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Could not find function get_collectri

Open cf98 opened this issue 4 months ago • 4 comments

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!

cf98 avatar Sep 30 '24 06:09 cf98