Bug in rtracklayer
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You • 0
@You-24633
Last seen 10 months ago
Germany

Dear developer of rtracklayer,

I met a bug resently with the import.bw function. I have more than 2000 bw files, and when I use a loop to load my files with import.bw, I encounter a bug and report an error after 417 runs of loop. The error message is as follow:

Error in seqinfo(ranges) : UCSC library operation failed In addition: Warning message: In seqinfo(ranges) : Too many pushAbortHandlers, can only handle 11

After detach and reload the package the function will work again. This makes me feel a bit weird.

Here shows my code for import the bw files:


for (i in seq_len(length(n4))) {
    bw.path <- paste0(n, "/", n4[[i]])
    g <- tryCatch({import.bw(bw.path, as = "RleList")},
                  error=function(cond){
                      return(RleList(Rle(values=rep(0, 200))))
                  })

    all.bw <- c(all.bw, g)
}

> import.bw(bw.path, as = "RleList")
Error in seqinfo(ranges) : UCSC library operation failed
In addition: Warning message:
In seqinfo(ranges) : Too many pushAbortHandlers, can only handle 11

I was wondering whether it is possible to somehow avoid this bug. Thank you : )

sessionInfo( )
R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 10.16

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] grid parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocParallel_1.25.3 ComplexHeatmap_2.8.0 Boruta_7.0.0
[4] ggpubr_0.4.0 ggrepel_0.9.1 ggthemr_1.1.0
[7] patchwork_1.1.1 ranger_0.12.1 Rsamtools_2.7.1
[10] BSgenome.Hsapiens.UCSC.hg38_1.4.3 adabag_4.2 doParallel_1.0.16
[13] iterators_1.0.13 foreach_1.5.1 caret_6.0-86
[16] lattice_0.20-44 rpart_4.1-15 cliProfiler_0.99.0
[19] bookdown_0.21 UpSetR_1.4.0 RColorBrewer_1.1-2
[22] DESeq2_1.32.0 SummarizedExperiment_1.21.1 MatrixGenerics_1.3.0
[25] matrixStats_0.58.0 ggseqlogo_0.1 BSgenome.Mmusculus.UCSC.mm10_1.4.0 [28] BSgenome_1.59.2 rtracklayer_1.52.0 Biostrings_2.59.2
[31] XVector_0.31.1 stringr_1.4.0 gridExtra_2.3
[34] dplyr_1.0.6 GenomicFeatures_1.44.0 AnnotationDbi_1.54.0
[37] Biobase_2.51.0 knitr_1.31 keras_2.4.0
[40] xlsx_0.6.5 ggplot2_3.3.5 GenomicRanges_1.43.3
[43] GenomeInfoDb_1.27.5 IRanges_2.25.6 S4Vectors_0.29.6
[46] BiocGenerics_0.37.0

loaded via a namespace (and not attached): [1] rappdirs_0.3.3 ModelMetrics_1.2.2.2 R.methodsS3_1.8.1 tidyr_1.1.3
[5] bit64_4.0.5 R.utils_2.10.1 DelayedArray_0.17.7 data.table_1.14.2
[9] KEGGREST_1.32.0 RCurl_1.98-1.2 generics_0.1.0 cowplot_1.1.1
[13] RSQLite_2.2.7 shadowtext_0.0.8 ggpointdensity_0.1.0 tensorflow_2.4.0
[17] bit_4.0.4 enrichplot_1.12.1 lubridate_1.7.10 assertthat_0.2.1
[21] viridis_0.6.1 gower_0.2.2 xfun_0.20 hms_1.1.0
[25] rJava_1.0-4 evaluate_0.14 fansi_0.4.2 restfulr_0.0.13
[29] progress_1.2.2 dbplyr_2.1.1 readxl_1.3.1 igraph_1.2.6
[33] DBI_1.1.1 geneplotter_1.70.0 purrr_0.3.4 ellipsis_0.3.2
[37] backports_1.2.1 annotate_1.70.0 biomaRt_2.48.0 vctrs_0.3.8
[41] Cairo_1.5-12.2 abind_1.4-5 cachem_1.0.1 withr_2.4.1
[45] ggforce_0.3.3 GenomicAlignments_1.27.2 treeio_1.16.1 prettyunits_1.1.1
[49] cluster_2.1.2 DOSE_3.18.1 ape_5.5 lazyeval_0.2.2
[53] crayon_1.4.1 genefilter_1.74.0 labeling_0.4.2 recipes_0.1.15
[57] pkgconfig_2.0.3 tweenr_1.0.2 vipor_0.4.5 nlme_3.1-153
[61] nnet_7.3-16 rlang_0.4.10 lifecycle_1.0.0 downloader_0.4
[65] filelock_1.0.2 BiocFileCache_2.0.0 ggrastr_0.2.3 cellranger_1.1.0
[69] polyclip_1.10-0 Matrix_1.3-3 aplot_0.0.6 carData_3.0-4
[73] beeswarm_0.2.3 base64enc_0.1-3 whisker_0.4 GlobalOptions_0.1.2
[77] png_0.1-7 viridisLite_0.4.0 rjson_0.2.20 bitops_1.0-6
[81] R.oo_1.24.0 pROC_1.17.0.1 blob_1.2.1 shape_1.4.6
[85] qvalue_2.24.0 rstatix_0.7.0 ggsignif_0.6.3 scales_1.1.1
[89] memoise_2.0.0 magrittr_2.0.1 plyr_1.8.6 zlibbioc_1.37.0
[93] compiler_4.1.0 scatterpie_0.1.6 BiocIO_1.1.2 clue_0.3-60
[97] cli_2.5.0 MASS_7.3-54 tidyselect_1.1.0 stringi_1.5.3
[101] forcats_0.5.1 yaml_2.2.1 GOSemSim_2.18.0 locfit_1.5-9.4
[105] fastmatch_1.1-0 tools_4.1.0 rio_0.5.26 circlize_0.4.13
[109] rstudioapi_0.13 foreign_0.8-81 eulerr_6.1.0 prodlim_2019.11.13
[113] farver_2.0.3 ggraph_2.0.5 digest_0.6.27 rvcheck_0.1.8
[117] BiocManager_1.30.10 lava_1.6.8.1 Rcpp_1.0.6 car_3.0-10
[121] broom_0.7.6 httr_1.4.2 colorspace_2.0-0 XML_3.99-0.5
[125] reticulate_1.20 splines_4.1.0 tidytree_0.3.4 graphlayouts_0.7.1
[129] xlsxjars_0.6.1 xtable_1.8-4 jsonlite_1.7.2 ggtree_3.0.2
[133] tidygraph_1.2.0 timeDate_3043.102 zeallot_0.1.0 ipred_0.9-9
[137] R6_2.5.0 pillar_1.6.1 htmltools_0.5.2 glue_1.4.2
[141] fastmap_1.1.0 clusterProfiler_4.0.0 class_7.3-19 codetools_0.2-18
[145] fgsea_1.18.0 utf8_1.1.4 tibble_3.1.2 ggbeeswarm_0.6.0
[149] curl_4.3 tfruns_1.5.0 zip_2.1.1 GO.db_3.13.0
[153] openxlsx_4.2.3 survival_3.2-11 rmarkdown_2.6 munsell_0.5.0
[157] DO.db_2.9 GetoptLong_1.0.5 GenomeInfoDbData_1.2.4 haven_2.4.1
[161] reshape2_1.4.4 gtable_0.3.0

rtracklayer • 209 views
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