i can't confirm this

> library(GenomicRanges)
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 object is masked from 'package:stats':

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

Loading required package: IRanges
Loading required package: GenomeInfoDb
> library(GenomicFeatures)
Loading required package: AnnotationDbi
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")'.

> grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)),
+                    r2=GRanges("chr2",IRanges(3,4)))
> grl[[1]] <- GRanges("chr1",IRanges(10,11))
> sessionInfo()
R version 3.1.0 alpha (2014-03-19 r65222)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso88591       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso88591        LC_COLLATE=en_US.iso88591
 [5] LC_MONETARY=en_US.iso88591    LC_MESSAGES=en_US.iso88591
 [7] LC_PAPER=en_US.iso88591       LC_NAME=C
 [9] LC_ADDRESS=C                  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices datasets  tools     utils
[8] methods   base

other attached packages:
 [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17   Biobase_2.23.6
 [4] GenomicRanges_1.15.44   GenomeInfoDb_0.99.30    IRanges_1.21.43
 [7] BiocGenerics_0.9.3      weaver_1.29.1           codetools_0.2-8
[10] digest_0.6.4            BiocInstaller_1.13.3

loaded via a namespace (and not attached):
 [1] BatchJobs_1.2             BBmisc_1.5
 [3] BiocParallel_0.5.19       biomaRt_2.19.3
 [5] Biostrings_2.31.21        bitops_1.0-6
 [7] brew_1.0-6                BSgenome_1.31.13
 [9] DBI_0.2-7                 fail_1.2
[11] foreach_1.4.1             GenomicAlignments_0.99.37
[13] iterators_1.0.6           plyr_1.8.1
[15] Rcpp_0.11.1               RCurl_1.95-4.1
[17] Rsamtools_1.15.41         RSQLite_0.11.4
[19] rtracklayer_1.23.22       sendmailR_1.1-2
[21] stats4_3.1.0              stringr_0.6.2
[23] XML_3.98-1.1              XVector_0.3.7
[25] zlibbioc_1.9.0



On Wed, Apr 9, 2014 at 3:23 AM, Michael Stadler <michael.stadler@fmi.ch>wrote:

> Dear Bioc gurus,
>
> Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some
> unit tests, which turns out to be reproducible independent of QuasR and
> might be related to R getting the wrong method for "[[<-".
>
> The following works fine...
> library(GenomicRanges)
> grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)),
>                    r2=GRanges("chr2",IRanges(3,4)))
> grl[[1]] <- GRanges("chr1",IRanges(10,11))
>
>
> ...but this produces an error:
> library(GenomicRanges)
> library(GenomicFeatures)
> grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)),
>                    r2=GRanges("chr2",IRanges(3,4)))
> grl[[1]] <- GRanges("chr1",IRanges(10,11))
> #Error in as.list(x, use.names = FALSE) :
> #  could not find function ".as.list.CompressedList"
>
> My guess is that loading the GenomicFeatures library in addition to
> GenomicRanges influences the methods dispatch, but with my limited
> understanding of R and S4 classes I was not able to narrow it further down.
>
> I noticed that I am using a slightly older version of R (r65206)
> compared to the build system (r65358), however I also see the error with
> the most recent release candidate (r65385).
>
> Michael
>
>
> My session info:
> R version 3.1.0 alpha (2014-03-17 r65206)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17   Biobase_2.23.6
> [4] GenomicRanges_1.15.44   GenomeInfoDb_0.99.30    IRanges_1.21.43
> [7] BiocGenerics_0.9.3      RColorBrewer_1.0-5
>
> loaded via a namespace (and not attached):
>  [1] BBmisc_1.5                BSgenome_1.31.13
>  [3] BatchJobs_1.2             BiocParallel_0.5.19
>  [5] Biostrings_2.31.21        DBI_0.2-7
>  [7] GenomicAlignments_0.99.37 RCurl_1.95-4.1
>  [9] RSQLite_0.11.4            Rcpp_0.11.1
> [11] Rsamtools_1.15.41         XML_3.98-1.1
> [13] XVector_0.3.7             biomaRt_2.19.3
> [15] bitops_1.0-6              brew_1.0-6
> [17] codetools_0.2-8           digest_0.6.4
> [19] fail_1.2                  foreach_1.4.1
> [21] iterators_1.0.6           plyr_1.8.1
> [23] rtracklayer_1.23.22       sendmailR_1.1-2
> [25] stats4_3.1.0              stringr_0.6.2
> [27] tools_3.1.0               zlibbioc_1.9.0
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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