Updated_HGNC_Symbols tries to download from non-existent site.
Abiologist opened this issue · 1 comments
# insert reproducible example here
library(Seurat)
library(scCustomize)
library(qs)
test_symbols <- c("MCM2", "MCM7", "CCNL1")
results <- scCustomize::Updated_HGNC_Symbols(input_data = test_symbols)Updated_HGNC_Symbols gives error:
Downloading HGNC data from:
https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
|================================================================| 100%
Error: download failed; see warnings()
In addition: Warning messages:
1: download failed
web resource path: ‘https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt’
local file path: ‘/Users/jsc/Library/Caches/org.R-project.R/R/scCustomize/file4d512279d26’
reason: Not Found (HTTP 404).
2: bfcdownload() failed
rid: BFC1
file: ‘https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt’
reason: download failed
sessionInfo() output
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
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: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] qs_0.27.2 scCustomize_2.1.2.9041 Seurat_5.1.0
[4] SeuratObject_5.0.2 sp_2.1-4
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.9 shape_1.4.6.1
[4] magrittr_2.0.3 spatstat.utils_3.1-0 ggbeeswarm_0.7.2
[7] farver_2.1.2 GlobalOptions_0.1.2 vctrs_0.6.5
[10] ROCR_1.0-11 memoise_2.0.1 spatstat.explore_3.3-2
[13] paletteer_1.6.0 janitor_2.2.0 htmltools_0.5.8.1
[16] forcats_1.0.0 curl_5.2.3 sctransform_0.4.1
[19] parallelly_1.38.0 KernSmooth_2.23-24 htmlwidgets_1.6.4
[22] ica_1.0-3 plyr_1.8.9 cachem_1.1.0
[25] plotly_4.10.4 zoo_1.8-12 lubridate_1.9.3
[28] igraph_2.1.1 mime_0.12 lifecycle_1.0.4
[31] pkgconfig_2.0.3 Matrix_1.7-1 R6_2.5.1
[34] fastmap_1.2.0 fitdistrplus_1.2-1 future_1.34.0
[37] shiny_1.9.1 snakecase_0.11.1 digest_0.6.37
[40] colorspace_2.1-1 rematch2_2.1.2 patchwork_1.3.0
[43] tensor_1.5 RSpectra_0.16-2 irlba_2.3.5.1
[46] RSQLite_2.3.7 filelock_1.0.3 progressr_0.14.0
[49] fansi_1.0.6 spatstat.sparse_3.1-0 timechange_0.3.0
[52] httr_1.4.7 polyclip_1.10-7 abind_1.4-8
[55] compiler_4.4.1 withr_3.0.1 bit64_4.5.2
[58] DBI_1.2.3 fastDummies_1.7.4 MASS_7.3-61
[61] tools_4.4.1 vipor_0.4.7 lmtest_0.9-40
[64] beeswarm_0.4.0 httpuv_1.6.15 future.apply_1.11.2
[67] goftest_1.2-3 glue_1.8.0 nlme_3.1-166
[70] promises_1.3.0 grid_4.4.1 Rtsne_0.17
[73] cluster_2.1.6 reshape2_1.4.4 generics_0.1.3
[76] gtable_0.3.5 spatstat.data_3.1-2 tidyr_1.3.1
[79] RApiSerialize_0.1.4 data.table_1.16.2 stringfish_0.16.0
[82] utf8_1.2.4 spatstat.geom_3.3-3 RcppAnnoy_0.0.22
[85] ggrepel_0.9.6 RANN_2.6.2 pillar_1.9.0
[88] stringr_1.5.1 spam_2.11-0 RcppHNSW_0.6.0
[91] ggprism_1.0.5 later_1.3.2 circlize_0.4.16
[94] splines_4.4.1 dplyr_1.1.4 BiocFileCache_2.12.0
[97] lattice_0.22-6 bit_4.5.0 survival_3.7-0
[100] deldir_2.0-4 tidyselect_1.2.1 miniUI_0.1.1.1
[103] pbapply_1.7-2 gridExtra_2.3 scattermore_1.2
[106] matrixStats_1.4.1 stringi_1.8.4 lazyeval_0.2.2
[109] codetools_0.2-20 tibble_3.2.1 cli_3.6.3
[112] RcppParallel_5.1.9 uwot_0.2.2 xtable_1.8-4
[115] reticulate_1.39.0 munsell_0.5.1 Rcpp_1.0.13
[118] globals_0.16.3 spatstat.random_3.3-2 dbplyr_2.5.0
[121] png_0.1-8 ggrastr_1.0.2 spatstat.univar_3.0-1
[124] parallel_4.4.1 blob_1.2.4 ggplot2_3.5.1
[127] dotCall64_1.2 listenv_0.9.1 viridisLite_0.4.2
[130] scales_1.3.0 ggridges_0.5.6 leiden_0.4.3.1
[133] purrr_1.0.2 rlang_1.1.4 cowplot_1.1.3
>
Hi @Abiologist,
Thanks for submitting issue. It appears HGNC did change the URL for the text file which caused the error. I have just updated the release version with fix for the issue. You can download with:
devtools::install_github("samuel-marsh/scCustomize", ref = "release/3.0.0")
If you continue to have any issues after updating to the release version please let me know here and I'll reopen the issue.
Best,
Sam