[Bioc-devel] a possible bug in development version of GenomicAlignments

Obenchain, Valerie Valerie.Obenchain at RoswellPark.org
Fri Dec 1 17:38:38 CET 2017


I believe this regression was fixed with the most recent commit to S4Vectors:

commit beacd33e43592c67c9e97517a58bf201ec0b4887 (HEAD -> master, origin/master, origin/HEAD)
Author: Hervé Pagès <hpages at fredhutch.org><mailto:hpages at fredhutch.org>
Date:   Thu Nov 30 16:00:50 2017 -0800

    Fix regression in new implementation of "[[<-" for List objects
    where 'x[[i]] <- value' was degrading 'value' to the class returned
    by 'elementType(x)' if 'value' was inheriting from that class, instead
    of preserving its class.

The fix is in version 0.17.12 and is available from git.bioconductor.org immediately or via biocLite() tomorrow (Dec 2) around 3pm EST.


On 11/30/2017 03:44 PM, Ou, Jianhong wrote:

Hi, is this a bug in the development version of GenomicAlignments or compressedList? Or I missed anything?

Here is how to repeat the error:


gal1 <- GAlignments(

+     seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),

+         c(1, 3, 2, 4)),

+     pos=1:10, cigar=paste0(10:1, "M"),

+     strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),

+     names=head(letters, 10), score=1:10)

gal2 <- GAlignments(

+     seqnames=Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,

+     cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),

+     strand=Rle(strand(c("-", "+")), c(4, 3)),

+     names=tail(letters, 7), score=1:7)

galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)

galist[["Gaps"]] <- gal2

Error in .wrap_in_length_one_list_like_object(value, names(x)[[i]], x) :

  failed to coerce 'list(value)' to a GAlignmentsList object of length 1


R Under development (unstable) (2017-11-29 r73795)

Platform: x86_64-apple-darwin17.2.0 (64-bit)

Running under: macOS High Sierra 10.13.1

Matrix products: default

BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib


[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] GenomicAlignments_1.15.1   Rsamtools_1.31.0

 [3] Biostrings_2.47.0          XVector_0.19.1

 [5] SummarizedExperiment_1.9.2 DelayedArray_0.5.6

 [7] matrixStats_0.52.2         Biobase_2.39.0

 [9] GenomicRanges_1.31.1       GenomeInfoDb_1.15.1

[11] IRanges_2.13.4             S4Vectors_0.17.10

[13] BiocGenerics_0.25.0

loaded via a namespace (and not attached):

 [1] lattice_0.20-35         bitops_1.0-6            grid_3.5.0

 [4] zlibbioc_1.25.0         Matrix_1.2-12           BiocParallel_1.13.0

 [7] tools_3.5.0             RCurl_1.95-4.8          compiler_3.5.0

[10] GenomeInfoDbData_0.99.2

Yours Sincerely,

Jianhong Ou

TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
UMASS Medical School
364 Plantation Street Worcester,
MA 01605

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