issue with toppFun - curl error - failed to perform HTTP request. Caused by error in `curl::curl_fetch_memory()`

[lsumoy]

I recently installed your package and get the following error upon trying to use your package:

library(scToppR)
toppData <- toppFun(toppFun.input.df,

•                 gene_col = "gene_symbol",
  

•                 cluster_col = "comparison",
  

•                 p_val_col = "p_val",
  

•                 logFC_col = "avg_log2FC",
  

•                 key_type = "SYMBOL")
  

<error/httr2_failure>
Error in httr2::req_perform():
! Failed to perform HTTP request.
Caused by error in curl::curl_fetch_memory():
! SSL peer certificate or SSH remote key was not OK [toppgene.cchmc.org]:
SSL certificate problem: self-signed certificate in certificate chain

Backtrace:
▆

1. └─scToppR::toppFun(...)
2. └─scToppR::get_Entrez(gene_list)

3. └─httr2::req_perform(httr2::req_body_json(req, list(Symbols = genes)))
   

4.   └─httr2:::handle_resp(req, resp, error_call = error_call)
   

5.     └─rlang::cnd_signal(resp)
   

R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS: /software/debian-12/general/R-4.5.0-bioc-3.21/lib/R/lib/libRblas.so
LAPACK: /software/debian-12/general/R-4.5.0-bioc-3.21/lib/R/lib/libRlapack.so; LAPACK version 3.12.1

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Madrid
tzcode source: system (glibc)

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

other attached packages:
[1] scToppR_0.99.8 readxl_1.4.5
[3] openxlsx_4.2.8.1 wheatmap_0.2.0
[5] ggplot2_4.0.2 sesame_1.26.0
[7] sesameData_1.26.0 knowYourCG_1.4.0
[9] DMRcatedata_2.26.0 IlluminaHumanMethylationEPICv2anno.20a1.hg38_1.0.0
[11] minfi_1.54.1 bumphunter_1.50.0
[13] locfit_1.5-9.12 iterators_1.0.14
[15] foreach_1.5.2 Biostrings_2.76.0
[17] XVector_0.48.0 SummarizedExperiment_1.38.1
[19] Biobase_2.68.0 MatrixGenerics_1.20.0
[21] matrixStats_1.5.0 ExperimentHub_2.16.1
[23] AnnotationHub_3.16.1 BiocFileCache_2.16.2
[25] dbplyr_2.5.2 DMRcate_3.4.1
[27] GenomicRanges_1.60.0 GenomeInfoDb_1.44.3
[29] IRanges_2.42.0 S4Vectors_0.46.0
[31] BiocGenerics_0.54.1 generics_0.1.4

loaded via a namespace (and not attached):
[1] fs_1.6.7 ProtGenerics_1.40.0
[3] bitops_1.0-9 devtools_2.5.0
[5] httr_1.4.8 RColorBrewer_1.1-3
[7] tools_4.5.0 doRNG_1.8.6.3
[9] backports_1.5.0 utf8_1.2.6
[11] R6_2.6.1 HDF5Array_1.36.0
[13] lazyeval_0.2.2 Gviz_1.52.0
[15] rhdf5filters_1.20.0 permute_0.9-10
[17] withr_3.0.2 prettyunits_1.2.0
[19] gridExtra_2.3 base64_2.0.2
[21] preprocessCore_1.70.0 cli_3.6.5
[23] S7_0.2.1 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[25] readr_2.2.0 genefilter_1.90.0
[27] askpass_1.2.1 Rsamtools_2.24.1
[29] foreign_0.8-91 siggenes_1.82.0
[31] illuminaio_0.50.0 R.utils_2.13.0
[33] rentrez_1.2.4 dichromat_2.0-0.1
[35] sessioninfo_1.2.3 scrime_1.3.7
[37] BSgenome_1.76.0 limma_3.64.3
[39] rstudioapi_0.18.0 RSQLite_2.4.6
[41] BiocIO_1.18.0 gtools_3.9.5
[43] zip_2.3.3 dplyr_1.2.0
[45] Matrix_1.7-4 interp_1.1-6
[47] abind_1.4-8 R.methodsS3_1.8.2
[49] lifecycle_1.0.5 yaml_2.3.12
[51] edgeR_4.6.3 rhdf5_2.52.1
[53] SparseArray_1.8.1 grid_4.5.0
[55] blob_1.3.0 crayon_1.5.3
[57] lattice_0.22-9 beachmat_2.24.0
[59] GenomicFeatures_1.60.0 annotate_1.86.1
[61] KEGGREST_1.48.1 pillar_1.11.1
[63] knitr_1.51 beanplot_1.3.1
[65] rjson_0.2.23 pak_0.9.2
[67] codetools_0.2-20 glue_1.8.0
[69] remotes_2.5.0 data.table_1.18.2.1
[71] vctrs_0.7.1 png_0.1-9
[73] cellranger_1.1.0 gtable_0.3.6
[75] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 cachem_1.1.0
[77] xfun_0.56 S4Arrays_1.8.1
[79] mime_0.13 survival_3.8-6
[81] statmod_1.5.1 ellipsis_0.3.2
[83] nlme_3.1-168 usethis_3.2.1
[85] bit64_4.6.0-1 bsseq_1.44.1
[87] progress_1.2.3 filelock_1.0.3
[89] nor1mix_1.3-3 otel_0.2.0
[91] rpart_4.1.24 colorspace_2.1-2
[93] DBI_1.3.0 Hmisc_5.2-5
[95] nnet_7.3-20 processx_3.8.6
[97] tidyselect_1.2.1 bit_4.6.0
[99] compiler_4.5.0 curl_7.0.0
[101] httr2_1.2.2 htmlTable_2.4.3
[103] h5mread_1.0.1 xml2_1.5.2
[105] desc_1.4.3 DelayedArray_0.34.1
[107] rtracklayer_1.68.0 checkmate_2.3.4
[109] scales_1.4.0 quadprog_1.5-8
[111] callr_3.7.6 rappdirs_0.3.4
[113] stringr_1.6.0 digest_0.6.39
[115] rmarkdown_2.30 GEOquery_2.76.0
[117] htmltools_0.5.9 pkgconfig_2.0.3
[119] jpeg_0.1-11 base64enc_0.1-6
[121] sparseMatrixStats_1.20.0 fastmap_1.2.0
[123] ensembldb_2.32.0 rlang_1.1.7
[125] htmlwidgets_1.6.4 UCSC.utils_1.4.0
[127] DelayedMatrixStats_1.30.0 farver_2.1.2
[129] jsonlite_2.0.0 BiocParallel_1.42.2
[131] mclust_6.1.2 R.oo_1.27.1
[133] VariantAnnotation_1.54.1 RCurl_1.98-1.17
[135] magrittr_2.0.4 Formula_1.2-5
[137] GenomeInfoDbData_1.2.14 patchwork_1.3.2
[139] Rhdf5lib_1.30.0 Rcpp_1.1.1
[141] viridis_0.6.5 stringi_1.8.7
[143] MASS_7.3-65 pkgbuild_1.4.8
[145] plyr_1.8.9 org.Hs.eg.db_3.21.0
[147] ggrepel_0.9.7 forcats_1.0.1
[149] deldir_2.0-4 splines_4.5.0
[151] multtest_2.64.0 hms_1.1.4
[153] ps_1.9.1 rngtools_1.5.2
[155] pkgload_1.5.0 reshape2_1.4.5
[157] biomaRt_2.64.0 BiocVersion_3.21.1
[159] missMethyl_1.42.0 XML_3.99-0.22
[161] evaluate_1.0.5 latticeExtra_0.6-31
[163] biovizBase_1.56.0 BiocManager_1.30.27
[165] tzdb_0.5.0 tidyr_1.3.2
[167] openssl_2.3.5 purrr_1.2.1
[169] reshape_0.8.10 xtable_1.8-8
[171] restfulr_0.0.16 AnnotationFilter_1.32.0
[173] viridisLite_0.4.3 tibble_3.3.1
[175] memoise_2.0.1 AnnotationDbi_1.70.0
[177] GenomicAlignments_1.44.0 cluster_2.1.8.2