Hello,
I am trying to read my data, but I keep getting an error message for one of my folders (other folders worked and successfully uploaded as an object). But not sure what is causing the problem.
> RGset <- read.metharray.exp(file.path(baseDir, "205624890058"))
Error: BiocParallel errors
1 remote errors, element index: 8
0 unevaluated and other errors
first remote error:
Error in readChar(con, nchars = n): invalid UTF-8 input in readChar()
Timing stopped at: 0.602 0.023 0.625
Thank you!
Session Info:
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 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 LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] missMethyl_1.36.0 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1
[4] minfi_1.48.0 bumphunter_1.44.0 locfit_1.5-9.9
[7] iterators_1.0.14 foreach_1.5.2 Biostrings_2.70.3
[10] XVector_0.42.0 SummarizedExperiment_1.32.0 Biobase_2.62.0
[13] MatrixGenerics_1.14.0 matrixStats_1.3.0 GenomicRanges_1.54.1
[16] GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2
[19] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 magrittr_2.0.3 GenomicFeatures_1.54.4 BiocIO_1.12.0 zlibbioc_1.48.2 vctrs_0.6.5 multtest_2.58.0
[8] memoise_2.0.1 Rsamtools_2.18.0 DelayedMatrixStats_1.24.0 RCurl_1.98-1.14 askpass_1.2.0 S4Arrays_1.2.1 progress_1.2.3
[15] curl_5.2.1 Rhdf5lib_1.24.2 SparseArray_1.2.4 rhdf5_2.46.1 nor1mix_1.3-3 plyr_1.8.9 cachem_1.1.0
[22] GenomicAlignments_1.38.2 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-3 R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.11
[29] digest_0.6.35 siggenes_1.76.0 reshape_0.8.9 AnnotationDbi_1.64.1 RSQLite_2.3.6 org.Hs.eg.db_3.18.0 base64_2.0.1
[36] filelock_1.0.3 fansi_1.0.6 httr_1.4.7 abind_1.4-5 compiler_4.3.2 beanplot_1.3.1 rngtools_1.5.2
[43] bit64_4.0.5 BiocParallel_1.36.0 DBI_1.2.2 HDF5Array_1.30.1 biomaRt_2.58.2 MASS_7.3-60 openssl_2.2.0
[50] rappdirs_0.3.3 DelayedArray_0.28.0 rjson_0.2.21 tools_4.3.2 glue_1.7.0 quadprog_1.5-8 restfulr_0.0.15
[57] nlme_3.1-163 rhdf5filters_1.14.1 grid_4.3.2 generics_0.1.3 tzdb_0.4.0 preprocessCore_1.64.0 tidyr_1.3.1
[64] data.table_1.15.4 hms_1.1.3 xml2_1.3.6 utf8_1.2.4 pillar_1.9.0 stringr_1.5.1 limma_3.58.1
[71] genefilter_1.84.0 splines_4.3.2 dplyr_1.1.4 BiocFileCache_2.10.2 lattice_0.22-5 renv_1.0.3 survival_3.5-7
[78] rtracklayer_1.62.0 bit_4.0.5 GEOquery_2.70.0 annotate_1.80.0 tidyselect_1.2.1 scrime_1.3.5 statmod_1.5.0
[85] stringi_1.8.4 yaml_2.3.8 codetools_0.2-19 tibble_3.2.1 BiocManager_1.30.23 cli_3.6.2 xtable_1.8-4
[92] Rcpp_1.0.12 dbplyr_2.5.0 png_0.1-8 XML_3.99-0.16.1 readr_2.1.5 blob_1.2.4 prettyunits_1.2.0
[99] mclust_6.1.1 doRNG_1.8.6 sparseMatrixStats_1.14.0 bitops_1.0-7 illuminaio_0.44.0 purrr_1.0.2 crayon_1.5.2
[106] rlang_1.1.3 KEGGREST_1.42.0
Hello,
I am trying to read my data, but I keep getting an error message for one of my folders (other folders worked and successfully uploaded as an object). But not sure what is causing the problem.
Thank you!
Session Info: