JuliaCall
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Published
20 hours ago •
Non-Contradiction
Non-Contradiction
`julia_setup` erorr in Rstudio
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
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