golgotha
golgotha copied to clipboard
Published
20 hours ago •
bnosac
bnosac
Loading golgotcha crashes due to python dependencies
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
The transformers python module needs the tokenizers python package which requires to install Rust nowadays
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
I tried that and same error. I used: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
