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

Thu Jan 7 19:43:41 CET 2016

Yes, the methods table is cached on package _install_ rather than load, so package B depending on package A has the wrong table when package A is updated by moving a generic.

Package B (and all other dependencies) need a version bump to trigger re-installation; the culprits can be hard to track, partly because the problem is a bit Heisenberg-ian -- once a package is re-installed, you can't easily go back to the broken version. I missed XVector when troubleshooting this earlier, but Herve bumped it's version yesterday. 

FWIW I referenced this dependency graph http://bioconductor.org/help/newsletters/2015_October/#hts-core-package-stack when trying to work through this.

Martin
________________________________________
From: Bioc-devel [bioc-devel-bounces at r-project.org] on behalf of Kasper Daniel Hansen [kasperdanielhansen at gmail.com]
Sent: Thursday, January 07, 2016 11:09 AM
To: Michael Love
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel]       Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’

I got this a lot a couple of days ago (except I had 3 warnings; you have
2).  Reinstalling some packages like XVector etc. would make one or more
warnings go away, but then I started getting other similar warnings (for
example on as.character).  In the end I gave up, deleted my Bioc packages
and completely re-installed (which took a couple of hours of computer time
since I compile from source).

This was despite having a current installation on devel as reported by
biocValid().  I got the impression that something happens at install time
with the methods lookup, but I don't really know.

Best,
Kasper

On Thu, Jan 7, 2016 at 10:41 AM, Michael Love <michaelisaiahlove at gmail.com>
wrote:

> 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
>
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