decoupleR
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Could not find function get_collectri
I am following the decoupleR document here.
I installed the package through remotes::install_github()
command.
However, when I tried to run it, it just shows:
Error in get_collectri(organism = "human", split_complexes = FALSE) :
could not find function "get_collectri"
Here's the session info output:
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] OmnipathR_3.13.26 decoupleR_2.9.7
loaded via a namespace (and not attached):
[1] Rcpp_1.0.13 lubridate_1.9.3 lattice_0.22-5 tidyr_1.3.1 prettyunits_1.2.0 ps_1.6.0
[7] rprojroot_2.0.4 digest_0.6.37 utf8_1.2.4 R6_2.5.1 cellranger_1.1.0 backports_1.5.0
[13] RSQLite_2.3.7 evaluate_1.0.0 httr_1.4.7 pillar_1.9.0 rlang_1.1.4 progress_1.2.3
[19] curl_5.2.3 readxl_1.4.3 rstudioapi_0.13 callr_3.7.0 blob_1.2.4 R.utils_2.12.3
[25] R.oo_1.26.0 Matrix_1.6-5 checkmate_2.3.2 rmarkdown_2.28 stringr_1.5.1 readr_2.1.5
[31] igraph_2.0.3 bit_4.5.0 compiler_4.2.2 xfun_0.47 pkgconfig_2.0.3 pkgbuild_1.2.0
[37] htmltools_0.5.8.1 tidyselect_1.2.1 tibble_3.2.1 XML_3.99-0.17 fansi_1.0.6 crayon_1.5.3
[43] dplyr_1.1.4 tzdb_0.4.0 withr_3.0.1 later_1.3.2 R.methodsS3_1.8.2 rappdirs_0.3.3
[49] grid_4.2.2 jsonlite_1.8.9 lifecycle_1.0.4 DBI_1.2.3 magrittr_2.0.3 zip_2.3.1
[55] cli_3.6.3 stringi_1.8.4 cachem_1.1.0 remotes_2.4.0 xml2_1.3.6 logger_0.3.0
[61] generics_0.1.3 vctrs_0.6.5 tools_4.2.2 bit64_4.5.2 glue_1.7.0 purrr_1.0.2
[67] hms_1.1.3 yaml_2.3.10 processx_3.5.2 fastmap_1.2.0 timechange_0.3.0 BiocManager_1.30.15
[73] rvest_1.0.4 memoise_2.0.1 knitr_1.48
Can you help identify the issue? Please let me know if other information is needed.
Thank you!