), R Under development
(unstable) (2015-11-08
  r69614).

> biocValid()
[1] TRUE

> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
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 objects are masked from ‘package:stats’:

    IQR, mad, 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, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unlist, unsplit


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To
    cite Bioconductor, see 'citation("Biobase")', and for packages
    'citation("pkgname")'.

Warning messages:
1: multiple methods tables found for ‘relistToClass’
2: multiple methods tables found for ‘relistToClass’

> sessionInfo()
R Under development (unstable) (2015-11-08 r69614)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices datasets  utils
   methods
[9] base

other attached packages:
[1] BiocInstaller_1.21.2        DESeq2_1.11.14
SummarizedExperiment_1.1.12
[4] Biobase_2.31.3              GenomicRanges_1.23.9
GenomeInfoDb_1.7.3
[7] IRanges_2.5.18              S4Vectors_0.9.16
BiocGenerics_0.17.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2          RColorBrewer_1.1-2   plyr_1.8.3
XVector_0.11.1
 [5] tools_3.3.0          zlibbioc_1.17.0      rpart_4.1-10
annotate_1.49.0
 [9] RSQLite_1.0.0        gtable_0.1.2         lattice_0.20-33
DBI_0.3.1
[13] gridExtra_2.0.0      genefilter_1.53.0    cluster_2.0.3
locfit_1.5-9.1
[17] grid_3.3.0           nnet_7.3-11          AnnotationDbi_1.33.4
XML_3.98-1.3
[21] survival_2.38-3      BiocParallel_1.5.12  foreign_0.8-66
latticeExtra_0.6-26
[25] Formula_1.2-1        ggplot2_2.0.0        geneplotter_1.49.0
Hmisc_3.17-1
[29] scales_0.3.0         splines_3.3.0        colorspace_1.2-6
xtable_1.8-0
[33] acepack_1.3-3.3      munsell_0.4.2