wurst-theke / butchr Goto Github PK

Hi,

I am running the sample code. However, a error was thrown as "Error in py_get_item_impl(x, key, FALSE) : TypeError: 'module' object is not subscriptable". Would you please suggest how to get this fixed? Thanks.

Li

Hi dears,

I'm trying to run your example data as specified in the installation guide but I always get the following error after calling the run_NMF_tensor() function. Any idea how to fix it? I tried to research it online but I couldn't find anything.

library(tensorflow)
library(BiocStyle)
library(ButchR)
library(knitr)
library(ComplexHeatmap)
library(viridis)
library(tidyverse)

data(leukemia)

k_min <- 2
k_max <- 4

leukemia_nmf_exp <- run_NMF_tensor(X = leukemia$matrix, 
                                   ranks = k_min:k_max, 
                                   method = "NMF", 
                                   n_initializations = 10,  
                                   extract_features = TRUE)

Error in py_get_item_impl(x, key, FALSE) :
TypeError: 'module' object is not subscriptable

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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

traceback()

8: stop(structure(list(message = "TypeError: 'module' object is not subscriptable",
call = py_get_item_impl(x, key, FALSE), cppstack = structure(list(
file = "", line = -1L, stack = c("1 reticulate.so 0x000000010b2ad05e _ZN4Rcpp9exceptionC2EPKcb + 222",
"2 reticulate.so 0x000000010b2b56a5 _ZN4Rcpp4stopERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEE + 53",
"3 reticulate.so 0x000000010b2c2d00 _ZN12_GLOBAL__N_113py_get_commonEPN9libpython7_objectEbb + 160",
"4 reticulate.so 0x000000010b2c2f21 _Z16py_get_item_impl11PyObjectRefN4Rcpp12RObject_ImplINS0_15PreserveStorageEEEb + 177",
"5 reticulate.so 0x000000010b2a0593 _reticulate_py_get_item_impl + 131",
"6 libR.dylib 0x0000000109e3bf52 R_doDotCall + 1458",
"7 libR.dylib 0x0000000109e870ed bcEval + 104317",
"8 libR.dylib 0x0000000109e6d2c1 Rf_eval + 385",
"9 libR.dylib 0x0000000109e8d139 R_execClosure + 2169",
"10 libR.dylib 0x0000000109e8bf27 Rf_applyClosure + 471",
"11 libR.dylib 0x0000000109e7420e bcEval + 26782",
"12 libR.dylib 0x0000000109e6d2c1 Rf_eval + 385",
"13 libR.dylib 0x0000000109e8d139 R_execClosure + 2169",
"14 libR.dylib 0x0000000109e8bf27 Rf_applyClosure + 471",
"15 libR.dylib 0x0000000109e7420e bcEval + 26782",
"16 libR.dylib 0x0000000109e6d2c1 Rf_eval + 385",
"17 libR.dylib 0x0000000109e8d139 R_execClosure + 2169",
"18 libR.dylib 0x0000000109e8bf27 Rf_applyClosure + 471",
"19 libR.dylib 0x0000000109e7420e bcEval + 26782",
"20 libR.dylib 0x0000000109e6d2c1 Rf_eval + 385",
"21 libR.dylib 0x0000000109e8d139 R_execClosure + 2169",
"22 libR.dylib 0x0000000109e8bf27 Rf_applyClosure + 471",
"23 libR.dylib 0x0000000109ed7137 dispatchMethod + 775",
"24 libR.dylib 0x0000000109ed6d03 Rf_usemethod + 483",
"25 libR.dylib 0x0000000109e971f6 tryDispatch + 374",
"26 libR.dylib 0x0000000109e8560b bcEval + 97435",
"27 libR.dylib 0x0000000109e6d2c1 Rf_eval + 385",
"28 libR.dylib 0x0000000109e8d139 R_execClosure + 2169",
"29 libR.dylib 0x0000000109e8bf27 Rf_applyClosure + 471",
"30 libR.dylib 0x0000000109e7420e bcEval + 26782",
"31 libR.dylib 0x0000000109e6d2c1 Rf_eval + 385",
"32 libR.dylib 0x0000000109e8d139 R_execClosure + 2169",
"33 libR.dylib 0x0000000109e8bf27 Rf_applyClosure + 471",
"34 libR.dylib 0x0000000109e6d77b Rf_eval + 1595",
"35 libR.dylib 0x0000000109e90806 do_set + 2534",
"36 libR.dylib 0x0000000109e6d4b7 Rf_eval + 887",
"37 libR.dylib 0x0000000109ec28a7 Rf_ReplIteration + 807",
"38 libR.dylib 0x0000000109ec3ef1 R_ReplConsole + 161",
"39 libR.dylib 0x0000000109ec3e42 run_Rmainloop + 82",
"40 libR.dylib 0x0000000109ec3f7e Rf_mainloop + 14",
"41 rsession 0x0000000109975170 _ZN13rstudio_boost4asio6detail24descriptor_write_op_baseINS0_15const_buffers_1EE10do_performEPNS1_10reactor_opE + 691568",
"42 rsession 0x00000001099483f4 _ZN13rstudio_boost4asio6detail24descriptor_write_op_baseINS0_15const_buffers_1EE10do_performEPNS1_10reactor_opE + 507892",
"43 rsession 0x00000001090de8bb _ZN13rstudio_boost4asio6detail30reactive_socket_accept_op_baseINS0_12basic_socketINS0_2ip3tcpEEES5_E10do_performEPNS1_10reactor_opE + 562571",
"44 libdyld.dylib 0x00007fff20402f5d start + 1"
)), class = "Rcpp_stack_trace")), class = c("Rcpp::exception",
"C++Error", "error", "condition")))
7: py_get_item_impl(x, key, FALSE)
6: py_get_item(x, name)
5: py_get_attr_or_item(x, name, FALSE)
4: [[.python.builtin.object(tensorTheCleaver, module[1])
3: tensorTheCleaver[[module[1]]]
2: source_NMFtensor_function(method)
1: run_NMF_tensor(X = leukemia$matrix, ranks = k_min:k_max, method = "NMF",
n_initializations = 10, extract_features = TRUE)