Installation Problem

[LisaBlackmer]

I'm not sure why I'm struggling so much, but I can't seem to even install this package. Would you be able to tell me what I am doing wrong? I've never used conda in combination with R so that may be my problem, but I created a new conda environment (using miniconda) in my terminal (not in R) and activated it as described in the tutorial.

# create new conda environment for R
conda create -n hdWGCNA -c conda-forge r-base r-essentials

# activate conda environment
conda activate hdWGCNA

Then I switch to R and installed all of these packages successfully:

# install BiocManager
install.packages("BiocManager")

# install Bioconductor core packages
BiocManager::install()

# install additional packages:
BiocManager::install(c("WGCNA", "igraph", "devtools", "GeneOverlap", "ggrepel", "UCell"))
devtools::install_github("NightingaleHealth/ggforestplot")

# install Seurat v5 
install.packages("Seurat")

# alternatively, install Seurat v4
install.packages("Seurat", repos = c("https://satijalab.r-universe.dev', 'https://cloud.r-project.org"))

However, when I tried to install hdWGCNA

devtools::install_github('smorabit/hdWGCNA', ref='dev')

I got this error: "Downloading GitHub repo smorabit/hdWGCNA@dev
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/smorabit/hdWGCNA/tarball/dev' failed"

I also tried using:

remotes::install_github("smorabit/hdWGCNA")

But got the same error.

When I first run the code, a screen pops up asking me to log in with my git credentials, but my own log in info doesn't work so I just click "Deny"

Any idea what I'm doing wrong?
Here is my session info:
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5

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-arm64/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/Denver
tzcode source: internal

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

other attached packages:
[1] WGCNA_1.72-5 fastcluster_1.2.6 dynamicTreeCut_1.63-1 patchwork_1.2.0 cowplot_1.1.3
[6] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[11] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[16] Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4

loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.2 later_1.3.2 bitops_1.0-8
[5] polyclip_1.10-7 preprocessCore_1.64.0 rpart_4.1.23 fastDummies_1.7.3
[9] lifecycle_1.0.4 doParallel_1.0.17 globals_0.16.3 lattice_0.22-6
[13] MASS_7.3-60.0.1 backports_1.5.0 magrittr_2.0.3 rmarkdown_2.27
[17] Hmisc_5.1-3 plotly_4.10.4 remotes_2.5.0 httpuv_1.6.15
[21] sctransform_0.4.1 spam_2.10-0 sessioninfo_1.2.2 pkgbuild_1.4.4
[25] spatstat.sparse_3.1-0 reticulate_1.38.0 pbapply_1.7-2 DBI_1.2.3
[29] RColorBrewer_1.1-3 abind_1.4-5 pkgload_1.4.0 zlibbioc_1.48.2
[33] Rtsne_0.17 RCurl_1.98-1.16 BiocGenerics_0.48.1 nnet_7.3-19
[37] GenomeInfoDbData_1.2.11 IRanges_2.36.0 S4Vectors_0.40.2 ggrepel_0.9.5
[41] irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.0-5 goftest_1.2-3
[45] RSpectra_0.16-2 spatstat.random_3.3-1 fitdistrplus_1.2-1 parallelly_1.38.0
[49] leiden_0.4.3.1 codetools_0.2-20 tidyselect_1.2.1 base64enc_0.1-3
[53] matrixStats_1.3.0 stats4_4.3.2 spatstat.explore_3.3-1 jsonlite_1.8.8
[57] Formula_1.2-5 ellipsis_0.3.2 progressr_0.14.0 ggridges_0.5.6
[61] survival_3.7-0 iterators_1.0.14 foreach_1.5.2 tools_4.3.2
[65] ica_1.0-3 Rcpp_1.0.13 glue_1.7.0 gridExtra_2.3
[69] xfun_0.46 usethis_3.0.0 GenomeInfoDb_1.38.8 withr_3.0.1
[73] BiocManager_1.30.23 fastmap_1.2.0 fansi_1.0.6 digest_0.6.36
[77] timechange_0.3.0 R6_2.5.1 mime_0.12 colorspace_2.1-1
[81] scattermore_1.2 GO.db_3.18.0 tensor_1.5 spatstat.data_3.1-2
[85] RSQLite_2.3.7 utf8_1.2.4 generics_0.1.3 data.table_1.15.4
[89] httr_1.4.7 htmlwidgets_1.6.4 uwot_0.2.2 pkgconfig_2.0.3
[93] gtable_0.3.5 blob_1.2.4 impute_1.76.0 lmtest_0.9-40
[97] XVector_0.42.0 htmltools_0.5.8.1 profvis_0.3.8 dotCall64_1.1-1
[101] scales_1.3.0 Biobase_2.62.0 png_0.1-8 spatstat.univar_3.0-0
[105] knitr_1.48 rstudioapi_0.16.0 tzdb_0.4.0 reshape2_1.4.4
[109] checkmate_2.3.2 nlme_3.1-165 curl_5.2.1 cachem_1.1.0
[113] zoo_1.8-12 KernSmooth_2.23-24 parallel_4.3.2 miniUI_0.1.1.1
[117] foreign_0.8-87 AnnotationDbi_1.64.1 pillar_1.9.0 grid_4.3.2
[121] vctrs_0.6.5 RANN_2.6.1 urlchecker_1.0.1 promises_1.3.0
[125] xtable_1.8-4 cluster_2.1.6 htmlTable_2.4.3 evaluate_0.24.0
[129] cli_3.6.3 compiler_4.3.2 rlang_1.1.4 crayon_1.5.3
[133] future.apply_1.11.2 plyr_1.8.9 fs_1.6.4 stringi_1.8.4
[137] viridisLite_0.4.2 deldir_2.0-4 munsell_0.5.1 Biostrings_2.70.3
[141] lazyeval_0.2.2 devtools_2.4.5 spatstat.geom_3.3-2 Matrix_1.6-5
[145] RcppHNSW_0.6.0 hms_1.1.3 bit64_4.0.5 future_1.34.0
[149] KEGGREST_1.42.0 shiny_1.9.1 ROCR_1.0-11 igraph_2.0.3
[153] memoise_2.0.1 bit_4.0.5

[smorabit]

Hi,

Unfortunately this seems like a problem unrelated to hdWGCNA itself. I am not able to replicate your error on my computer, so it is difficult for me to offer a solution. I found this thread on another repository which might help you solve this problem: r-lib/remotes#130

[kueckelj]

Hi, I stumbled upon the same error. This worked for me:

options(timeout = 100000)
install.packages("tester") # has to be installed manually
download.file("https://github.com/smorabit/hdWGCNA/archive/refs/heads/dev.tar.gz", destfile = "hdWGCNA-dev.tar.gz")
install.packages("hdWGCNA-dev.tar.gz", repos = NULL, type = "source")

[LisaBlackmer]

Thank you both for your help! I tried the steps outlined by @kueckelj and they worked! Everything should be properly installed and ready to use now. Thanks again!