Thank you Valerie for your quick fix. 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 any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message. ________________________________ From: Obenchain, Valerie [valerie.obench...@roswellpark.org] Sent: Friday, December 01, 2017 11:38 AM To: Ou, Jianhong; bioc-devel@r-project.org Subject: Re: [Bioc-devel] a possible bug in development version of GenomicAlignments 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:11}} _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]]
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