problems running get_progeny after conda install

[JGASmits]

Hi, looking forward to using decoupleR, it looks very usefull!

I've tried to install the R library decouleR via conda However eventhough the library seems to load the 'get_progeny' function isn't known, run_wmean does seem to function however:

> library("decoupleR")
> net <- get_progeny(organism = 'human', top = 100)
Error in get_progeny(organism = "human", top = 100) : 
  could not find function "get_progeny"
> run_wmean()
Error in check_nas_infs(mat) : argument "mat" is missing, with no default

This seems confirmed when i list the exported functions:

> ls('package:decoupleR')
 [1] ":="                 "%>%"                "abort"              "as_label"           "as_name"            "convert_f_defaults" "convert_to_"       
 [8] "convert_to_aucell"  "convert_to_fgsea"   "convert_to_gsva"    "convert_to_mlm"     "convert_to_ora"     "convert_to_ulm"     "convert_to_viper"  
[15] "convert_to_wmean"   "convert_to_wsum"    "decouple"           "enquo"              "enquos"             "exec"               "expr"              
[22] "filter_regulons"    "intersect_regulons" "quo_is_missing"     "quo_is_null"        "run_aucell"         "run_consensus"      "run_fgsea"         
[29] "run_gsva"           "run_mdt"            "run_mlm"            "run_ora"            "run_udt"            "run_ulm"            "run_viper"         
[36] "run_wmean"          "run_wsum"           "sym"                "syms"     

The session info:

sessionInfo()

R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default BLAS/LAPACK: /vol/mbconda/jsmits/minR/lib/libopenblasp-r0.3.18.so

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 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] decoupleR_2.0.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 pillar_1.7.0 compiler_4.1.3 GenomeInfoDb_1.30.0 XVector_0.34.0
[6] MatrixGenerics_1.6.0 bitops_1.0-7 tools_4.1.3 zlibbioc_1.40.0 rpart_4.1.16
[11] lattice_0.20-45 lifecycle_1.0.1 tibble_3.1.6 gtable_0.3.0 pkgconfig_2.0.3
[16] rlang_1.0.2 Matrix_1.4-1 DelayedArray_0.20.0 cli_3.2.0 speedglm_0.3-4
[21] GenomeInfoDbData_1.2.7 ranger_0.13.1 dplyr_1.0.8 generics_0.1.2 vctrs_0.4.0
[26] S4Vectors_0.32.3 IRanges_2.28.0 stats4_4.1.3 grid_4.1.3 tidyselect_1.1.2
[31] glue_1.6.2 Biobase_2.54.0 R6_2.5.1 RobustRankAggreg_1.1 fansi_1.0.3
[36] tidyr_1.2.0 ggplot2_3.3.5 purrr_0.3.4 magrittr_2.0.3 MASS_7.3-56
[41] scales_1.1.1 matrixStats_0.61.0 ellipsis_0.3.2 BiocGenerics_0.40.0 GenomicRanges_1.46.1
[46] SummarizedExperiment_1.24.0 colorspace_2.0-3 utf8_1.2.2 RCurl_1.98-1.6 munsell_0.5.0
[51] crayon_1.5.1

Anny pointers on how i can fix this? 

[PauBadiaM]

Hi @JGASmits,

Thanks for checking out the package! Yes the problem here is that I haven't pushed the new changes (such as the addition of Omnipath to decoupleR) to BioC yet. You can install the latest version from GitHub instead with

devtools::install_github('saezlab/decoupleR')

With a version <2.1. it should work. Else you can wait until I push to BioC, which will happen soonish (today or Monday).

[JGASmits]

Thanks Pau for your swift reply. Before you push the github version to BioC there is still a small hickup there. After running the devtools install the error changes to the missing Omnipath package:

** testing if installed package keeps a record of temporary installation path

• DONE (decoupleR)

  library("decoupleR") net <- get_progeny(organism = 'human', top = 100) Error in loadNamespace(x) : there is no package called ‘OmnipathR’

However after installing OmnipathR with BiocManager it indeed works!