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Elisseeff-Lab / domino

A software package for connecting cell level features in single cell RNA sequencing data with receptor ligand activity. Please be aware that an improved package, dominoSignal, is available.
https://fertiglab.github.io/dominoSignal/
GNU General Public License v3.0
15 stars 8 forks source link

Could not find function "create_domino" #9

Closed melanieloth closed 3 years ago

melanieloth commented 3 years ago

Hello,

I am having issues when attempting the function create_domino.

When I run the function, I get the following error:

> pbmc_dom = create_domino(signaling_db = '/Users/melanie/cellphonedb/', 
+                          features = auc, counts = counts, z_scores = z_scores, clusters = clusters, 
+                          df = '/Users/melanie/dockerResults1/regulons.csv')
Error in create_domino(signaling_db = "/Users/melanie/cellphonedb/", features = auc,  : 
  could not find function "create_domino"

I am able to get documentation when I run ?create_domino , but when I run find('create_domino') I get the following:

> find('create_domino')
character(0)

Thanks, Melanie

Chris-Cherry commented 3 years ago

Hey Melanie,

That's strange. Just to check, you're able to install and load the package successfully correct? Could you also check for build_domino() and/or signaling_heatmap()?

Chris

melanieloth commented 3 years ago

Thanks for the quick response. I reinstalled and checked the functions, and I am still not having any luck.

Downloading GitHub repo Chris-Cherry/domino@HEAD
Skipping 1 packages not available: biomaRt
✓  checking for file ‘/private/var/folders/gp/_jcgrtgx3n3868tmrkdx5v4w0000gp/T/Rtmp7TtjER/remotes2ddf3f505f40/Chris-Cherry-domino-af4514f/DESCRIPTION’ ...
─  preparing ‘domino’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘domino_0.1.1.tar.gz’

Installing package into ‘/Users/melanie/Library/R/3.6/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘domino’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning: undefined slot classes in definition of "domino": counts(class "AnyMatrix")
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (domino)
> library(domino)
> library(biomaRt)
> create_domino()
Error in create_domino() : could not find function "create_domino"
> build_domino()
Error in build_domino() : could not find function "build_domino"
> find('build_domino')
character(0)
Chris-Cherry commented 3 years ago

Could you give me the sessionInfo()?

melanieloth commented 3 years ago 
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.42.1 devtools_2.3.2 usethis_1.6.3  CoGAPS_3.6.0   Seurat_3.2.2   domino_0.1.1  

loaded via a namespace (and not attached):
  [1] BiocFileCache_1.10.2        plyr_1.8.6                  igraph_1.2.6                lazyeval_0.2.2             
  [5] splines_3.6.3               BiocParallel_1.20.1         listenv_0.8.0               GenomeInfoDb_1.22.1        
  [9] ggplot2_3.3.2               digest_0.6.27               htmltools_0.5.0             fansi_0.4.1                
 [13] magrittr_2.0.1              memoise_1.1.0               tensor_1.5                  cluster_2.1.0              
 [17] ROCR_1.0-11                 remotes_2.2.0               globals_0.14.0              matrixStats_0.57.0         
 [21] askpass_1.1                 prettyunits_1.1.1           colorspace_2.0-0            rappdirs_0.3.1             
 [25] blob_1.2.1                  ggrepel_0.8.2               dplyr_1.0.2                 callr_3.5.1                
 [29] crayon_1.3.4                RCurl_1.98-1.2              jsonlite_1.7.1              spatstat_1.64-1            
 [33] spatstat.data_1.5-2         survival_3.2-7              zoo_1.8-8                   glue_1.4.2                 
 [37] polyclip_1.10-0             gtable_0.3.0                zlibbioc_1.32.0             XVector_0.26.0             
 [41] leiden_0.3.6                DelayedArray_0.12.3         pkgbuild_1.1.0              Rhdf5lib_1.8.0             
 [45] SingleCellExperiment_1.8.0  future.apply_1.6.0          BiocGenerics_0.32.0         abind_1.4-5                
 [49] scales_1.1.1                DBI_1.1.0                   miniUI_0.1.1.1              Rcpp_1.0.5                 
 [53] progress_1.2.2              viridisLite_0.3.0           xtable_1.8-4                reticulate_1.18            
 [57] bit_4.0.4                   rsvd_1.0.3                  stats4_3.6.3                htmlwidgets_1.5.2          
 [61] httr_1.4.2                  gplots_3.1.1                RColorBrewer_1.1-2          ellipsis_0.3.1             
 [65] ica_1.0-2                   XML_3.99-0.3                pkgconfig_2.0.3             dbplyr_2.0.0               
 [69] uwot_0.1.9                  deldir_0.2-3                AnnotationDbi_1.48.0        tidyselect_1.1.0           
 [73] rlang_0.4.9                 reshape2_1.4.4              later_1.1.0.1               munsell_0.5.0              
 [77] tools_3.6.3                 cli_2.2.0                   RSQLite_2.2.1               generics_0.1.0             
 [81] ggridges_0.5.2              stringr_1.4.0               fastmap_1.0.1               goftest_1.2-2              
 [85] bit64_4.0.5                 processx_3.4.5              fs_1.5.0                    fitdistrplus_1.1-3         
 [89] caTools_1.18.0              purrr_0.3.4                 RANN_2.6.1                  pbapply_1.4-3              
 [93] future_1.20.1               nlme_3.1-150                mime_0.9                    compiler_3.6.3             
 [97] rstudioapi_0.13             plotly_4.9.2.1              curl_4.3                    png_0.1-7                  
[101] testthat_3.0.0              spatstat.utils_1.17-0       tibble_3.0.4                stringi_1.5.3              
[105] ps_1.5.0                    desc_1.2.0                  lattice_0.20-41             Matrix_1.2-18              
[109] vctrs_0.3.5                 pillar_1.4.7                lifecycle_0.2.0             BiocManager_1.30.10        
[113] lmtest_0.9-38               RcppAnnoy_0.0.17            data.table_1.13.4           cowplot_1.1.0              
[117] bitops_1.0-6                irlba_2.3.3                 httpuv_1.5.4                patchwork_1.1.0            
[121] GenomicRanges_1.38.0        R6_2.5.0                    promises_1.1.1              KernSmooth_2.23-18         
[125] gridExtra_2.3               IRanges_2.20.2              parallelly_1.21.0           sessioninfo_1.1.1          
[129] codetools_0.2-18            MASS_7.3-53                 gtools_3.8.2                assertthat_0.2.1           
[133] pkgload_1.1.0               rhdf5_2.30.1                SummarizedExperiment_1.16.1 openssl_1.4.3              
[137] rprojroot_2.0.2             withr_2.3.0                 sctransform_0.3.1           S4Vectors_0.24.4           
[141] GenomeInfoDbData_1.2.2      hms_0.5.3                   mgcv_1.8-33                 parallel_3.6.3             
[145] grid_3.6.3                  rpart_4.1-15                tidyr_1.1.2                 Rtsne_0.15                 
[149] Biobase_2.46.0              shiny_1.5.0
Chris-Cherry commented 3 years ago

For some reason it looks like the functions aren't exported for your installation. Function documentation is available for non-exported functions even though the function doesn't exist in the workspace. I can't replicate the behavior though - could you copy your NAMESPACE file from the domino directory? Maybe that will provide a clue.

(For you that's /Users/melanie/Library/R/3.6/library/domino/NAMESPACE)

melanieloth commented 3 years ago

Thank you, Chris! I was able to resolve the issue and successfully run the Domino workflow.