Hi Jialin, Thanks for the report. This should be fixed in BioC 3.7 (S4Vectors 0.18.2 and IRanges 2.14.10) and BioC devel (S4Vectors 0.19.3 and IRanges 2.15.11).
The updated packages will become available via biocLite() in the next 24h (if everything goes as expected). Best, H. On 05/14/2018 07:38 PM, Jialin Ma wrote:
Sorry, forgot to attach the session info: sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-suse-linux-gnu (64-bit) Running under: openSUSE Tumbleweed Matrix products: default BLAS: /usr/lib64/R/lib/libRblas.so LAPACK: /usr/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicRanges_1.32.2 GenomeInfoDb_1.16.0 IRanges_2.14.8 [4] S4Vectors_0.18.1 BiocGenerics_0.26.0 magrittr_1.5 loaded via a namespace (and not attached): [1] zlibbioc_1.26.0 compiler_3.5.0 XVector_0.20.0 [4] tools_3.5.0 GenomeInfoDbData_1.1.0 RCurl_1.95- 4.10 [7] yaml_2.1.19 bitops_1.0-6 -------- Forwarded Message -------- From: Jialin Ma <marl...@gmx.cn> To: bioc-devel <bioc-devel@r-project.org> Subject: Problem showing a GRanges with a meta data column of data frame Date: Tue, 15 May 2018 10:17:35 +0800 Mailer: Evolution 3.24.4Hi all, I recently upgraded R to 3.5 and use the new release of Bioconductor. The new version of S4Vectors seems to have problem showing a GRanges with a meta-data column of a data frame. One simplified example is: gr <- GRanges('chr2', IRanges(1, 11)) gr$df <- data.frame(a = 32) rep(gr, 11) ## No error rep(gr, 12) ## Error when printing # GRanges object with 12 ranges and 1 metadata column: # Error in .Call2("vector_OR_factor_extract_ranges", x, start, width, PACKAGE = "S4Vectors") : # 'end' must be <= 'length(x)' Any help would be appreciated! Best regards, Jialin_______________________________________________ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=09DDSYiwyEgMDuRBEXo2G8cd-Yse5xe8Z_k_aT3ciew&s=zcOg_EezEKrtpGE_7wyqZHWJPaVh4cYJd739M3rPjqA&e=
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
