BUG: cannot open URL - Issues with "satijalab/azimuth", Seurat additional package installation
jb018 opened this issue · comments
Issue Description
I'm trying to install R package "azimuth" but encountered the following error. I attempted to access the URL manually, but it was unsuccessful.
Any assistance would be greatly appreciated
Reproducing Code Example
> remotes::install_github("satijalab/azimuth", "seurat5", quiet = TRUE)Error Message
Installing 30 packages: SparseArray, DelayedArray, Rhtslib, SummarizedExperiment, GenomicAlignments, Rsamtools, Biostrings, XVector, GenomicRanges, AnnotationDbi, KEGGREST, GO.db, annotate, rtracklayer, rhdf5filters, rhdf5, biomaRt, AnnotationFilter, GenomicFeatures, CNEr, BSgenome, beachmat, SingleCellExperiment, HDF5Array, DelayedMatrixStats, ensembldb, TFBSTools, glmGamPoi, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘SparseArray’ ‘DelayedArray’ ‘Rhtslib’
‘GenomicAlignments’ ‘Rsamtools’ ‘Biostrings’ ‘XVector’ ‘GenomicRanges’ ‘rtracklayer’ ‘rhdf5filters’ ‘rhdf5’ ‘CNEr’ ‘beachmat’ ‘HDF5Array’
‘TFBSTools’ ‘glmGamPoi’
installing the source packages ‘SparseArray’, ‘DelayedArray’, ‘Rhtslib’, ‘SummarizedExperiment’, ‘GenomicAlignments’, ‘Rsamtools’, ‘Biostrings’, ‘XVector’, ‘GenomicRanges’, ‘AnnotationDbi’, ‘KEGGREST’, ‘GO.db’, ‘annotate’, ‘rtracklayer’, ‘rhdf5filters’, ‘rhdf5’, ‘biomaRt’, ‘AnnotationFilter’, ‘GenomicFeatures’, ‘CNEr’, ‘BSgenome’, ‘beachmat’, ‘SingleCellExperiment’, ‘HDF5Array’, ‘DelayedMatrixStats’, ‘ensembldb’, ‘TFBSTools’, ‘glmGamPoi’, ‘EnsDb.Hsapiens.v86’, ‘BSgenome.Hsapiens.UCSC.hg38’
There were 31 warnings (use warnings() to see them)Additional Comments
No response
Session Info
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8 LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8
time zone: Australia/Brisbane
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeuratData_0.2.2.9001 Seurat_5.2.1 SeuratObject_5.0.2 sp_2.2-0 devtools_2.4.5 usethis_3.1.0
loaded via a namespace (and not attached):
[1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3 remotes_2.5.0 rlang_1.1.5 magrittr_2.0.3
[7] RcppAnnoy_0.0.22 spatstat.geom_3.3-5 matrixStats_1.5.0 ggridges_0.5.6 compiler_4.4.2 png_0.1-8
[13] callr_3.7.6 vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1 profvis_0.4.0 crayon_1.5.3
[19] pkgconfig_2.0.3 fastmap_1.2.0 ellipsis_0.3.2 promises_1.3.2 sessioninfo_1.2.3 ps_1.8.1
[25] purrr_1.0.4 cachem_1.1.0 jsonlite_1.8.9 goftest_1.2-3 later_1.4.1 spatstat.utils_3.1-2
[31] irlba_2.3.5.1 parallel_4.4.2 cluster_2.1.6 R6_2.5.1 ica_1.0-3 spatstat.data_3.1-4
[37] stringi_1.8.4 RColorBrewer_1.1-3 reticulate_1.40.0 spatstat.univar_3.1-1 parallelly_1.42.0 pkgload_1.4.0
[43] lmtest_0.9-40 scattermore_1.2 Rcpp_1.0.14 tensor_1.5 future.apply_1.11.3 zoo_1.8-12
[49] sctransform_0.4.1 httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2 igraph_2.1.4 tidyselect_1.2.1
[55] abind_1.4-8 rstudioapi_0.17.1 spatstat.random_3.3-2 spatstat.explore_3.3-4 codetools_0.2-20 miniUI_0.1.1.1
[61] curl_6.2.0 processx_3.8.5 listenv_0.9.1 pkgbuild_1.4.6 lattice_0.22-6 tibble_3.2.1
[67] plyr_1.8.9 shiny_1.10.0 ROCR_1.0-11 Rtsne_0.17 future_1.34.0 fastDummies_1.7.5
[73] desc_1.4.3 survival_3.7-0 polyclip_1.10-7 urlchecker_1.0.1 fitdistrplus_1.2-2 pillar_1.10.1
[79] KernSmooth_2.23-24 plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0 ggplot2_3.5.1 munsell_0.5.1
[85] scales_1.3.0 globals_0.16.3 xtable_1.8-4 glue_1.8.0 lazyeval_0.2.2 tools_4.4.2
[91] data.table_1.16.4 RSpectra_0.16-2 RANN_2.6.2 fs_1.6.5 dotCall64_1.2 cowplot_1.1.3
[97] grid_4.4.2 tidyr_1.3.1 colorspace_2.1-1 nlme_3.1-166 patchwork_1.3.0 cli_3.6.3
[103] rappdirs_0.3.3 spatstat.sparse_3.1-0 spam_2.11-1 viridisLite_0.4.2 dplyr_1.1.4 uwot_0.2.2
[109] gtable_0.3.6 digest_0.6.37 progressr_0.15.1 ggrepel_0.9.6 htmlwidgets_1.6.4 farver_2.1.2
[115] memoise_2.0.1 htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 mime_0.12 MASS_7.3-61
Hi @jb018,
It seems the issue is that your computer cannot reach bioconductor repo to install needed packages. Have you resolved this issue?
Best,
Sam