When passing python location I encounter '/c' not found

[Krutik6]

When trying to use_python I am running into some errors. This is very new and a bit confusing. I feel the route cause is in R, as I have used these environments in a python IDE and they are found with no issues.

library(reticulate)

use_python("C:/Users/kruti/anaconda3/envs/py3/python.exe")

Error in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  : 
  '/c' not found

#copied the python folder into the local enviroment and re-ran.
use_python("py3/python.exe")

Error in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  : 
  '/c' not found

I think the issue lies in system calling but am wondering if anyone has encountered such issues before.

> sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] purrr_1.0.2                 rjson_0.2.21                DESeq2_1.42.0              
 [4] SummarizedExperiment_1.32.0 Biobase_2.62.0              MatrixGenerics_1.14.0      
 [7] matrixStats_1.1.0           GenomicRanges_1.54.1        GenomeInfoDb_1.38.1        
[10] IRanges_2.36.0              S4Vectors_0.40.1            BiocGenerics_0.48.1        
[13] yaml_2.3.7                  tidyr_1.3.0                 dplyr_1.1.3                
[16] data.table_1.14.8           reticulate_1.36.0          

loaded via a namespace (and not attached):
 [1] rappdirs_0.3.3          utf8_1.2.4              generics_0.1.3          SparseArray_1.2.2      
 [5] bitops_1.0-7            lattice_0.21-9          magrittr_2.0.3          grid_4.3.2             
 [9] rprojroot_2.0.4         jsonlite_1.8.7          Matrix_1.6-5            fansi_1.0.5            
[13] scales_1.2.1            codetools_0.2-19        abind_1.4-5             cli_3.6.1              
[17] rlang_1.1.2             crayon_1.5.2            XVector_0.42.0          munsell_0.5.0          
[21] withr_2.5.2             DelayedArray_0.28.0     S4Arrays_1.2.0          tools_4.3.2            
[25] parallel_4.3.2          BiocParallel_1.36.0     colorspace_2.1-0        ggplot2_3.4.4          
[29] locfit_1.5-9.8          GenomeInfoDbData_1.2.11 here_1.0.1              vctrs_0.6.4            
[33] R6_2.5.1                png_0.1-8               lifecycle_1.0.4         zlibbioc_1.48.0        
[37] pkgconfig_2.0.3         gtable_0.3.4            pillar_1.9.0            glue_1.6.2             
[41] Rcpp_1.0.11             tibble_3.2.1            tidyselect_1.2.0        rstudioapi_0.15.0      
[45] compiler_4.3.2          RCurl_1.98-1.13        

[t-kalinowski]

Hi, thanks for reporting.

I'm unable to reproduce on Windows. This succeeded without error for me:

library(reticulate)
install_miniconda(force = TRUE)
use_python(conda_python("r-reticulate"))
py_run_string("1+1")
py_config()

Is there any additional information you can provide that might help us track this down?

Is this specific to anaconda? Have you tried install_python() and a virtualenv?

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