Error while reading the data using (read.metharray.exp)

[royamani]

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