Could not find function get_collectri

[cf98]

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!

[zkliesmete]

I have the same issue - the function get_collectri is not found. My decoupleR version is also 2.9.7, dorothea 1.10.0, R 4.2.3

Thank you!

[deeenes]

That's weird, get_collectri is exported since 20 April last year. So let's try to find out. Can you please both confirm that you have loaded the package after installation?

library(decoupleR)

'decoupleR' in .packages()

packageVersion('decoupleR')

And check if get_collectri is in its namespace:

'get_collectri' %in% names(decoupleR:::.__NAMESPACE__.$exports)

decoupleR:::get_collectri

If you still can't access get_collectri, is it the same situation with other exported functions?

decoupleR:::run_mlm