Hi, I believe this regression was fixed with the most recent commit to S4Vectors:
commit beacd33e43592c67c9e97517a58bf201ec0b4887 (HEAD -> master, origin/master, origin/HEAD) Author: Herv� Pag�s <hpa...@fredhutch.org><mailto:hpa...@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. Valerie 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: library(GenomicAlignments) 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 sessionInfo() 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 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] 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 Confidentiality Notice:\ This e-mail message, including ...{{dropped:20}}
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