Hello,

I'm having issues with downloading a series matrix file in R 4.2.3.

library(GEOquery)

geoMat <- getGEO("GSE51032")

I get the following error message.

Error in data.table::fread(text = dat[(series_table_begin_line + 1):(series_table_end_line - :

R character strings are limited to 2^31-1 bytes

sessionInfo()

R version 4.2.3 (2023-03-15 ucrt)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 [2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] GEOquery_2.66.0 minfi_1.44.0
[3] bumphunter_1.40.0 locfit_1.5-9.7
[5] iterators_1.0.14 foreach_1.5.2
[7] Biostrings_2.66.0 XVector_0.38.0
[9] SummarizedExperiment_1.28.0 Biobase_2.58.0
[11] MatrixGenerics_1.10.0 matrixStats_0.63.0
[13] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[15] IRanges_2.32.0 S4Vectors_0.36.2
[17] BiocGenerics_0.44.0 lubridate_1.9.2
[19] forcats_1.0.0 stringr_1.5.0
[21] purrr_1.0.1 readr_2.1.4
[23] tibble_3.2.0 ggplot2_3.4.1
[25] tidyverse_2.0.0 data.table_1.14.8
[27] tidyr_1.3.0 plyr_1.8.8
[29] dplyr_1.1.0 ncdf4_1.21

loaded via a namespace (and not attached): [1] colorspace_2.1-0 rjson_0.2.21
[3] siggenes_1.72.0 mclust_6.0.0
[5] base64_2.0.1 bit64_4.0.5
[7] AnnotationDbi_1.60.2 fansi_1.0.4
[9] xml2_1.3.3 R.methodsS3_1.8.2
[11] codetools_0.2-19 splines_4.2.3
[13] sparseMatrixStats_1.10.0 cachem_1.0.7
[15] scrime_1.3.5 Rsamtools_2.14.0
[17] annotate_1.76.0 dbplyr_2.3.2
[19] R.oo_1.25.0 png_0.1-8
[21] HDF5Array_1.26.0 compiler_4.2.3
[23] httr_1.4.5 Matrix_1.5-3
[25] fastmap_1.1.1 limma_3.54.2
[27] cli_3.6.0 prettyunits_1.1.1
[29] tools_4.2.3 gtable_0.3.3
[31] glue_1.6.2 GenomeInfoDbData_1.2.9
[33] rappdirs_0.3.3 doRNG_1.8.6
[35] Rcpp_1.0.10 vctrs_0.6.0
[37] rhdf5filters_1.10.0 multtest_2.54.0
[39] nlme_3.1-162 preprocessCore_1.60.2
[41] rtracklayer_1.58.0 DelayedMatrixStats_1.20.0 [43] timechange_0.2.0 lifecycle_1.0.3
[45] restfulr_0.0.15 rngtools_1.5.2
[47] XML_3.99-0.13 beanplot_1.3.1
[49] zlibbioc_1.44.0 MASS_7.3-58.2
[51] scales_1.2.1 hms_1.1.3
[53] rhdf5_2.42.0 RColorBrewer_1.1-3
[55] yaml_2.3.7 curl_5.0.0
[57] memoise_2.0.1 biomaRt_2.54.1
[59] reshape_0.8.9 stringi_1.7.12
[61] RSQLite_2.3.0 genefilter_1.80.3
[63] BiocIO_1.8.0 GenomicFeatures_1.50.4
[65] filelock_1.0.2 BiocParallel_1.32.6
[67] rlang_1.1.0 pkgconfig_2.0.3
[69] bitops_1.0-7 nor1mix_1.3-0
[71] lattice_0.20-45 Rhdf5lib_1.20.0
[73] GenomicAlignments_1.34.1 bit_4.0.5
[75] tidyselect_1.2.0 magrittr_2.0.3
[77] R6_2.5.1 generics_0.1.3
[79] DelayedArray_0.23.2 DBI_1.1.3
[81] pillar_1.9.0 withr_2.5.0
[83] survival_3.5-5 KEGGREST_1.38.0
[85] RCurl_1.98-1.10 crayon_1.5.2
[87] utf8_1.2.3 BiocFileCache_2.6.1
[89] tzdb_0.3.0 progress_1.2.2
[91] grid_4.2.3 blob_1.2.4
[93] digest_0.6.31 xtable_1.8-4
[95] R.utils_2.12.2 illuminaio_0.40.0
[97] openssl_2.0.6 munsell_0.5.0
[99] quadprog_1.5-8 askpass_1.1