When running dba.normalize in diffbind I am receiving the follow error:

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("DiffBind")

library(DiffBind)

Load sample sheet

sampleSheet <- read.csv("/Users/vwimalasena/Documents/Ewald/ChIP-seq/DiffBind/DiffBindSampleSheet3.csv")

Create a DBA object

dbaObj <- dba(sampleSheet="/Users/vwimalasena/Documents/Ewald/ChIP-seq/DiffBind/DiffBindSampleSheet3.csv", scoreCol = 5)

dbaObj <- dba.count(dbaObj)

BiocManager::install("csaw")

library(csaw)

dbaObj <- dba.normalize(dbaObj, spikein = TRUE)

output message with error

Generating counts for spike-ins... Error in socketConnection(host, port, TRUE, TRUE, "a+b", timeout = connect_timeout) : cannot open the connection

sessionInfo( )

output of sessionInfo

R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.3.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York tzcode source: internal

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

other attached packages: [1] BiocManager_1.30.22 csaw_1.34.0 DiffBind_3.10.1
[4] SummarizedExperiment_1.30.2 Biobase_2.60.0 MatrixGenerics_1.12.3
[7] matrixStats_1.3.0 GenomicRanges_1.52.1 GenomeInfoDb_1.36.4
[10] IRanges_2.34.1 S4Vectors_0.38.2 BiocGenerics_0.46.0

loaded via a namespace (and not attached): [1] amap_0.8-19 tidyselect_1.2.1 dplyr_1.1.4
[4] Biostrings_2.68.1 bitops_1.0-7 fastmap_1.1.1
[7] RCurl_1.98-1.14 apeglm_1.22.1 GenomicAlignments_1.36.0 [10] XML_3.99-0.16.1 digest_0.6.35 lifecycle_1.0.4
[13] invgamma_1.1 magrittr_2.0.3 compiler_4.3.1
[16] rlang_1.1.3 tools_4.3.1 utf8_1.2.4
[19] yaml_2.3.8 rtracklayer_1.60.1 S4Arrays_1.0.6
[22] htmlwidgets_1.6.4 interp_1.1-6 DelayedArray_0.26.7
[25] plyr_1.8.9 RColorBrewer_1.1-3 ShortRead_1.58.0
[28] abind_1.4-5 BiocParallel_1.34.2 KernSmooth_2.23-22
[31] numDeriv_2016.8-1.1 hwriter_1.3.2.1 grid_4.3.1
[34] fansi_1.0.6 latticeExtra_0.6-30 caTools_1.18.2
[37] colorspace_2.1-0 edgeR_3.42.4 ggplot2_3.5.0
[40] scales_1.3.0 gtools_3.9.5 MASS_7.3-60.0.1
[43] bbmle_1.0.25.1 cli_3.6.2 mvtnorm_1.2-4
[46] crayon_1.5.2 generics_0.1.3 metapod_1.8.0
[49] rstudioapi_0.16.0 rjson_0.2.21 bdsmatrix_1.3-7
[52] stringr_1.5.1 zlibbioc_1.46.0 parallel_4.3.1
[55] restfulr_0.0.15 XVector_0.40.0 vctrs_0.6.5
[58] Matrix_1.6-5 mixsqp_0.3-54 ggrepel_0.9.5
[61] irlba_2.3.5.1 systemPipeR_2.6.3 jpeg_0.1-10
[64] locfit_1.5-9.9 limma_3.56.2 glue_1.7.0
[67] emdbook_1.3.13 codetools_0.2-20 stringi_1.8.3
[70] gtable_0.3.4 deldir_2.0-4 BiocIO_1.10.0
[73] munsell_0.5.1 tibble_3.2.1 pillar_1.9.0
[76] htmltools_0.5.8.1 gplots_3.1.3.1 BSgenome_1.68.0
[79] GenomeInfoDbData_1.2.10 truncnorm_1.0-9 R6_2.5.1
[82] GreyListChIP_1.32.1 lattice_0.22-6 png_0.1-8
[85] Rsamtools_2.16.0 SQUAREM_2021.1 ashr_2.2-63
[88] Rcpp_1.0.12 coda_0.19-4.1 DESeq2_1.40.2
[91] pkgconfig_2.0.3