Error in substring(line, 1, 1): invalid multibyte string at '<eb><f2>�<87><04>' #8
Description
1. Bug description
Error when importing peak files from ENCODE.
Console output
Processing id(s).
1 unique ENCODE id(s) identified.
Querying 1 id(s) from: ENCODE
Importing metadata via AnnotationHub.
snapshotDate(): 2022-04-21
loading from cache
Filtering by: file_type
Returning filtered metadata: 454,413 entries.
129,530 rows remain after filtering by genome build: GRCh38
Searching ENCODE metadata for: ENCSR000AKP
Identified 8 files: narrowpeak
Identified 6 files: bigwig
Processing id: >>> ENCSR000AKP <<<
Importing pre-computed narrowPeak files.
Error: BiocParallel errors
1 remote errors, element index: 1
0 unevaluated and other errors
first remote error:
Error in substring(line, 1, 1): invalid multibyte string at '<eb><f2>�<87><04>'
Expected behaviour
Import all peak files
2. Reproducible example
Code
reference <- PeakyFinders::import_peaks(ids = "ENCSR000AKP"
builds = "GRCh38")
3. Session info
Details
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] PeakyFinders_0.99.1 EpiCompare_0.99.20 Matrix_1.4-1 GenomicRanges_1.48.0 ggplot2_3.3.6
[6] dplyr_1.0.9 GenomeInfoDb_1.32.2 IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 R.utils_2.11.0
[3] reticulate_1.25 tidyselect_1.1.2
[5] RSQLite_2.2.14 AnnotationDbi_1.58.0
[7] htmlwidgets_1.5.4 grid_4.2.0
[9] BiocParallel_1.30.3 scatterpie_0.1.7
[11] munsell_0.5.0 codetools_0.2-18
[13] withr_2.5.0 colorspace_2.0-3
[15] GOSemSim_2.22.0 Biobase_2.56.0
[17] filelock_1.0.2 MACSr_1.4.0
[19] knitr_1.39 rstudioapi_0.13
[21] DOSE_3.22.0 MatrixGenerics_1.8.0
[23] GenomeInfoDbData_1.2.8 polyclip_1.10-0
[25] seqPattern_1.28.0 bit64_4.0.5
[27] farver_2.1.0 rprojroot_2.0.3
[29] basilisk_1.8.0 vctrs_0.4.1
[31] treeio_1.20.0 generics_0.1.2
[33] xfun_0.31 BiocFileCache_2.4.0
[35] regioneR_1.28.0 R6_2.5.1
[37] graphlayouts_0.8.0 locfit_1.5-9.5
[39] bitops_1.0-7 BRGenomics_1.8.0
[41] cachem_1.0.6 fgsea_1.22.0
[43] gridGraphics_0.5-1 DelayedArray_0.22.0
[45] assertthat_0.2.1 promises_1.2.0.1
[47] BiocIO_1.6.0 scales_1.2.0
[49] ggraph_2.0.5 enrichplot_1.16.1
[51] gtable_0.3.0 tidygraph_1.2.1
[53] rlang_1.0.2 genefilter_1.78.0
[55] splines_4.2.0 rtracklayer_1.56.0
[57] lazyeval_0.2.2 GEOquery_2.64.2
[59] impute_1.70.0 BiocManager_1.30.18
[61] yaml_2.3.5 reshape2_1.4.4
[63] GenomicFeatures_1.48.3 httpuv_1.6.5
[65] qvalue_2.28.0 tools_4.2.0
[67] ggplotify_0.1.0 gridBase_0.4-7
[69] ellipsis_0.3.2 gplots_3.1.3
[71] RColorBrewer_1.1-3 Rcpp_1.0.8.3
[73] plyr_1.8.7 progress_1.2.2
[75] zlibbioc_1.42.0 purrr_0.3.4
[77] RCurl_1.98-1.7 basilisk.utils_1.8.0
[79] prettyunits_1.1.1 viridis_0.6.2
[81] SummarizedExperiment_1.26.1 ggrepel_0.9.1
[83] magrittr_2.0.3 data.table_1.14.2
[85] DO.db_2.9 matrixStats_0.62.0
[87] pkgload_1.2.4 hms_1.1.1
[89] patchwork_1.1.1 mime_0.12
[91] evaluate_0.15 xtable_1.8-4
[93] XML_3.99-0.9 gridExtra_2.3
[95] testthat_3.1.4 compiler_4.2.0
[97] biomaRt_2.52.0 tibble_3.1.7
[99] KernSmooth_2.23-20 crayon_1.5.1
[101] shadowtext_0.1.2 R.oo_1.24.0
[103] htmltools_0.5.2 ggfun_0.0.6
[105] later_1.3.0 tzdb_0.3.0
[107] tidyr_1.2.0 geneplotter_1.74.0
[109] aplot_0.1.6 DBI_1.1.2
[111] ExperimentHub_2.4.0 tweenr_1.0.2
[113] ChIPseeker_1.32.0 genomation_1.28.0
[115] dbplyr_2.2.0 MASS_7.3-57
[117] rappdirs_0.3.3 boot_1.3-28
[119] readr_2.1.2 brio_1.1.3
[121] cli_3.3.0 R.methodsS3_1.8.1
[123] parallel_4.2.0 igraph_1.3.1
[125] pkgconfig_2.0.3 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[127] dir.expiry_1.4.0 GenomicAlignments_1.32.0
[129] plotly_4.10.0 xml2_1.3.3
[131] ggtree_3.4.0 annotate_1.74.0
[133] XVector_0.36.0 yulab.utils_0.0.4
[135] stringr_1.4.0 digest_0.6.29
[137] Biostrings_2.64.0 rmarkdown_2.14
[139] fastmatch_1.1-3 tidytree_0.3.9
[141] restfulr_0.0.14 curl_4.3.2
[143] shiny_1.7.1 Rsamtools_2.12.0
[145] gtools_3.9.2.1 rjson_0.2.21
[147] lifecycle_1.0.1 nlme_3.1-157
[149] jsonlite_1.8.0 limma_3.52.1
[151] desc_1.4.1 viridisLite_0.4.0
[153] BSgenome_1.64.0 fansi_1.0.3
[155] pillar_1.7.0 lattice_0.20-45
[157] KEGGREST_1.36.0 fastmap_1.1.0
[159] httr_1.4.3 plotrix_3.8-2
[161] survival_3.3-1 GO.db_3.15.0
[163] interactiveDisplayBase_1.34.0 glue_1.6.2
[165] png_0.1-7 BiocVersion_3.15.2
[167] bit_4.0.4 ggforce_0.3.3
[169] stringi_1.7.6 blob_1.2.3
[171] DESeq2_1.36.0 AnnotationHub_3.4.0
[173] caTools_1.18.2 memoise_2.0.1
[175] ape_5.6-2