gongx030 / ensemblemerge Goto Github PK

params_merge <- new('BBKNNMerge', normalize = params_normalize)
x_merged <- Merge(x, params_merge) # x_merged is a Seurat object

Python  package leidenalg must have version >= 0.8.8

Error in py_call_impl(callable, dots$args, dots$keywords): ValueError: X_pca does not have enough Dimensions. Provide a Representation with equal or more dimensions than`n_pcs` or lower `n_pcs` 

Detailed traceback:
  File "/usr/local/lib/python3.7/dist-packages/scanpy/tools/_umap.py", line 187, in umap
    silent=True,
  File "/usr/local/lib/python3.7/dist-packages/scanpy/tools/_utils.py", line 53, in _choose_representation
    f'{use_rep} does not have enough Dimensions. Provide a '

Traceback:

1. Merge(x, params_merge)
2. Merge(x, params_merge)
3. sc$tl$umap(adata)
4. py_call_impl(callable, dots$args, dots$keywords)

Notebook not found
There was an error loading this notebook. Ensure that the file is accessible and try again.
https://github.com/gongx030/ensemblemerge_docs/blob/main/notebooks/normalization.ipynb

sprintf('pip install torch') %>% system()
sprintf('pip install scvi-tools==0.14.5') %>% system()
reticulate::import('scvi')

Error in py_module_import(module, convert = convert): ImportError: cannot import name '_CONSTANTS' from 'scvi._constants' (/usr/local/lib/python3.7/dist-packages/scvi/_constants.py)

Detailed traceback:
  File "/usr/local/lib/R/site-library/reticulate/python/rpytools/loader.py", line 44, in _import_hook
    level=level
  File "/usr/local/lib/python3.7/dist-packages/scvi/__init__.py", line 6, in <module>
    from ._constants import _CONSTANTS

Traceback:

1. reticulate::import("scvi")
2. py_module_import(module, convert = convert)

**Downloading GitHub repo gongx030/ensemblemerge@HEAD

Error: Failed to install 'ensemblemerge' from GitHub:
  HTTP error 404.
  Not Found

  Did you spell the repo owner (`yulijia`) and repo name (`SIMLR`) correctly?
  - If spelling is correct, check that you have the required permissions to access the repo.**
Traceback:

1. devtools::install_github("gongx030/ensemblemerge", auth_token = "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")

2. pkgbuild::with_build_tools({
 .     ellipsis::check_dots_used(action = getOption("devtools.ellipsis_action", 
 .         rlang::warn))
 .     {
 .         remotes <- lapply(repo, github_remote, ref = ref, subdir = subdir, 
 .             auth_token = auth_token, host = host)
 .         install_remotes(remotes, auth_token = auth_token, host = host, 
 .             dependencies = dependencies, upgrade = upgrade, force = force, 
 .             quiet = quiet, build = build, build_opts = build_opts, 
 .             build_manual = build_manual, build_vignettes = build_vignettes, 
 .             repos = repos, type = type, ...)
 .     }
 . }, required = FALSE)

3. install_remotes(remotes, auth_token = auth_token, host = host, 
 .     dependencies = dependencies, upgrade = upgrade, force = force, 
 .     quiet = quiet, build = build, build_opts = build_opts, build_manual = build_manual, 
 .     build_vignettes = build_vignettes, repos = repos, type = type, 
 .     ...)

4. tryCatch(res[[i]] <- install_remote(remotes[[i]], ...), error = function(e) {
 .     stop(remote_install_error(remotes[[i]], e))
 . })

5. tryCatchList(expr, classes, parentenv, handlers)

6. tryCatchOne(expr, names, parentenv, handlers[[1L]])

7. value[[3L]](cond)

library(ensemblemerge)
library(dplyr)

params_preprocess <- new('SeuratPreprocess', batch = 'batch')
so <- Preprocess(so, params_preprocess)

Error in Preprocess(so, params_preprocess): could not find function "Preprocess"

# integration
params_merge <- new('SeuratMerge', normalize = params_normalize)
x_merged <- Merge(x, params_merge) # x_merged is a Seurat object

Error in getGlobalsAndPackages(expr, envir = envir, globals = globals): The total size of the 7 globals exported for future expression (‘FUN()’) is 2.35 GiB.. This exceeds the maximum allowed size of 500.00 MiB (option 'future.globals.maxSize'). The three largest globals are ‘object.list’ (2.35 GiB of class ‘list’), ‘anchor.features’ (125.67 KiB of class ‘character’) and ‘FUN’ (35.52 KiB of class ‘function’)

params_embed <- new('PCAEmbed', normalize = params_normalize)
so <- Embed(so, params_doubletdetect)

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘Embed’ for signature ‘"Seurat", "DoubletFinderDoubletDetect"’
Traceback:

1. Embed(so, params_doubletdetect)

2. (function (classes, fdef, mtable) 
 . {
 .     methods <- .findInheritedMethods(classes, fdef, mtable)
 .     if (length(methods) == 1L) 
 .         return(methods[[1L]])
 .     else if (length(methods) == 0L) {
 .         cnames <- paste0("\"", vapply(classes, as.character, 
 .             ""), "\"", collapse = ", ")
 .         stop(gettextf("unable to find an inherited method for function %s for signature %s", 
 .             sQuote(fdef@generic), sQuote(cnames)), domain = NA)
 .     }
 .     else stop("Internal error in finding inherited methods; didn't return a unique method", 
 .         domain = NA)
 . })(list(structure("Seurat", package = "SeuratObject"), structure("DoubletFinderDoubletDetect", package = "ensemblemerge")), 
 .     new("standardGeneric", .Data = function (x, params, ...) 
 .     standardGeneric("Embed"), generic = structure("Embed", package = "ensemblemerge"), 
 .         package = "ensemblemerge", group = list(), valueClass = character(0), 
 .         signature = c("x", "params"), default = NULL, skeleton = (function (x, 
 .             params, ...) 
 .         stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
 .             "Embed"), domain = NA))(x, params, ...)), <environment>)

3. stop(gettextf("unable to find an inherited method for function %s for signature %s", 
 .     sQuote(fdef@generic), sQuote(cnames)), domain = NA)