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julia_setup erorr in Rstudio #212

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Zepeng-Mu opened this issue Oct 27, 2023 · 3 comments
Open

julia_setup erorr in Rstudio #212

Zepeng-Mu opened this issue Oct 27, 2023 · 3 comments

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@Zepeng-Mu
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Hi,

I'm encountering this error in julia_setup:

> j <- julia_setup(JULIA_HOME = "/scratch/midway3/zepengmu/miniconda3/envs/R42/bin")
Julia version 1.8.2 at location /scratch/midway3/zepengmu/miniconda3/envs/R42/bin will be used.
Loading setup script for JuliaCall...
WARNING: replacing module JuliaCall.
LoadError("/scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R/library/JuliaCall/julia/setup.jl", 16, ArgumentError("Package Suppressor not found in current path.\n- Run `import Pkg; Pkg.add(\"Suppressor\")` to install the Suppressor package.")) Error in .julia$cmd(paste0(Rhomeset, "Base.include(Main,\"", system.file("julia/setup.jl",  : 
  Error happens when you try to execute command ENV["R_HOME"] = "/scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R";Base.include(Main,"/scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R/library/JuliaCall/julia/setup.jl") in Julia.
                        To have more helpful error messages,
                        you could considering running the command in Julia directly
In addition: Warning message:
In system2(file.path(.julia$bin_dir, "julia"), shQuote(command),  :
  running command ''/scratch/midway3/zepengmu/miniconda3/envs/R42/bin/julia' '--startup-file=no' '/scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R/library/JuliaCall/julia/install_dependency.jl' '/scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R' 2>&1' had status 1

However, this only happens in RStudio. In Julia REPL, I can run using Supressor without any problem. Also, running ENV["R_HOME"] = "/scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R";Base.include(Main,"/scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R/library/JuliaCall/julia/setup.jl") in Julia returns no error. I can also run my R script from terminal using Rscript and again julia_setup returns no error.

I should say previously I was able to run my script in RStudio, but in terminal some packages like MixedModels I am using cannot be found. I had to install it again in terminal, but then the script stopped working in RStudio.

julia version 1.8.2

Session Info 
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.0 (2022-04-22)
 os       Ubuntu 22.04.3 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2023-10-27
 rstudio  2023.09.1+494 Desert Sunflower (server)
 pandoc   3.1.1 @ /usr/local/bin/pandoc

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version  date (UTC) lib source
 Biobase              * 2.56.0   2022-04-26 [1] Bioconductor
 BiocGenerics         * 0.42.0   2022-04-26 [1] Bioconductor
 bitops                 1.0-7    2021-04-24 [1] CRAN (R 4.2.0)
 boot                   1.3-28.1 2022-11-22 [1] CRAN (R 4.2.3)
 cachem                 1.0.8    2023-05-01 [1] CRAN (R 4.2.3)
 callr                  3.7.3    2022-11-02 [1] CRAN (R 4.2.3)
 cli                    3.6.1    2023-03-23 [1] CRAN (R 4.2.3)
 colorspace             2.1-0    2023-01-23 [1] CRAN (R 4.2.3)
 crayon                 1.5.2    2022-09-29 [1] CRAN (R 4.2.3)
 data.table           * 1.14.8   2023-02-17 [1] CRAN (R 4.2.3)
 DelayedArray           0.22.0   2022-04-26 [1] Bioconductor
 devtools               2.4.5    2022-10-11 [1] CRAN (R 4.2.1)
 digest                 0.6.33   2023-07-07 [1] CRAN (R 4.2.0)
 dplyr                * 1.1.3    2023-09-03 [1] CRAN (R 4.2.0)
 ellipsis               0.3.2    2021-04-29 [1] CRAN (R 4.2.3)
 fansi                  1.0.4    2023-01-22 [1] CRAN (R 4.2.3)
 fastmap                1.1.1    2023-02-24 [1] CRAN (R 4.2.3)
 forcats              * 1.0.0    2023-01-29 [1] CRAN (R 4.2.3)
 fs                     1.6.3    2023-07-20 [1] CRAN (R 4.2.0)
 generics               0.1.3    2022-07-05 [1] CRAN (R 4.2.3)
 GenomeInfoDb         * 1.34.9   2023-02-02 [1] Bioconductor
 GenomeInfoDbData       1.2.8    2022-09-10 [1] Bioconductor
 GenomicRanges        * 1.50.2   2022-12-16 [1] Bioconductor
 ggplot2              * 3.4.3    2023-08-14 [1] CRAN (R 4.2.0)
 glue                   1.6.2    2022-02-24 [1] CRAN (R 4.2.3)
 gtable                 0.3.4    2023-08-21 [1] CRAN (R 4.2.0)
 hms                    1.1.3    2023-03-21 [1] CRAN (R 4.2.3)
 htmltools              0.5.6    2023-08-10 [1] CRAN (R 4.2.0)
 htmlwidgets            1.6.2    2023-03-17 [1] CRAN (R 4.2.3)
 httpuv                 1.6.11   2023-05-11 [1] CRAN (R 4.2.3)
 IRanges              * 2.32.0   2022-11-01 [1] Bioconductor
 JuliaCall            * 0.17.5   2023-10-27 [1] Github (Non-Contradiction/JuliaCall@c05473b)
 knitr                  1.44     2023-09-11 [1] CRAN (R 4.2.0)
 later                  1.3.1    2023-05-02 [1] CRAN (R 4.2.3)
 lattice                0.21-8   2023-04-05 [1] CRAN (R 4.2.3)
 lifecycle              1.0.3    2022-10-07 [1] CRAN (R 4.2.3)
 lme4                 * 1.1-32   2022-12-12 [1] Github (lme4/lme4@aab627f)
 lubridate            * 1.9.2    2023-02-10 [1] CRAN (R 4.2.3)
 magrittr               2.0.3    2022-03-30 [1] CRAN (R 4.2.3)
 MASS                   7.3-60   2023-05-04 [1] CRAN (R 4.2.3)
 Matrix               * 1.6-1.1  2023-09-18 [1] CRAN (R 4.2.0)
 MatrixGenerics       * 1.8.1    2022-06-26 [1] Bioconductor
 matrixStats          * 1.0.0    2023-06-02 [1] CRAN (R 4.2.3)
 memoise                2.0.1    2021-11-26 [1] CRAN (R 4.2.3)
 mime                   0.12     2021-09-28 [1] CRAN (R 4.2.3)
 miniUI                 0.1.1.1  2018-05-18 [1] CRAN (R 4.2.3)
 minqa                  1.2.5    2022-10-19 [1] CRAN (R 4.2.0)
 munsell                0.5.0    2018-06-12 [1] CRAN (R 4.2.3)
 nlme                   3.1-162  2023-01-31 [1] CRAN (R 4.2.3)
 nloptr                 2.0.3    2022-05-26 [1] CRAN (R 4.2.0)
 pbmcapply            * 1.5.1    2022-12-30 [1] Github (kvnkuang/pbmcapply@c302c2e)
 pillar                 1.9.0    2023-03-22 [1] CRAN (R 4.2.3)
 pkgbuild               1.4.2    2023-06-26 [1] CRAN (R 4.2.3)
 pkgconfig              2.0.3    2019-09-22 [1] CRAN (R 4.2.3)
 pkgload                1.3.2    2022-11-16 [1] CRAN (R 4.2.3)
 prettyunits            1.2.0    2023-09-24 [1] CRAN (R 4.2.0)
 processx               3.8.1    2023-04-18 [1] CRAN (R 4.2.3)
 profvis                0.3.8    2023-05-02 [1] CRAN (R 4.2.3)
 promises               1.2.1    2023-08-10 [1] CRAN (R 4.2.0)
 ps                     1.7.5    2023-04-18 [1] CRAN (R 4.2.3)
 purrr                * 1.0.2    2023-08-10 [1] CRAN (R 4.2.0)
 R6                     2.5.1    2021-08-19 [1] CRAN (R 4.2.3)
 Rcpp                   1.0.11   2023-07-06 [1] CRAN (R 4.2.0)
 RCurl                  1.98-1.9 2022-10-03 [1] CRAN (R 4.2.0)
 readr                * 2.1.4    2023-02-10 [1] CRAN (R 4.2.3)
 remotes                2.4.2    2021-11-30 [1] CRAN (R 4.2.3)
 rlang                  1.1.1    2023-04-28 [1] CRAN (R 4.2.3)
 rstudioapi             0.14     2022-08-22 [1] CRAN (R 4.2.3)
 S4Vectors            * 0.34.0   2022-04-26 [1] Bioconductor
 scales                 1.2.1    2022-08-20 [1] CRAN (R 4.2.3)
 sessioninfo            1.2.2    2021-12-06 [1] CRAN (R 4.2.3)
 shiny                  1.7.4    2022-12-15 [1] CRAN (R 4.2.3)
 stringi                1.7.12   2023-01-11 [1] CRAN (R 4.2.0)
 stringr              * 1.5.0    2022-12-02 [1] CRAN (R 4.2.3)
 SummarizedExperiment * 1.28.0   2022-11-01 [1] Bioconductor
 tibble               * 3.2.1    2023-03-20 [1] CRAN (R 4.2.3)
 tidyr                * 1.3.0    2023-01-24 [1] CRAN (R 4.2.3)
 tidyselect             1.2.0    2022-10-10 [1] CRAN (R 4.2.3)
 tidyverse            * 2.0.0    2023-02-22 [1] CRAN (R 4.2.0)
 timechange             0.2.0    2023-01-11 [1] CRAN (R 4.2.3)
 tzdb                   0.4.0    2023-05-12 [1] CRAN (R 4.2.3)
 urlchecker             1.0.1    2021-11-30 [1] CRAN (R 4.2.3)
 usethis                2.2.1    2023-06-23 [1] CRAN (R 4.2.3)
 utf8                   1.2.3    2023-01-31 [1] CRAN (R 4.2.3)
 vctrs                  0.6.3    2023-06-14 [1] CRAN (R 4.2.3)
 withr                  2.5.1    2023-09-26 [1] CRAN (R 4.2.0)
 xfun                   0.40     2023-08-09 [1] CRAN (R 4.2.0)
 xtable                 1.8-4    2019-04-21 [1] CRAN (R 4.2.3)
 XVector                0.36.0   2022-04-26 [1] Bioconductor
 zlibbioc               1.42.0   2022-04-26 [1] Bioconductor

 [1] /scratch/midway3/zepengmu/miniconda3/envs/R42/lib/R/library

─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
@ronirg
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ronirg commented Nov 13, 2023

I have the same issue.

@gravary
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gravary commented Nov 1, 2024

I'm also having the same issue, notably it was working up until I manually cleared a temp directory

@gravary
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gravary commented Nov 1, 2024

I'm also having the same issue, notably it was working up until I manually cleared a temp directory

restarted system and issue is cleared, might be a issue with tempdir structure

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@gravary @Zepeng-Mu @ronirg