Loading golgotcha crashes due to python dependencies

[laresbernardo]

Hi! I've just installed the package successfully and then when loading golgotcha it returned an error:

> devtools::install_github("bnosac/golgotha", INSTALL_opts = "--no-multiarch")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo bnosac/golgotha@HEAD
✓  checking for file ‘/private/var/folders/3w/x0bjsdv52v3b3kjbw87y3wfw0000gn/T/RtmpGIic1l/remotes866533484609/bnosac-golgotha-6f9f2bf/DESCRIPTION’ ...
─  preparing ‘golgotha’:
✓  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘golgotha_0.2.0.tar.gz’
   
Installing package into ‘/Users/bernardolares/Library/R/4.0/library’
(as ‘lib’ is unspecified)
* installing *source* package ‘golgotha’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (golgotha)
> library(golgotha)
Loading required package: reticulate
Configuring package 'golgotha': please wait ...
Collecting torch
  Downloading torch-1.9.0-cp39-none-macosx_10_9_x86_64.whl (127.9 MB)
Collecting transformers==2.4.1
  Downloading transformers-2.4.1-py3-none-any.whl (475 kB)
Collecting boto3
  Downloading boto3-1.18.16-py3-none-any.whl (131 kB)
Collecting tqdm>=4.27
  Downloading tqdm-4.62.0-py2.py3-none-any.whl (76 kB)
Requirement already satisfied: numpy in ./Library/r-miniconda/envs/r-reticulate/lib/python3.9/site-packages (from transformers==2.4.1) (1.21.1)
Collecting sentencepiece
  Downloading sentencepiece-0.1.96-cp39-cp39-macosx_10_6_x86_64.whl (1.1 MB)
Collecting tokenizers==0.0.11
  Downloading tokenizers-0.0.11.tar.gz (30 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
    Preparing wheel metadata: started
    Preparing wheel metadata: finished with status 'done'
Collecting filelock
  Downloading filelock-3.0.12-py3-none-any.whl (7.6 kB)
Collecting sacremoses
  Downloading sacremoses-0.0.45-py3-none-any.whl (895 kB)
Collecting requests
  Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB)
Collecting regex!=2019.12.17
  Downloading regex-2021.8.3-cp39-cp39-macosx_10_9_x86_64.whl (285 kB)
Requirement already satisfied: typing-extensions in ./Library/r-miniconda/envs/r-reticulate/lib/python3.9/site-packages (from torch) (3.10.0.0)
Collecting botocore<1.22.0,>=1.21.16
  Downloading botocore-1.21.16-py3-none-any.whl (7.8 MB)
Collecting jmespath<1.0.0,>=0.7.1
  Downloading jmespath-0.10.0-py2.py3-none-any.whl (24 kB)
Collecting s3transfer<0.6.0,>=0.5.0
  Downloading s3transfer-0.5.0-py3-none-any.whl (79 kB)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in ./Library/r-miniconda/envs/r-reticulate/lib/python3.9/site-packages (from botocore<1.22.0,>=1.21.16->boto3->transformers==2.4.1) (2.8.2)
Collecting urllib3<1.27,>=1.25.4
  Downloading urllib3-1.26.6-py2.py3-none-any.whl (138 kB)
Requirement already satisfied: six>=1.5 in ./Library/r-miniconda/envs/r-reticulate/lib/python3.9/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.22.0,>=1.21.16->boto3->transformers==2.4.1) (1.16.0)
Requirement already satisfied: certifi>=2017.4.17 in ./Library/r-miniconda/envs/r-reticulate/lib/python3.9/site-packages (from requests->transformers==2.4.1) (2021.5.30)
Collecting charset-normalizer~=2.0.0
  Downloading charset_normalizer-2.0.4-py3-none-any.whl (36 kB)
Collecting idna<4,>=2.5
  Downloading idna-3.2-py3-none-any.whl (59 kB)
Collecting click
  Downloading click-8.0.1-py3-none-any.whl (97 kB)
Requirement already satisfied: joblib in ./Library/r-miniconda/envs/r-reticulate/lib/python3.9/site-packages (from sacremoses->transformers==2.4.1) (1.0.1)
Building wheels for collected packages: tokenizers
  Building wheel for tokenizers (PEP 517): started
  Building wheel for tokenizers (PEP 517): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /Users/bernardolares/Library/r-miniconda/envs/r-reticulate/bin/python /Users/bernardolares/Library/r-miniconda/envs/r-reticulate/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /var/folders/3w/x0bjsdv52v3b3kjbw87y3wfw0000gn/T/tmp4_14r7ur
       cwd: /private/var/folders/3w/x0bjsdv52v3b3kjbw87y3wfw0000gn/T/pip-install-hydjbfqr/tokenizers_800ac7fe01f240cf9fe99c8faeb338df
  Complete output (20 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib
  creating build/lib/tokenizers
  copying tokenizers/__init__.py -> build/lib/tokenizers
  running build_ext
  running build_rust
  error: can't find Rust compiler
  
  If you are using an outdated pip version, it is possible a prebuilt wheel is available for this package but pip is not able to install from it. Installing from the wheel would avoid the need for a Rust compiler.
  
  To update pip, run:
  
      pip install --upgrade pip
  
  and then retry package installation.
  
  If you did intend to build this package from source, try installing a Rust compiler from your system package manager and ensure it is on the PATH during installation. Alternatively, rustup (available at https://rustup.rs) is the recommended way to download and update the Rust compiler toolchain.
  ----------------------------------------
  ERROR: Failed building wheel for tokenizers
Failed to build tokenizers
ERROR: Could not build wheels for tokenizers which use PEP 517 and cannot be installed directly
Error: package or namespace load failed for ‘golgotha’:
 .onLoad failed in loadNamespace() for 'golgotha', details:
  call: NULL
  error: Error installing package(s): 'torch', 'transformers==2.4.1'

My sessionInfo():

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  11.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] reticulate_1.20 Robyn_3.0.0     ggplot2_3.3.5   dplyr_1.0.7     lares_5.0.2    

loaded via a namespace (and not attached):
 [1] bitops_1.0-7       fs_1.5.0           usethis_2.0.1      lubridate_1.7.10   devtools_2.4.0    
 [6] doParallel_1.0.16  httr_1.4.2         rprojroot_2.0.2    tools_4.0.3        doRNG_1.8.2       
[11] utf8_1.2.2         R6_2.5.0           rpart_4.1-15       lazyeval_0.2.2     DBI_1.1.0         
[16] colorspace_2.0-2   withr_2.4.2        tidyselect_1.1.1   prettyunits_1.1.1  processx_3.5.2    
[21] curl_4.3.2         compiler_4.0.3     glmnet_4.1-2       cli_3.0.1          rvest_1.0.0       
[26] xml2_1.3.2         desc_1.3.0         labeling_0.4.2     scales_1.1.1       callr_3.7.0       
[31] rappdirs_0.3.3     stringr_1.4.0      digest_0.6.27      pkgconfig_2.0.3    parallelly_1.27.0 
[36] sessioninfo_1.1.1  fastmap_1.0.1      rlang_0.4.11       rstudioapi_0.13    rPref_1.3         
[41] shape_1.4.6        prophet_1.0        farver_2.1.0       generics_0.1.0     jsonlite_1.7.2    
[46] zip_2.2.0          RCurl_1.98-1.3     magrittr_2.0.1     patchwork_1.1.1    Matrix_1.2-18     
[51] Rcpp_1.0.7         munsell_0.5.0      fansi_0.5.0        lifecycle_1.0.0    stringi_1.7.3     
[56] pROC_1.17.0.1      yaml_2.2.1         pkgbuild_1.2.0     plyr_1.8.6         grid_4.0.3        
[61] parallel_4.0.3     listenv_0.8.0      crayon_1.4.1       lattice_0.20-41    splines_4.0.3     
[66] ps_1.6.0           pillar_1.6.2       igraph_1.2.6       rngtools_1.5       codetools_0.2-18  
[71] pkgload_1.2.1      glue_1.4.2         doFuture_0.12.0    RcppParallel_5.1.4 rpart.plot_3.0.9  
[76] data.table_1.14.0  remotes_2.3.0      png_0.1-7          vctrs_0.3.8        nloptr_1.2.2.2    
[81] foreach_1.5.1      testthat_3.0.4     gtable_0.3.0       purrr_0.3.4        tidyr_1.1.3       
[86] future_1.21.0      assertthat_0.2.1   cachem_1.0.4       openxlsx_4.2.4     h2o_3.32.1.3      
[91] survival_3.2-7     minpack.lm_1.2-1   tibble_3.1.3       iterators_1.0.13   memoise_2.0.0     
[96] corrplot_0.90      globals_0.14.0     ellipsis_0.3.2  

[jwijffels]

The transformers python module needs the tokenizers python package which requires to install Rust nowadays

[laresbernardo]

What should be the steps to follow? Can we include this step to Installation section? I tried running the installation on Terminal, restarted RStudio, and still getting the error. Any recommendation? Thanks @jwijffels

[jwijffels]

Install rust

[SatoshiReport]

I tried that and same error. I used: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh