Can you post an example dataset that triggers the error reproducibly? On Tue, Jul 14, 2020 at 4:44 AM Charles Plessy <charles.ple...@oist.jp> wrote:
> Hello, > > a user of the CAGEr package reported an error that occurs when it calls > the `export.bw` function of rtracklayer: > > rsession: 1730343 1730344 doesn't intersect 1892288 1899678, chromId 6 > chromSize 5022195: Resource temporarily unavailable > Error in isSingleString(path) : UCSC library operation failed > In addition: Warning message: > In isSingleString(path) : Internal error ucsc/bbiWrite.c 414 > > This is triggered by a GRanges object that has 236595 lines and 13304 > seqlevels. My attempts to bisect the object to find a defective line > did not succeed; but it seems important that I keep most of the contents > to trigger the error. I therefore wonder if the problem is either the > number of lines or the number of seqlevels. > > Not being very familiar with the BigWig format and the internals of > rtracklayer, I am a bit lost. > > Can somebody suggest me a way to solve the problem ? > > Have a nice day, > > Charles > > R version 4.0.2 (2020-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Debian GNU/Linux bullseye/sid > > Matrix products: default > BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 > LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > LC_TIME=en_GB.UTF-8 > [4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 > LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C > > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > methods > [9] base > > other attached packages: > [1] CAGEr_1.31.3 MultiAssayExperiment_1.15.2 > [3] SummarizedExperiment_1.19.5 DelayedArray_0.15.6 > [5] matrixStats_0.56.0 Matrix_1.2-18 > [7] Biobase_2.49.0 GenomicRanges_1.41.5 > [9] GenomeInfoDb_1.25.8 IRanges_2.23.10 > [11] S4Vectors_0.27.12 BiocGenerics_0.35.4 > > loaded via a namespace (and not attached): > [1] Rcpp_1.0.5 stringdist_0.9.5.5 lattice_0.20-41 > > [4] formula.tools_1.7.1 Rsamtools_2.5.3 > Biostrings_2.57.2 > [7] gtools_3.8.2 digest_0.6.25 R6_2.4.1 > > [10] plyr_1.8.6 ggplot2_3.3.2 pillar_1.4.5 > > [13] zlibbioc_1.35.0 rlang_0.4.7 rstudioapi_0.11 > > [16] data.table_1.12.8 vegan_2.5-6 splines_4.0.2 > > [19] BiocParallel_1.23.2 RCurl_1.98-1.2 munsell_0.5.0 > > [22] compiler_4.0.2 rtracklayer_1.49.3 pkgconfig_2.0.3 > > [25] mgcv_1.8-31 tidyselect_1.1.0 tibble_3.0.2 > > [28] GenomeInfoDbData_1.2.3 XML_3.99-0.4 reshape_0.8.8 > > [31] permute_0.9-5 crayon_1.3.4 dplyr_1.0.0 > > [34] GenomicAlignments_1.25.3 MASS_7.3-51.6 bitops_1.0-6 > > [37] grid_4.0.2 nlme_3.1-148 gtable_0.3.0 > > [40] lifecycle_0.2.0 magrittr_1.5 scales_1.1.1 > > [43] KernSmooth_2.23-17 stringi_1.4.6 som_0.3-5.1 > > [46] XVector_0.29.3 ellipsis_0.3.1 generics_0.0.2 > > [49] vctrs_0.3.1 tools_4.0.2 BSgenome_1.57.4 > > [52] glue_1.4.1 purrr_0.3.4 colorspace_1.4-1 > > [55] cluster_2.1.0 operator.tools_1.6.3 beanplot_1.2 > > [58] memoise_1.1.0 VGAM_1.1-3 > > -- > Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp > Okinawa Institute of Science and Technology Graduate University > Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu > Toots from work - ~ ~~ ~ - https://mastodon.technology/@charles_plessy > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel